bluuebunny/crossref_metadata_2025 huggingface dataset:
Extension of the reconstruction field of view and truncation correction using sinogram decomposition
Authors: Zamyatin Alexander A. , Nakanishi Satoru
Published: May 2007

We propose a novel truncation correction algorithm that completes unmeasured data outside of the scan field of view, which allows extending the reconstruction field of view. When a patient extends outside the detector coverage the projection data are transversely truncated, which causes severe artifacts. The proposed method utilizes the idea of sinogram decomposition, where we consider sinogram curves corresponding to image points outside the field of view. We propose two ways to estimate the truncated data, one based on the minimum value along the sinogram curve, and the other based on the data values near the edge of truncation. Both estimation methods are combined to achieve uniform image quality improvement from the edge of truncation to the outer side of the extended region. In our evaluation with simulated and real projection data we compare the proposed method with existing methods and investigate the dependence on the amount of truncation. The evaluation shows that the proposed method handles cases when truncation is present on both sides of the detector, or when a high‐contrast object is located outside the field of view.
Novel ultrahigh resolution data acquisition and image reconstruction for multi‐detector row CT
Authors: Flohr T. G. , Stierstorfer K. , Süß C. , Schmidt B. , Primak A. N. , McCollough C. H.
Published: May 2007

We present and evaluate a special ultrahigh resolution mode providing considerably enhanced spatial resolution both in the scan plane and in the ‐axis direction for a routine medical multi‐detector row computed tomography (CT) system. Data acquisition is performed by using a flying focal spot both in the scan plane and in the ‐axis direction in combination with tantalum grids that are inserted in front of the multi‐row detector to reduce the aperture of the detector elements both in‐plane and in the ‐axis direction. The dose utilization of the system for standard applications is not affected, since the grids are moved into place only when needed and are removed for standard scanning. By means of this technique, image slices with a nominal section width of (measured full width at half maximum=) can be reconstructed in spiral mode on a CT system with a detector configuration of . The measured 2% value of the in‐plane modulation transfer function (MTF) is , the measured 2% value of the longitudinal ( axis) MTF is . In a resolution phantom with metal line pair test patterns, spatial resolution of can be demonstrated both in the scan plane and along the axis. This corresponds to an object size of that can be resolved. The new mode is intended for ultrahigh resolution bone imaging, in particular for wrists, joints, and inner ear studies, where a higher level of image noise due to the reduced aperture is an acceptable trade‐off for the clinical benefit brought about by the improved spatial resolution.
Development of an ultrasmall ‐band linear accelerator guide for a four‐dimensional image‐guided radiotherapy system with a gimbaled x‐ray head
Authors: Kamino Yuichiro , Miura Sadao , Kokubo Masaki , Yamashita Ichiro , Hirai Etsuro , Hiraoka Masahiro , Ishikawa Junzo
Published: May 2007

We are developing a four‐dimensional image‐guided radiotherapy system with a gimbaled x‐ray head. It is capable of pursuing irradiation and delivering irradiation precisely with the help of an agile moving x‐ray head on the gimbals. Requirements for the accelerator guide were established, system design was developed, and detailed design was conducted. An accelerator guide was manufactured and basic beam performance and leakage radiation from the accelerator guide were evaluated at a low pulse repetition rate. The accelerator guide including the electron gun is long and weighs about . The length of the accelerating structure is . The accelerating structure is a standing wave type and is composed of the axial‐coupled injector section and the side‐coupled acceleration cavity section. The injector section is composed of one prebuncher cavity, one buncher cavity, one side‐coupled half cavity, and two axial coupling cavities. The acceleration cavity section is composed of eight side‐coupled nose reentrant cavities and eight coupling cavities. The electron gun is a diode‐type gun with a cerium hexaboride direct heating cathode. The accelerator guide can be operated without any magnetic focusing device. Output beam current was with a transmission efficiency of 58%, and the average energy was . Beam energy was distributed from 4.95 to . The beam profile, measured from the beam output hole on the axis of the accelerator guide, was full width at half maximum (FWHM) width. The beam loading line was , where is output beam current. The maximum radiation leakage of the accelerator guide at from the axis of the accelerator guide was calculated as at the rated x‐ray output of from the measured value. This leakage requires no radiation shielding for the accelerator guide itself per IEC 60601‐2‐1.
An investigation of temporal regularization techniques for dynamic PET reconstructions using temporal splines
Authors: Verhaeghe Jeroen , D'Asseler Yves , Vandenberghe Stefaan , Staelens Steven , Lemahieu Ignace
Published: May 2007

The use of a temporal B‐spline basis for the reconstruction of dynamic positron emission tomography data was investigated. Maximum likelihood (ML) reconstructions using an expectation maximization framework and maximum A‐posteriori (MAP) reconstructions using the generalized expectation maximization framework were evaluated. Different parameters of the B‐spline basis of such as order, number of basis functions and knot placing were investigated in a reconstruction task using simulated dynamic list‐mode data. We found that a higher order basis reduced both the bias and variance. Using a higher number of basis functions in the modeling of the time activity curves (TACs) allowed the algorithm to model faster changes of the TACs, however, the TACs became noisier. We have compared ML, Gaussian postsmoothed ML and MAP reconstructions. The noise level in the ML reconstructions was controlled by varying the number of basis functions. The MAP algorithm penalized the integrated squared curvature of the reconstructed TAC. The postsmoothed ML was always outperformed in terms of bias and variance properties by the MAP and ML reconstructions. A simple adaptive knot placing strategy was also developed and evaluated. It is based on an arc length redistribution scheme during the reconstruction. The free knot reconstruction allowed a more accurate reconstruction while reducing the noise level especially for fast changing TACs such as blood input functions. Limiting the number of temporal basis functions combined with the adaptive knot placing strategy is in this case advantageous for regularization purposes when compared to the other regularization techniques.
In vivo dosimeters for HDR brachytherapy: A comparison of a diamond detector, MOSFET, TLD, and scintillation detector
Authors: Lambert Jamil , Nakano Tatsuya , Law Sue , Elsey Justin , McKenzie David R. , Suchowerska Natalka
Published: May 2007

The large dose gradients in brachytherapy necessitate a detector with a small active volume for accurate dosimetry. The dosimetric performance of a novel scintillation detector (BrachyFOD™) is evaluated and compared to three commercially available detectors, a diamond detector, a MOSFET, and TLDs. An HDR brachytherapy source is used to measure the depth dependence, angular dependence, and temperature dependence of the detectors. Of the commercially available detectors, the diamond detector was found to be the most accurate, but has a large physical size. The TLDs cannot provide real time readings and have depth dependent sensitivity. The MOSFET used in this study was accurate to within 5% for distances of 20 to from the source in water but gave errors of 30%–40% for distances greater than from the source. The BrachyFOD™ was found to be accurate to within 3% for distances of 10 to from an HDR brachytherapy source in water. It has an angular dependence of less than 2% and the background signal created by Čerenkov radiation and fluorescence of the plastic optical fiber is insignificant compared to the signal generated in the scintillator. Of the four detectors compared in this study the BrachyFOD™ has the most favorable combination of characteristics for dosimetry in HDR brachytherapy.
Quality in radiation oncology
Authors: Pawlicki Todd , Mundt Arno J.
Published: May 2007

A modern approach to quality was developed in the United States at Bell Telephone Laboratories during the first part of the 20th century. Over the years, those quality techniques have been adopted and extended by almost every industry. Medicine in general and radiation oncology in particular have been slow to adopt modern quality techniques. This work contains a brief description of the history of research on quality that led to the development of organization‐wide quality programs such as Six Sigma. The aim is to discuss the current approach to quality in radiation oncology as well as where quality should be in the future. A strategy is suggested with the goal to provide a threshold improvement in quality over the next 10 years.
Ultracold Neutral Plasmas
Authors: Killian Thomas C.
Published: May 2007

Ultracold neutral plasmas occupy an exotic regime of plasma physics in which electrons form a swarming, neutralizing background for ions that sluggishly move in a correlated manner. Strong interactions between the charged particles give rise to surprising dynamics such as oscillations of the average kinetic energy during equilibration and extremely fast recombination. Such phenomena offer stimulating and challenging problems for computational scientists, and the physics can be applied to other environments, such as the interior of gas giant planets and plasmas created by short-pulse laser irradiation of solid, liquid, and cluster targets.
Regulation of NF-κB Activation in T Cells via Association of the Adapter Proteins ADAP and CARMA1
Authors: Medeiros Ricardo B. , Burbach Brandon J. , Mueller Kristen L. , Srivastava Rupa , Moon James J. , Highfill Sarah , Peterson Erik J. , Shimizu Yoji
Published: May 2007

The adapter protein ADAP regulates T lymphocyte adhesion and activation. We present evidence for a previously unrecognized function for ADAP in regulating T cell receptor (TCR)–mediated activation of the transcription factor NF-κB. Stimulation of ADAP-deficient mouse T cells with antibodies to CD3 and CD28 resulted in impaired nuclear translocation of NF-κB, a reduced DNA binding, and delayed degradation and decreased phosphorylation of IκB (inhibitor of NF-κB). TCR-stimulated assembly of the CARMA1–BCL-10–MALT1 complex was substantially impaired in the absence of ADAP. We further identified a region of ADAP that is required for association with the CARMA1 adapter and NF-κB activation but is not required for ADAP-dependent regulation of adhesion. These findings provide new insights into ADAP function and the mechanism by which CARMA1 regulates NF-κB activation in T cells.
The Golden Weed, America's Most Deadly Drug
Authors: Proctor Robert N.
Published: May 2007

The Cigarette Century. The Rise, Fall, and Deadly Persistence of the Product That Defined America.By Allan M. Brandt. Basic Books, New York, 2007. 640 pp. $36, C$43.50. ISBN 9780465070473.

In this history of changing attitudes toward smoking, Brandt describes how the tobacco industry promoted "the most deadly addiction on the planet."
Synthesis of Tetrahexahedral Platinum Nanocrystals with High-Index Facets and High Electro-Oxidation Activity
Authors: Tian Na , Zhou Zhi-You , Sun Shi-Gang , Ding Yong , Wang Zhong Lin
Published: May 2007

The shapes of noble metal nanocrystals (NCs) are usually defined by polyhedra that are enclosed by {111} and {100} facets, such as cubes, tetrahedra, and octahedra. Platinum NCs of unusual tetrahexahedral (THH) shape were prepared at high yield by an electrochemical treatment of Pt nanospheres supported on glassy carbon by a square-wave potential. The single-crystal THH NC is enclosed by 24 high-index facets such as {730}, {210}, and/or {520} surfaces that have a large density of atomic steps and dangling bonds. These high-energy surfaces are stable thermally (to 800°C) and chemically and exhibit much enhanced (up to 400%) catalytic activity for equivalent Pt surface areas for electro-oxidation of small organic fuels such as formic acid and ethanol.
Local Replenishment of Coral Reef Fish Populations in a Marine Reserve
Authors: Almany Glenn R. , Berumen Michael L. , Thorrold Simon R. , Planes Serge , Jones Geoffrey P.
Published: May 2007

The scale of larval dispersal of marine organisms is important for the design of networks of marine protected areas. We examined the fate of coral reef fish larvae produced at a small island reserve, using a mass-marking method based on maternal transmission of stable isotopes to offspring. Approximately 60% of settled juveniles were spawned at the island, for species with both short (<2 weeks) and long (>1 month) pelagic larval durations. If natal homing of larvae is a common life-history strategy, the appropriate spatial scales for the management and conservation of coral reefs are likely to be much smaller than previously assumed.
Comparison of Immunoglobulin G Responses to the Spike and Nucleocapsid Proteins of Severe Acute Respiratory Syndrome (SARS) Coronavirus in Patients with SARS
Authors: Zhao Jincun , Wang Wei , Wang Wenling , Zhao Zhendong , Zhang Yan , Lv Ping , Ren Furong , Gao Xiao-Ming
Published: May 2007

Both the nucleocapsid (N) and the spike (S) proteins of severe acute respiratory syndrome (SARS)-associated coronavirus (SARS-CoV) are able to induce strong humoral responses in humans following an infection. To compare the immunoglobulin G (IgG) responses to the S and N proteins of SARS-CoV in SARS patients during the manifestation/convalescent period with those during the postinfection period, serum samples were collected from hospitalized SARS patients within 6 weeks after the onset of illness (set 1; 57 sequential samples from 19 patients) or 2 to 3 months after their recovery (set 2; 33 postinfection samples from 33 subjects). Serum samples from 100 healthy blood donors (set 3), collected in 2002, were also included. The specific IgG response to whole virus, the fragment from positions 450 to 650 of the S protein (S450-650), and the full-length N protein of SARS-CoV were measured by enzyme-linked immunosorbent assays (ELISAs). Western blot assays were carried out to confirm the ELISA results. Fifty-one of the serum samples in set 1 (89%) bound to the N protein, a proportion similar to that which recognized whole virus (79%) and the S-protein fragment (77%). All 33 serum samples from set 2 were strongly positive for N-protein-specific IgG, while 27 (82%) were positive for anti-S450-650 IgG. Two of the serum samples from set 3 were strongly positive for anti-N-protein IgG but not anti-S450-650 IgG. Similar levels of IgG responses to the S and N proteins were observed in SARS patients during the manifestation and convalescent stages. In the postinfection period, however, a number of patients had much lower serum IgG levels against S450-650 than against the N protein.
Real-Time PCR for Diagnosis of Human Bocavirus Infections and Phylogenetic Analysis
Authors: Neske Florian , Blessing Kerstin , Tollmann Franz , Schubert Jörg , Rethwilm Axel , Kreth Hans Wolfgang , Weissbrich Benedikt
Published: May 2007

The human bocavirus (hBoV) was first described in 2005 in respiratory tract samples. The clinical relevance of hBoV is still unclear. The aim of our study was to establish a real-time PCR assay for the detection and quantification of hBoV DNA, to apply the real-time assay for the analysis of stool and serum samples for the presence of hBoV DNA, and to perform a phylogenetic analysis of the hBoV positive samples. A total of 834 nasopharyngeal aspirates (NPA), 10 serum samples, and 31 stool samples of children with acute respiratory diseases were retrospectively tested. For phylogenetic analysis, 968 bp of the VP2 gene were sequenced from 69 hBoV-positive NPA samples. The qualitative results of the real-time hBoV PCR were in good agreement with a conventional hBoV PCR. We found that 12% of the NPA were positive for hBoV DNA. The median viral load in the NPA was 4.9 × 10
3
copies/ml (range, 2.7 × 10° to 1.5 × 10
11
copies/ml). There was no difference of the hBoV load in NPA between children with or without known coinfection, but the load was significantly higher in children with bronchitis than in children with the diagnosis of febrile seizures. hBoV DNA was found in 1 of 10 serum samples and in 14 of 31 stool samples. hBoV sequence identity was >99% in the VP2 region. In conclusion, hBoV DNA can be found in NPA samples at very high titers. In addition to being found in the respiratory tract, hBoV was found in stool samples. The clinical relevance of these findings remains to be determined.
Quality Control and Reference Guidelines for CLSI Broth Microdilution Method (M38-A Document) for Susceptibility Testing of Anidulafungin against Molds
Authors: Espinel-Ingroff A. , Fothergill A. , Ghannoum M. , Manavathu E. , Ostrosky-Zeichner L. , Pfaller M. A. , Rinaldi M. G. , Schell W. , Walsh T. J.
Published: May 2007

The CLSI (formerly NCCLS) M38-A document for antifungal susceptibility testing of filamentous fungi does not describe guidelines for echinocandins. A multicenter study (eight centers) evaluated inter- and intralaboratory reproducibilities of two reading times (24 and 48 h or 48 and 72 h) and two end points (MICs and minimum effective concentrations [MECs]) for evaluating anidulafungin against molds. Anidulafungin MICs (≥50% inhibition) and MECs (morphological hyphal changes) were determined for seven
Aspergillus
isolates (four species) and one isolate each of
Fusarium moniliforme
,
Fusarium solani
, and
Paecilomyces variotii
and for two
Scedosporium apiospermum
isolates. The inter- and intralaboratory reproducibilities of 10 replicate tests performed in each laboratory on 10 different days for each isolate was 100% at 24 h (MECs, ≤0.015 μg/ml) for six
Aspergillus
and
P. variotii
isolates. The reproducibility was 94 to 96.7% at 72 h (MECs, 1 to 8 μg/ml) for
S. apiospermum
and 96.7 to 97.5% at 48 h (MICs, ≥32 μg/ml) for both
Fusarium
isolates. Introduction of these identified optimum testing conditions for anidulafungin into future versions of the M38 document is warranted.
Ultrasensitive p24 Antigen Assay for Diagnosis of Perinatal Human Immunodeficiency Virus Type 1 Infection
Authors: Fiscus Susan A. , Wiener Jeffrey , Abrams Elaine J. , Bulterys Marc , Cachafeiro Ada , Respess Richard A.
Published: May 2007

We evaluated an ultrasensitive p24 antigen enzyme immunosorbent assay on 802 plasma specimens from 582 infants and children of 0 to 180 days of age. Overall sensitivity and specificity were 91.7% and 98.5%, respectively. After exclusion of infants of less than 7 days of age, the sensitivity and specificity were 93.7% and 98.3%, respectively.
The Other Group G Streptococcus: Increased Detection ofStreptococcus canisUlcer Infections in Dog Owners
Authors: Lam Maggie M. , Clarridge Jill E. , Young E. J. , Mizuki Sally
Published: May 2007

β-Hemolytic Lancefield group GStreptococcus dysgalactiaeandStreptococcus caniscannot be distinguished when only Lancefield typing is performed. Phenotypic testing and 16S rRNA gene sequencing identifiedS. canisassociated with ulcer infections in dog owners. BecauseS. canismay be incorrectly identified (published biochemical descriptions are inconsistent), there may be an underestimation of the true number of infections. Identification of group G streptococci to the species level could have epidemiological and clinical implications.
The Herpes Simplex Virus Type 1 BgKLVariant, Unlike the BgOLVariant, Shows a Higher Association with Orolabial Infection than with Infections at Other Sites, Supporting the Variant-Dispersion-Replacement Hypothesis
Authors: Ozawa Shigeru , Eda Hiroyuki , Ishii Yasuyuki , Ban Fumihiko , Funabashi Toshiyuki , Hata Seiichiro , Hayashi Kozaburo , Iga Hiroki , Ikushima Takao , Ishiko Hiroaki , Itagaki Tomoo , Kawana Rinji , Kobayashi Shunsaku , Ogino Takeo , Sekizawa Tsuyoshi , Shimomura Yoshikazu , Shiota Hiroshi , Mori Ryoichi , Nakakita Takashi , Numazaki Yoshio , Ozaki Yoshikatsu , Yamamoto Shigeru , Yoshino Kamesaburo , Yanagi Kazuo
Published: May 2007

The identification and geographic distribution of the herpes simplex virus type 1 (HSV-1) BglII restriction fragment length polymorphism (RFLP) variants named BgKLand BgOLin clinical isolates from orolabial and cutaneous sites were described in our previous reports, in which the dispersion and replacement of HSV-1 variants were proposed. The base substitution sites deduced from the BgKLmultiple RFLP variations were mapped to the UL12 (DNase), RL2 (α0 transactivator), and latency-associated transcript genes in the present study. The results show that the relative frequencies (RFs) of BgKLare significantly higher in orolabial and cutaneous HSV-1 infections than in ocular infections. For the BgOLvariant, the opposite was found; i.e., the RF of BgOLwas significantly lower in orolabial and cutaneous infections than in ocular infections. No significant differences in the RFs of non-BgKL:non-BgOLisolates were observed. The ratio of the BgKLRF to the BgOLRF was much higher for the orolabial and cutaneous infection groups than for the ocular infection group, whereas the BgKLRF-to-non-BgKL:non-BgOLRF ratios for the former groups were slightly higher than those for the latter group. The higher efficiency of orolabial and cutaneous infections caused by BgKLcompared to the efficiency of infections caused by BgOLallows BgKLto spread more efficiently in human populations and to displace BgOL, because the mouth and lips are the most common HSV-1 infection sites in children. The present study supports our HSV-1 dispersion-and-replacement hypothesis and suggests that HSV-1, the latency-reactivation of which allows variants to accumulate in human populations, has evolved under competitive conditions, providing a new perspective on the polymorphism or variation of HSV-1.
Comparison of Results of Detection of Rhinovirus by PCR and Viral Culture in Human Nasal Wash Specimens from Subjects with and without Clinical Symptoms of Respiratory Illness
Authors: Wright Peter F. , Deatly Anne M. , Karron Ruth A. , Belshe Robert B. , Shi Jian R. , Gruber William C. , Zhu Yuwei , Randolph Valerie B.
Published: May 2007

Human rhinoviruses (HRV) cause acute upper respiratory illness. The frequency of HRV-associated illnesses appears greater when PCR assays are used to detect rhinoviruses. The present study performed PCR-based detection of HRV upon entry of subjects into respiratory syncytial virus and parainfluenza type 3 vaccine trials when subjects were symptom-free and upon subsequent development of clinical symptoms of respiratory illness during the trial. The background of HRV PCR positivity in symptom-free individuals (30/139 [22%]) was only slightly lower than in those with respiratory illness (28/77 [36%]). For subjects with multiple samples, it was estimated that HRV was detectable by PCR for approximately 100 days before, during, and after clinical symptoms were documented. PCR is a remarkably more sensitive method of detecting HRV than is tissue culture. The presence of HRV RNA may not always reflect an association with infectious virus production. The limited association of HRV RNA with illness suggests caution in assigning causality of HRV PCR positivity to clinical symptoms of respiratory illness.
Chloroviruses Encode a Bifunctional dCMP-dCTP Deaminase That Produces Two Key Intermediates in dTTP Formation
Authors: Zhang Yuanzheng , Maley Frank , Maley Gladys F. , Duncan Garry , Dunigan David D. , Van Etten James L.
Published: May 2007

The chlorovirus PBCV-1, like many large double-stranded DNA-containing viruses, contains several genes that encode putative proteins involved in nucleotide biosynthesis. This report describes the characterization of the PBCV-1 dCMP deaminase, which produces dUMP, a key intermediate in the synthesis of dTTP. As predicted, the recombinant protein has dCMP deaminase activity that is activated by dCTP and inhibited by dTTP. Unexpectedly, however, the viral enzyme also has dCTP deaminase activity, producing dUTP. Typically, these two reactions are catalyzed by proteins in separate enzyme classes; to our knowledge, this is the first example of a protein having both deaminase activities. Kinetic experiments established that (i) the PBCV-1 enzyme has a higher affinity for dCTP than for dCMP, (ii) dCTP serves as a positive heterotropic effector for the dCMP deaminase activity and a positive homotropic effector for the dCTP deaminase activity, and (iii) the enzymatic efficiency of the dCMP deaminase activity is about four times higher than that of the dCTP deaminase activity. Inhibitor studies suggest that the same active site is involved in both dCMP and dCTP deaminations. The discovery that the PBCV-1 dCMP deaminase has two activities, together with a previous report that the virus also encodes a functional dUTP triphosphatase (Y. Zhang, H. Moriyama, K. Homma, and J. L. Van Etten, J. Virol. 79:9945-9953, 2005), means that PBCV-1 is the first virus to encode enzymes involved in all three known pathways to form dUMP.
Sensitive Assays for Simian Foamy Viruses Reveal a High Prevalence of Infection in Commensal, Free-Ranging Asian Monkeys
Authors: Jones-Engel Lisa , Steinkraus Katherine A. , Murray Shannon M. , Engel Gregory A. , Grant Richard , Aggimarangsee Nantiya , Lee Benjamin P. Y.-H. , May Cynthia , Schillaci Michael A. , Somgird Chaleamchat , Sutthipat Tulyawat , Vojtech Lucia , Zhao JianYuan , Linial Maxine L.
Published: May 2007

Foamy viruses (FV) are retroviruses that naturally infect many hosts, including most nonhuman primates (NHPs). Zoonotic infection by primate FV has been documented in people in Asia who reported contact with free-ranging macaques. FV transmission in Asia is a concern, given abundant human-NHP contact, particularly at monkey temples and in urban settings. We have developed three assays capable of detecting the presence of FV in Asian NHP species that are commensal with humans: enzyme-linked immunosorbent assay (ELISA), Western blot assays using recombinant viral Gag protein, and an indicator cell line that can detect macaque FV. The recombinant ELISA correlates very well with the presence of FV sequences detected by PCR. We have used these assays to demonstrate both that FV is highly prevalent among free-ranging NHPs and that seroconversion occurs at a young age in these animals. These assays should also prove useful for large-scale analysis of the prevalence of FV infections in human populations in Asia that are commensal with free-ranging NHPs.
A Novel Bcl-2-Like Inhibitor of Apoptosis Is Encoded by the Parapoxvirus Orf Virus
Authors: Westphal Dana , Ledgerwood Elizabeth C. , Hibma Merilyn H. , Fleming Stephen B. , Whelan Ellena M. , Mercer Andrew A.
Published: May 2007

Apoptotic cell death forms part of the host defense against virus infection. We tested orf virus, a member of the poxvirus family, for the ability to inhibit apoptosis and found that orf virus-infected cells were fully resistant to UV-induced changes in cell morphology, caspase activation, and DNA fragmentation. By using a library of vaccinia virus-orf virus recombinants, we identified an orf virus gene (
ORFV125
) whose presence was linked with the inhibition of apoptosis. The 173-amino-acid predicted protein had no clear homologs in public databases other than those encoded by other parapoxviruses. However, ORFV125 possessed a distinctive C-terminal domain which was necessary and sufficient to direct the protein to the mitochondria. We determined that ORFV125 alone could fully inhibit UV-induced DNA fragmentation, caspase activation, and cytochrome
c
release and that its mitochondrial localization was required for its antiapoptotic function. In contrast, ORFV125 did not prevent UV-induced activation of c-Jun NH
2
-terminal kinase, an event occurring upstream of the mitochondria. These features are comparable to the antiapoptotic properties of the mitochondrial regulator Bcl-2. Furthermore, bioinformatic analyses revealed sequence and secondary-structure similarities to Bcl-2 family members, including characteristic residues of all four Bcl-2 homology domains. Consistent with this, the viral protein inhibited the UV-induced activation of the proapoptotic Bcl-2 family members Bax and Bak. ORFV125 is the first parapoxvirus apoptosis inhibitor to be identified, and we propose that it is a new antiapoptotic member of the Bcl-2 family.
A Single Amino Acid of the Human Immunodeficiency Virus Type 2 Capsid Affects Its Replication in the Presence of Cynomolgus Monkey and Human TRIM5αs
Authors: Song Haihan , Nakayama Emi E. , Yokoyama Masaru , Sato Hironori , Levy Jay A. , Shioda Tatsuo
Published: May 2007

Human immunodeficiency virus type 2 (HIV-2) strains vary widely in their abilities to grow in Old World monkey (OWM) cells such as those of cynomolgus monkeys (CM). We evaluated eight HIV-2 isolates for their sensitivities to CM TRIM5α, an anti-HIV factor in OWM cells. We found that different HIV-2 isolates showed differences in their sensitivities to CM TRIM5α. Sequence analysis showed that TRIM5α-sensitive viruses had proline at the 120th position of the capsid protein (CA), whereas TRIM5α-resistant viruses had either alanine or glutamine. Mutagenesis studies indicated that the single amino acid at the 120th position indeed affected the sensitivity of the virus to CM TRIM5α.
Novel Strategy for Treatment of Viral Central Nervous System Infection by Using a Cell-Permeating Inhibitor of c-Jun N-Terminal Kinase
Authors: Beckham J. David , Goody Robin J. , Clarke Penny , Bonny Christophe , Tyler Kenneth L.
Published: May 2007

Viral encephalitis is a major cause of morbidity and mortality worldwide, yet there is no proven efficacious therapy for most viral infections of the central nervous system (CNS). Many of the viruses that cause encephalitis induce apoptosis and activate c-Jun N-terminal kinase (JNK) following infection. We have previously shown that reovirus infection of epithelial cell lines activates JNK-dependent apoptosis. We now show that reovirus infection resulted in activation of JNK and caspase-3 in the CNS. Treatment of reovirus-infected mice with a cell-permeating peptide that competitively inhibits JNK activity resulted in significantly prolonged survival of intracerebrally infected mice following an otherwise lethal challenge with T3D (100× 50% lethal dose). Protection correlated with reduced CNS injury, reduced neuronal apoptosis, and reduced c-Jun activation without altering the viral titer or viral antigen distribution. Given the efficacy of the inhibitor in protecting mice from viral encephalitis, JNK inhibition represents a promising and novel treatment strategy for viral encephalitis.
Cytokine-Independent Upregulation of MDA5 in Viral Infection
Authors: Yount Jacob S. , Moran Thomas M. , López Carolina B.
Published: May 2007

The RNA helicases RIG-I and MDA5 detect virus infection of dendritic cells (DCs) leading to cytokine induction. Maximal sensitivity for virus detection by these helicases is obtained after their upregulation, which is thought to occur primarily through type I interferon (IFN) signaling. Here we demonstrate that in response to paramyxovirus infection, RIG-I upregulation requires type I IFN whereas MDA5 expression is increased by Sendai virus infection independently of signaling mediated by type I IFN, STAT1, tumor necrosis factor alpha, or NF-κB. This MDA5 upregulation is largely lost in IRF3 knockout DCs and is achieved in type I IFN-deficient cells expressing constitutively active IRF3.
An RNA Stem-Loop within the Bovine Coronavirus nsp1 Coding Region Is a
cis
-Acting Element in Defective Interfering RNA Replication
Authors: Brown Cary G. , Nixon Kimberley S. , Senanayake Savithra D. , Brian David A.
Published: May 2007

Higher-order
cis
-acting RNA replication structures have been identified in the 3′- and 5′-terminal untranslated regions (UTRs) of a bovine coronavirus (BCoV) defective interfering (DI) RNA. The UTRs are identical to those in the viral genome, since the 2.2-kb DI RNA is composed of only the two ends of the genome fused between an internal site within the 738-nucleotide (nt) 5′-most coding region (the nsp1, or p28, coding region) and a site just 4 nt upstream of the 3′-most open reading frame (ORF) (the N gene). The joined ends of the viral genome in the DI RNA create a single continuous 1,635-nt ORF, 288 nt of which come from the 738-nt nsp1 coding region. Here, we have analyzed features of the 5′-terminal 288-nt portion of the nsp1 coding region within the continuous ORF that are required for DI RNA replication. We observed that (i) the 5′-terminal 186 nt of the nsp1 coding region are necessary and sufficient for DI RNA replication, (ii) two
Mfold
-predicted stem-loops within the 186-nt sequence, named SLV (nt 239 to 310) and SLVI (nt 311 to 340), are supported by RNase structure probing and by nucleotide covariation among closely related group 2 coronaviruses, and (iii) SLVI is a required higher-order structure for DI RNA replication based on mutation analyses. The function of SLV has not been evaluated. We conclude that SLVI within the BCoV nsp1 coding region is a higher-order
cis
-replication element for DI RNA and postulate that it functions similarly in the viral genome.
Maturation of Blood-Derived Dendritic Cells Enhances Human Immunodeficiency Virus Type 1 Capture and Transmission
Authors: Izquierdo-Useros Nuria , Blanco Julià , Erkizia Itziar , Fernández-Figueras Maria Teresa , Borràs Francesc E. , Naranjo-Gómez Mar , Bofill Margarita , Ruiz Lidia , Clotet Bonaventura , Martinez-Picado Javier
Published: May 2007

Dendritic cells (DCs) are specialized antigen-presenting cells. However, DCs exposed to human immunodeficiency virus type 1 (HIV-1) are also able to transmit a vigorous cytopathic infection to CD4
+
T cells, a process that has been frequently related to the ability of DC-SIGN to bind HIV-1 envelope glycoproteins. The maturation of DCs can increase the efficiency of HIV-1 transmission through
trans
infection. We aimed to comparatively study the effect of maturation in monocyte-derived DCs (MDDCs) and blood-derived myeloid DCs during the HIV-1 capture process. In vitro capture and transmission of envelope-pseudotyped HIV-1 and its homologous replication-competent virus to susceptible target cells were assessed by p24
gag
detection, luciferase activity, and both confocal and electron microscopy. Maturation of MDDCs or myeloid DCs enhanced the active capture of HIV-1 in a DC-SIGN- and viral envelope glycoprotein-independent manner, increasing the life span of trapped virus. Moreover, higher viral transmission of mature DCs to CD4
+
T cells was highly dependent on active viral capture, a process mediated through cholesterol-enriched domains. Mature DCs concentrated captured virus in a single large vesicle staining for CD81 and CD63 tetraspanins, while immature DCs lacked these structures, suggesting different intracellular trafficking processes. These observations help to explain the greater ability of mature DCs to transfer HIV-1 to T lymphocytes, a process that can potentially contribute to the viral dissemination at lymph nodes in vivo, where viral replication takes place and there is a continuous interaction between susceptible T cells and mature DCs.
Primary Cell Model for Activation-Inducible Human Immunodeficiency Virus
Authors: Burke Bryan , Brown Helen J. , Marsden Matthew D. , Bristol Gregory , Vatakis Dimitrios N. , Zack Jerome A.
Published: May 2007

Quiescent T lymphocytes containing latent human immunodeficiency virus (HIV) provide a long-lived viral reservoir. This reservoir may be the source of active infection that is reinitiated following the cessation of antiretroviral therapy. Therefore, it is important to understand the mechanisms involved in latent infection to develop new strategies to eliminate the latent HIV reservoir. We have previously demonstrated that latently infected quiescent lymphocytes can be generated during thymopoiesis in vivo in the SCID-hu mouse system. However, there is still a pressing need for an in vitro model of HIV latency in primary human cells. Here, we present a novel in vitro model that recapitulates key aspects of dormant HIV infection. Using an enhanced green fluorescent protein-luciferase fusion protein-containing reporter virus, we have generated a stable infection in primary human CD4
+
CD8
+
thymocytes in the absence of viral gene expression. T-cell activation induces a >200-fold induction of reporter activity. The induced reporter activity originates from a fully reverse-transcribed and integrated genome. We further demonstrate that this model can be useful to study long terminal repeat regulation, as previously characterized NF-κB response element mutations decrease the activation of viral gene expression. This model can therefore be used to study intricate molecular aspects of activation-inducible HIV infection in primary cells.
Relationship between blood pressure and blood flow in newborn preterm infants
Authors: Groves A M , Kuschel C A , Knight D B , Skinner J R
Published: May 2007

Background:

Arterial blood pressure remains the most frequently monitored indicator of neonatal circulatory status. However, studies of systemic perfusion in neonates have often shown only weakly positive associations with blood pressure.

Objectives:

To examine the relationship between invasively monitored arterial blood pressure and four measurements of systemic perfusion: left and right ventricular outputs, superior vena caval (SVC) flow and descending aortic (DAo) flow.

Design:

Echocardiographic assessments of perfusion were performed four times in the first 48 h of postnatal life in a cohort of 34 preterm (<30 weeks) infants. Arterial blood pressure was monitored invasively over the exact duration of the echocardiogram.

Results:

In the first 48 h of postnatal life there was no evidence of a positive association between blood pressure and volume of blood flow in any of the four vessels studied. At 5 h postnatal age there was a weak but significant inverse correlation between volume of SVC flow and arterial blood pressure (p = 0.04). A similar but non-significant trend was seen at 12 h postnatal age.

Conclusions:

Infants with reduced systemic perfusion tend to have normal or high blood pressure in the first hours of life, suggesting that a high systemic vascular resistance may lead to reduced blood flow. Low blood pressure does not correlate with poor perfusion in the first 48 h of postnatal life in sick preterm infants.
Implication of the satellite cell in dystrophic muscle fibrosis: a self-perpetuating mechanism of collagen overproduction
Authors: Alexakis Catherine , Partridge Terence , Bou-Gharios George
Published: May 2007

Because of its mechanical function, skeletal muscle is heavily influenced by the composition of its extracellular matrix (ECM). Fibrosis generated by chronic damage, such as occurs in muscular dystrophies, is thus particularly disastrous in this tissue. Here, we examined the interrelationship between the muscle satellite cell and the production of collagen type I, a major component of fibrotic ECM, by using both C2C12, a satellite cell-derived cell line, and primary muscle satellite cells. In C2C12 cells, we found that expression of collagen type I mRNA decreases substantially during skeletal muscle differentiation. On a single-cell level, collagen type I and myogenin became mutually exclusive after 3 days in differentiation medium, whereas addition of collagen markedly suppressed differentiation of C2C12 cells. Primary cultures of satellite cells associated with isolated single fibers of the young (4 wk old) mdx dystrophic mouse and of C57BL/10ScSn wild-type controls expressed collagen type I and type III mRNA and protein. This pattern persisted in wild-type mice at all ages. But, curiously, in older (18-mo-old) mdx mice, although the myogenic cells continued to express type III collagen, type I expression became restricted to nonmyogenic cells. These cells typically constituted part of a cellular sheet surrounding the old mdx fibers. This combination of features strongly suggests that the progression to fibrosis in dystrophic muscle involves changes in the mechanisms controlling matrix production, which generates positive feedback that results in a reprogramming of myoblasts to a profibrotic function.
Vaticanol B, a resveratrol tetramer, regulates endoplasmic reticulum stress and inflammation
Authors: Tabata Yoshiyuki , Takano Katsura , Ito Tetsuro , Iinuma Munekazu , Yoshimoto Tanihiro , Miura Hikari , Kitao Yasuko , Ogawa Satoshi , Hori Osamu
Published: May 2007

Enhanced endoplasmic reticulum (ER) stress has been implicated in various pathological situations including inflammation. During a search for compounds that regulate ER stress, we identified vaticanol B, a tetramer of resveratrol, as an agent that protects against ER stress-induced cell death. Vaticanol B suppressed the induction of unfolded protein response-targeted genes such as glucose-regulated protein 78 ( GRP78) and C/EBP-homologous protein ( CHOP) after cells were treated with ER stressors. Analysis in the mouse macrophage cell line RAW 264.7 revealed that vaticanol B also possesses a strong anti-inflammatory activity. Production of a variety of inflammatory modulators such as tumor necrosis factor-α, nitric oxide, and prostaglandin E2 was inhibited by vaticanol B to a much greater extent than by monomeric or dimeric resveratrol after exposure of cells to lipopolysaccharide. Further investigations to determine the common mechanisms underlying the regulation of ER stress and inflammation by vaticanol B disclosed an important role for vaticanol B in regulation of basic gene expression and in prevention of the protein leakage from the ER into the cytosol in both conditions. These results suggest that vaticanol B is a novel anti-inflammatory agent that improves the ER environment by reducing the protein load on the ER and by maintaining the membrane integrity of the ER.
The role of mitochondria in pharmacotoxicology: a reevaluation of an old, newly emerging topic
Authors: Scatena Roberto , Bottoni Patrizia , Botta Giorgia , Martorana Giuseppe E. , Giardina Bruno
Published: May 2007

In addition to their well-known critical role in energy metabolism, mitochondria are now recognized as the location where various catabolic and anabolic processes, calcium fluxes, various oxygen-nitrogen reactive species, and other signal transduction pathways interact to maintain cell homeostasis and to mediate cellular responses to different stimuli. It is important to consider how pharmacological agents affect mitochondrial biochemistry, not only because of toxicological concerns but also because of potential therapeutic applications. Several potential targets could be envisaged at the mitochondrial level that may underlie the toxic effects of some drugs. Recently, antiviral nucleoside analogs have displayed mitochondrial toxicity through the inhibition of DNA polymerase-γ (pol-γ). Other drugs that target different components of mitochondrial channels can disrupt ion homeostasis or interfere with the mitochondrial permeability transition pore. Many known inhibitors of the mitochondrial electron transfer chain act by interfering with one or more of the respiratory chain complexes. Nonsteroidal anti-inflammatory drugs (NSAIDs), for example, may behave as oxidative phosphorylation uncouplers. The mitochondrial toxicity of other drugs seems to depend on free radical production, although the mechanisms have not yet been clarified. Meanwhile, drugs targeting mitochondria have been used to treat mitochondrial dysfunctions. Importantly, drugs that target the mitochondria of cancer cells have been developed recently; such drugs can trigger apoptosis or necrosis of the cancer cells. Thus the aim of this review is to highlight the role of mitochondria in pharmacotoxicology, and to describe whenever possible the main molecular mechanisms underlying unwanted and/or therapeutic effects.
Systems genetic analysis of peripheral iron parameters in the mouse
Authors: Jones Byron C. , Beard John L. , Gibson Jennifer N. , Unger Erica L. , Allen Richard P. , McCarthy Kristin A. , Earley Christopher J.
Published: May 2007

Iron homeostasis is one of the most critical functions in living systems. Too little iron can lead to anemia and tissue-specific disorders, such as splenomegaly. Excessive systemic iron is characteristic of hemochromatosis and is implicated in the brain in Parkinson's disease. With the exception of some single gene diseases like hemochromatosis, we know little about genetic-based, individual differences in iron-related parameters and their impact on biology. To model genetic control of iron homeostasis, we measured liver, spleen, and plasma iron concentrations, hematocrit and hemoglobin, transferrin saturation, and total iron-binding capacity in several BXD/Ty recombinant inbred mouse strains derived from C57BL/6 and DBA/2 progenitors. At 120 days of age, the animals were killed for iron analysis. All measures showed genetic-based variability consistent with polygenic influence. Analysis of principal components of the seven measures revealed three factors that we named availability, transport, and storage. Quantitative trait loci (QTL) analysis revealed one suggestive QTL on chromosome 5 for availability, two suggestive QTL (one on chromosome 1 and the other on chromosome 7) for transport, and one weak QTL on chromosome 2 for storage. The results show that iron homeostasis is a complex trait and is influenced by multiple genes.
Calcineurin-Aα activation enhances the structure and function of regenerating muscles after myotoxic injury
Authors: Stupka Nicole , Schertzer Jonathan D. , Bassel-Duby Rhonda , Olson Eric N. , Lynch Gordon S.
Published: May 2007

Calcineurin signaling is essential for successful muscle regeneration. Although calcineurin inhibition compromises muscle repair, it is not known whether calcineurin activation can enhance muscle repair after injury. Tibialis anterior (TA) muscles from adult wild-type (WT) and transgenic mice overexpressing the constitutively active calcineurin-Aα transgene under the control of the mitochondrial creatine kinase promoter (MCK-CnAα*) were injected with the myotoxic snake venom Notexin to destroy all muscle fibers. The TA muscle of the contralateral limb served as the uninjured control. Muscle structure was assessed at 5 and 9 days postinjury, and muscle function was tested in situ at 9 days postinjury. Calcineurin stimulation enhanced muscle regeneration and altered levels of myoregulatory factors (MRFs). Recovery of myofiber size and force-producing capacity was hastened in injured muscles of MCK-CnAα* mice compared with control. Myogenin levels were greater 5 days postinjury and myocyte enhancer factor 2a (MEF2a) expression was greater 9 days postinjury in muscles of MCK-CnAα* mice compared with WT mice. Higher MEF2a expression in regenerating muscles of MCK-CnAα* mice 9 days postinjury may be related to an increase of slow fiber genes. Calcineurin activation in uninjured and injured TA muscles slowed muscle contractile properties, reduced fatigability, and enhanced force recovery after 4 min of intermittent maximal stimulation. Therefore, calcineurin activation can confer structural and functional benefits to regenerating skeletal muscles, which may be mediated in part by differential expression of MRFs.