bluuebunny/crossref_metadata_2025_split huggingface dataset:
Adenovirus E3/19K Promotes Evasion of NK Cell Recognition by Intracellular Sequestration of the NKG2D Ligands Major Histocompatibility Complex Class I Chain-Related Proteins A and B
Authors: McSharry Brian P. , Burgert Hans-Gerhard , Owen Douglas P. , Stanton Richard J. , Prod'homme Virginie , Sester Martina , Koebernick Katja , Groh Veronika , Spies Thomas , Cox Steven , Little Ann-Margaret , Wang Eddie C. Y. , Tomasec Peter , Wilkinson Gavin W. G. 
Published: February 2008

ABSTRACTThe adenovirus (Ad) early transcription unit 3 (E3) encodes multiple immunosubversive functions that are presumed to facilitate the establishment and persistence of infection. Indeed, the capacity of E3/19K to inhibit transport of HLA class I (HLA-I) to the cell surface, thereby preventing peptide presentation to CD8+T cells, has long been recognized as a paradigm for viral immune evasion. However, HLA-I downregulation has the potential to render Ad-infected cells vulnerable to natural killer (NK) cell recognition. Furthermore, expression of the immediate-early Ad gene E1A is associated with efficient induction of ligands for the key NK cell-activating receptor NKG2D. Here we show that while infection with wild-type Ad enhances synthesis of the NKG2D ligands, major histocompatibility complex class I chain-related proteins A and B (MICA and MICB), their expression on the cell surface is actively suppressed. Both MICA and MICB are retained within the endoplasmic reticulum as immature endoglycosidase H-sensitive forms. By analyzing a range of cell lines and viruses carrying mutated versions of the E3 gene region, E3/19K was identified as the gene responsible for this activity. The structural requirements within E3/19K necessary to sequester MICA/B and HLA-I are similar. In functional assays, deletion of E3/19K rendered Ad-infected cells more sensitive to NK cell recognition. We report the first NK evasion function in theAdenoviridaeand describe a novel function for E3/19K. Thus, E3/19K has a dual function: inhibition of T-cell recognition and NK cell activation.
Rapid Adaptive Amplification of Preexisting Variation in an RNA Virus
Authors: Dutta Ranendra N. , Rouzine Igor M. , Smith Sarah D. , Wilke Claus O. , Novella Isabel S. 
Published: February 2008

ABSTRACT

The amount and nature of preexisting variation in a population of RNA viruses is an important determinant of the virus's ability to adapt rapidly to a changed environment. However, direct quantification of this preexisting variation may be cumbersome, because potentially beneficial alleles are typically rare, and isolation of a large number of subclones is required. Here, we propose a simpler method. We infer the initial population structure of vesicular stomatitis virus (VSV) by fitting a mathematical model of asexual evolution to an extensive set of measurements of VSV fitness dynamics under various conditions, including new and previously published data. The inferred variation of fitness in the initial population agrees very well with the results of direct experiments with subclone fitness quantification. From the same procedure, we also estimate the mean fitness effect of beneficial mutations (selection coefficient
s
), the percentage of sites in the genome that are under moderate positive or negative selection, and the percentage of sites where beneficial mutations may potentially occur. For VSV strain MARM U evolving in BHK-21 cells, the three parameters have values of 0.39, 9%, and 0.06%, respectively. The method can be generalized and applied easily to other rapidly evolving microbes, including both asexual microorganisms and those with recombination.
Autographa californica
Multiple Nucleopolyhedrovirus Nucleocapsid Protein BV/ODV-C42 Mediates the Nuclear Entry of P78/83
Authors: Wang Yun , Wang Qian , Liang Changyong , Song Jianhua , Li Ni , Shi Hui , Chen Xinwen 
Published: February 2008

ABSTRACT

Autographa californica
multiple nucleopolyhedrovirus (AcMNPV)
BV/ODV-c42
(
orf101
;
c42
), which encodes a 41.5-kDa viral nucleocapsid protein with a putative nuclear localization signal (NLS) motif at the C terminus, is a highly conserved gene among members of the
Baculoviridae
family. C42 is demonstrated to be essential for AcMNPV propagation and can bind to nucleocapsid protein P78/83, a viral activator for the actin-related protein 2/3 (ARP2/3) complex to initiate nuclear actin polymerization, which is essential for viral nucleocapsid morphogenesis during AcMNPV infection. Here, we report the identification of a novel pathway through which
c42
functions in nucleocapsid assembly. Cotransfection of Sf9 cells with
c42
and
p78/83
plasmids demonstrated that C42 was capable of recruiting P78/83 to the nuclei of uninfected cells and that the NLS motif of C42 was essential for this process. To validate this nuclear relocation mode in bacmid-transfected cells, a
c42
-disrupted bacmid (vAc
c42ko-gfp
) and rescued bacmids with wild-type
c42
(vAc
c42res-gfp
) or with NLS coding sequence-mutated
c42
(vAc
c42nls-gfp
) were prepared. By immuno-staining, P78/83 was found to be localized in the cytoplasm of either vAc
c42ko-gfp
- or vAc
c42nls-gfp
-transfected cells, whereas P78/83 was relocated to the nuclei of vAc
c42res-gfp
-transfected cells. Furthermore, F-actin-specific staining confirmed that there was no actin polymerization activity in the nuclei of either vAc
c42ko-gfp
- or vAc
c42nls-gfp
-transfected cells, which might be attributed to the absence of nuclear P78/83, an activator of the ARP2/3 complex to initiate nuclear actin polymerization. We therefore hypothesize a mode of action where C42 binds to P78/83 in the cytoplasm to form a protein complex and cotransports to the nucleus under the direction of the NLS motif in C42 during AcMNPV infection.
Indoor air quality in prisons before and after implementation of a smoking ban law
Authors: Proescholdbell S K , Foley K L , Johnson J , Malek S H 
Published: February 2008

Objective:To ascertain whether a new indoor smoking ban law in North Carolina correctional facilities was successfully implemented and whether the indoor air quality has improved as a result.Method:Before the law came into effect, we tested the air quality of 22 dormitory and common areas within six North Carolina prisons using standard protocols for testing particulate matter. We measured particulate matter 2.5 μm in diameter (PM2.5) using state of the art TSI SidePak monitors. After the law went into effect, the same locations within each prison were tested again. Written inmate surveys were also conducted at two prisons, one with partial smoking ban (indoors only) and one with a total smoking ban (indoors and outdoors).Results:The findings indicate that, on average, levels of respirable suspended particulates (RSPs), an accepted marker for secondhand smoke (SHS) levels, decreased 77% in these prisons after the law took effect compared to levels obtained before ban implementation. Several areas were tobacco-free before the implementation of this ban. In those areas no significant decreases in RSPs were noted.Conclusion:Laws banning tobacco use in correctional facilities can significantly reduce indoor SHS exposure among inmates, visitors and staff and potentially lead to reduced use. To date, 24 US states have enacted 100% smoke-free correctional facility polices for all indoor areas even though inmates and staff have much higher tobacco use prevalence rates than the general population. With an estimated nine million people incarcerated worldwide, prison smoking bans could have a substantial impact in terms of health outcomes and long-term costs if they can effectively reduce exposure to secondhand smoke.
ON THE COMPUTATION OF THE RELATIVE ENTROPY OF PROBABILISTIC AUTOMATA
Authors: CORTES CORINNA , MOHRI MEHRYAR , RASTOGI ASHISH , RILEY MICHAEL 
Published: February 2008

We present an exhaustive analysis of the problem of computing the relative entropy of two probabilistic automata. We show that the problem of computing the relative entropy of unambiguous probabilistic automata can be formulated as a shortest-distance problem over an appropriate semiring, give efficient exact and approximate algorithms for its computation in that case, and report the results of experiments demonstrating the practicality of our algorithms for very large weighted automata. We also prove that the computation of the relative entropy of arbitrary probabilistic automata is PSPACE-complete. The relative entropy is used in a variety of machine learning algorithms and applications to measure the discrepancy of two distributions. We examine the use of the symmetrized relative entropy in machine learning algorithms and show that, contrarily to what is suggested by a number of publications in that domain, the symmetrized relative entropy is neither positive definite symmetric nor negative definite symmetric, which limits its use and application in kernel methods. In particular, the convergence of training for learning algorithms is not guaranteed when the symmetrized relative entropy is used directly as a kernel, or as the operand of an exponential as in the case of Gaussian Kernels. Finally, we show that our algorithm for the computation of the entropy of an unambiguous probabilistic automaton can be generalized to the computation of the norm of an unambiguous probabilistic automaton by using a monoid morphism. In particular, this yields efficient algorithms for the computation of the Lp-norm of a probabilistic automaton.
Abandoned quarries in the Athens urban area: safety assessment and rational land-planning design
Authors: Loupasakis C. , Karfakis J. 
Published: February 2008

Numerous quarries, active and abandoned, have been excavated all over Greece. Based on the practices of the past, most of these quarries were excavated close to the construction activity, thus near expanding cities or major transportation axes. The gradual incorporation of the abandoned quarries into the cities generated the need for change of their usage to be environmentally compatible. The land-planning development of the sites without taking into consideration the geotechnical characteristics of the slopes led to the incorrect selection of the new use or to the misplacement of infrastructure. The main purpose of this paper is to present the geotechnical problems that occurred at constructed facilities and to analyse the influence of correct land-planning design on the reduction of rock fall hazard and the cost of slope support measures.
The problems arising from the unsuitable land-planning design of facilities in abandoned quarries are presented by means of case studies from the Athens urban environment. Most of the data are from the case study of the stability problems of the slopes surrounding the infrastructure of the Attiko Alsos Park, constructed in the abandoned quarries of the Turkovounia hill. To highlight that the problems at Attiko Alsos Park are not atypical, two other old quarry sites are briefly reviewed.
Cloud-Top Temperatures for Precipitating Winter Clouds
Authors: Hanna Jay W. , Schultz David M. , Irving Antonio R. 
Published: February 2008

Abstract
To explore the role of cloud microphysics in a large dataset of precipitating clouds, a 6-month dataset of satellite-derived cloud-top brightness temperatures from the longwave infrared band (channel 4) on the Geostationary Operational Environmental Satellite (GOES) is constructed over precipitation-reporting surface observation stations, producing 144 738 observations of snow, rain, freezing rain, and sleet. The distributions of cloud-top brightness temperatures were constructed for each precipitation type, as well as light, moderate, and heavy snow and rain. The light-snow distribution has a maximum at −16°C, whereas the moderate- and heavy-snow distributions have a bimodal distribution with a primary maximum around −16° to −23°C and a secondary maximum at −35° to −45°C. The light, moderate, and heavy rain, as well as the freezing rain and sleet, distributions are also bimodal with roughly the same temperature maxima, although the colder mode dominates when compared with the snow distributions. The colder of the bimodal peaks trends to lower temperatures with increasing rainfall intensity: −45°C for light rain, −47°C for moderate rain, and −50°C for heavy rain. Like the distributions for snow, the colder peak increases in amplitude relative to the warmer peak at heavier rainfall intensities. The steep slope in the snow distribution for cloud-tops warmer than −15°C is likely due to the combined effects of above-freezing cloud-top temperatures not producing snow, the activation of ice nuclei, the maximum growth rate for ice crystals at temperatures near −15°C, and ice multiplication processes from −3° to −8°C. In contrast, the rain distributions have a gentle slope toward higher cloud-top brightness temperatures (−5° to 0°C), likely due to the warm-rain process. Last, satellite-derived cloud-top brightness temperatures are compared with coincident radiosonde-derived cloud-top temperatures. Although most differences between these two are small, some are as large as ±60°C. The cause of these differences remains unclear, and several hypotheses are offered.
Overview and First Results of the Montreal Urban Snow Experiment 2005
Authors: Lemonsu A. , Bélair S. , Mailhot J. , Benjamin M. , Morneau G. , Harvey B. , Chagnon F. , Jean M. , Voogt J. 
Published: February 2008

Abstract
Within the framework of a large urban meteorology program recently launched in Canada, the Montreal Urban Snow Experiment (MUSE) campaign has been conducted in order to document the thermoradiative exchanges in a densely built-up area of Montreal in late winter and spring conditions. The targeted period is of particular scientific interest because it covers the transition period from a mainly snow-covered urban environment to a mainly snow-free environment. The campaign is based on four weeks of observations from 17 March to 14 April 2005. It couples automatic and continuous measurements of radiation and turbulent fluxes, radiative surface temperatures, and air temperature and humidity with manual observations performed during intensive observation periods to supplement the surface temperature observations and to characterize the snow properties. The footprints of radiation and turbulent flux measurements are computed using the surface–sensor–sun urban model and the flux-source area model, respectively. The analysis of the radiometer footprint underscores the difficulty of correctly locating this type of instrument in urban environments, so that the sensor sees a representative combination of the urban and nonurban surfaces. Here, the alley contribution to the upward radiation tends to be overestimated to the detriment of the road contribution. The turbulent footprints cover homogeneous zones in terms of surface characteristics, whatever the wind direction. The initial analysis of the energy balance displays the predominance of the residual term (QRes = Q* − QH − QE) in comparison with the turbulent sensible (QH) and latent (QE) heat fluxes, since its daytime contribution exceeds 50% of the net radiation (Q*). The investigation of energy balances observed at the beginning and at the end of the experiment (i.e., with and without snow) also indicates that the snow plays a significant role in the flux partitioning and the daily pattern of fluxes. Without snow, the energy balance is characteristic of energy balances that have been already observed in densely built-up areas, notably because of the hysteresis observed for QRes and QH in relation to Q* and because of the high contribution of QRes, which includes the effect of heat storage inside the urban structures. With snow, the flux partitioning is modified by the snowmelt process leading to contributions of the residual term and latent heat flux, which are larger than in the case without snow to the detriment of the sensible heat flux.
The Influence of Nonanatomical Insertion and Incongruence of Meniscal Transplants on the Articular Cartilage in an Ovine Model
Authors: von Lewinski Gabriela , Kohn Dieter , Wirth Carl Joachim , Lazovic Djordje 
Published: February 2008

Background Adequate size matching and anatomically correct positioning must be recognized as essential factors influencing the outcome of meniscal transplantation. Hypothesis Nonanatomical insertion and incongruence of meniscal transplants has an influence on the development of degenerative changes. Study Design Controlled laboratory study. Methods Ten female sheep were used for this animal study. Both knees (N = 20) were divided into 3 groups, subjected to either meniscectomy (group I; n = 10), to a medial meniscal autograft transplantation with a nonanatomical insertion of the anterior and posterior horn (group II; n = 5), or a meniscal autograft transplantation from the opposite knee as an incongruent meniscal autograft (group III; n = 5). After 6 months, radiographic (Fairbank's criteria), macroscopic (Jackson score), and histological evaluation by light microscopy (Mankin score) and scanning electron microscopy of the articular cartilage was performed. Results All applied evaluation methods demonstrated that nonanatomical insertion of meniscal transplants resulted in the highest amount of degenerative cartilage changes. The histological assessment even revealed a significantly enlarged cartilage damage for the non-anatomic-positioned meniscal transplants in relation to the meniscectomized knees. Furthermore, the incongruent meniscal transplants demonstrated a significantly better cartilage situation than nonanatomically inserted meniscal transplants. Conclusion The histological evaluation demonstrated clearly that a nonanatomically inserted meniscal transplant leads to degenerative cartilage changes that are worse than that after meniscectomy. Clinical Relevance Precise anatomic positioning is mandatory for the potential chondroprotective effect of meniscal transplants.
Observer Reliability in Ankle and Calcaneocuboid Stress Radiography
Authors: Lohrer Heinz , Nauck Tanja , Arentz Sabine , Schöll Jakob 
Published: February 2008

Background Stress radiographic measurements play an important role in assessing the degree of joint instability in scientific investigations and for decision making in treatment. However, their validity and reliability are still a matter of intensive debate. Hypothesis There is no difference regarding interobserver and intraobserver reliability with respect to anterior talar drawer, talar tilt, and calcaneocuboid stress radiographs. Study Design Cohort study (diagnosis); Level of evidence, 4. Methods Eighty-nine anterior talar drawer, 89 talar tilt, and 76 calcaneocuboid stress radiographs were selected. Analyses for anterior talar drawer (1 measurement technique), talar tilt (1 measurement technique), and lateral calcaneocuboid instability (4 measurement techniques) were performed by 4 independent raters. One rater repeated the measurements after 1 month. Intraclass and interclass correlation coefficients (ICCs) with calculated confidence intervals assessed intratester and intertester reliability of each measure. Results Ankle stress radiographic interobserver agreement was ICC = 0.73 to 0.97 for anterior talar drawer test and ICC = 0.78 to 0.97 for talar tilt. Interobserver reliability for calcaneocuboid angle measurement methods was lower (ICC = 0.35–0.91) than for the calcaneocuboid joint-space distance measurements (ICC = 0.81–0.95). Intraobserver ICC varied between 0.78 and 0.97 for ankle stress testing and was 0.67 to 0.94 for calcaneocuboid stress radiography, respectively. Conclusions Ankle stress radiographic measurements were proven to be reliable. Insufficient reproducibility was found for angular calcaneocuboid stress radiography measurements, while lateral calcaneocuboid joint-space distances offered accurate reliability. Clinical Relevance Measurement errors can be avoided using standardized stress radiography and measurement techniques with proven reliability.
A PAI-1 (SERPINE1) polymorphism predicts osteonecrosis in children with acute lymphoblastic leukemia: a report from the Children's Oncology Group
Authors: French Deborah , Hamilton Leo H. , Mattano Leonard A. , Sather Harland N. , Devidas Meenakshi , Nachman James B. , Relling Mary V. 
Published: February 2008

AbstractAs glucocorticoid use increased in acute lymphoblastic leukemia, osteonecrosis became an increasingly frequent complication. Besides increased age, host risk factors are poorly defined. We tested whether 12 polymorphisms were associated with osteonecrosis among patients 10 years and older treated on the CCG1882 protocol. Candidate genes (TYMS, MTHFR, ABCB1, BGLAP, ACP5, LRP5, ESR1, PAI-1, VDR, PTH, and PTHR) were chosen based on putative mechanisms underlying osteonecrosis risk. All children received dexamethasone, with doses varying by treatment arm. A PAI-1 polymorphism (rs6092) was associated with risk of osteonecrosis in univariate (P = .002; odds ratio = 2.79) and multivariate (P = .002; odds ratio = 2.89) analyses (adjusting for gender, age, and treatment arm). Overall, 21 of 78 (26.9%) children with PAI-1 GA/AA genotypes, versus 25 of 214 (11.7%) children with GG genotype, developed osteonecrosis. PAI-1 polymorphisms and PAI-1 serum levels have previously been associated with thrombosis. We conclude that PAI-1 genetic variation may contribute to risk of osteonecrosis.
Radiologic and nuclear events: contingency planning for hematologists/oncologists
Authors: Weinstock David M. , Case Cullen , Bader Judith L. , Chao Nelson J. , Coleman C. Norman , Hatchett Richard J. , Weisdorf Daniel J. , Confer Dennis L. 
Published: February 2008

Abstract
Untoward events involving radioactive material, either accidental or intentional, are potentially devastating. Hematologists and oncologists are uniquely suited to help manage radiation victims, as myelosuppression is a frequent complication of radiation exposure. In the aftermath of a large event, such as a nuclear detonation, there may be a national call for surge capacity that involves hematologists/oncologists across the country in the disaster response. In preparation, the National Marrow Donor Program and American Society for Blood and Marrow Transplantation have established the Radiation Injury Treatment Network (RITN), a voluntary consortium of transplant centers, donor centers, and umbilical cord blood banks. RITN is partnered with the Office of the Assistant Secretary for Preparedness and Response in the United States Department of Health and Human Services to develop treatment guidelines, educate healthcare professionals, coordinate situation response, and provide comprehensive evaluation and care for radiation injury victims. We outline the current plans for event response and describe scenarios, including catastrophic events that would require extensive support from hematologists/oncologists across the country. In addition, we highlight important reference resources and discuss current efforts to develop medical countermeasures against radiation toxicity. Practitioners and institutions across the country are encouraged to become involved and participate in the planning.