bluuebunny/crossref_metadata_2025_split huggingface dataset:
No Evidence for Consistent Virus-Specific Immunity in Simian Immunodeficiency Virus-Exposed, Uninfected Rhesus Monkeys
Authors: Letvin Norman L. , Rao Srini S. , Dang Vi , Buzby Adam P. , Korioth-Schmitz Birgit , Dombagoda Dilani , Parvani Jenny G. , Clarke Ryon H. , Bar Liat , Carlson Kevin R. , Kozlowski Pamela A. , Hirsch Vanessa M. , Mascola John R. , Nabel Gary J. 
Published: August 2007

ABSTRACT
Defining the immune correlates of the protection against human immunodeficiency virus type 1 (HIV-1) acquisition in individuals who are exposed to HIV-1 but do not become infected may provide important direction for the creation of an HIV-1 vaccine. We have employed the simian immunodeficiency virus (SIV)/rhesus monkey model to determine whether monkeys can be repeatedly exposed to a primate lentivirus by a mucosal route and escape infection and whether virus-specific immune correlates of protection from infection can be identified in uninfected monkeys. Five of 18 rhesus monkeys exposed 18 times by intrarectal inoculation to SIVmac251 or SIVsmE660 were resistant to infection, indicating that the exposed/uninfected phenotype can be reproduced in a nonhuman primate AIDS model. However, routine peripheral blood lymphocyte gamma interferon enzyme-linked immunospot (ELISPOT), tetramer, and intracellular cytokine staining assays, as well as cytokine-augmented ELISPOT and peptide-stimulated tetramer assays, failed to define a systemic antigen-specific cellular immune correlate to this protection. Further, local cell-mediated immunity could not be demonstrated by tetramer assays of these protected monkeys, and local humoral immunity was not associated with protection against acquisition of virus in another cohort of mucosally exposed monkeys. Therefore, resistance to mucosal infection in these monkeys may not be mediated by adaptive virus-specific immune mechanisms. Rather, innate immune mechanisms or an intact epithelial barrier may be responsible for protection against mucosal infection in this population of monkeys.
The Role of DNA-PKcs and Artemis in Opening Viral DNA Hairpin Termini in Various Tissues in Mice
Authors: Inagaki Katsuya , Ma Congrong , Storm Theresa A. , Kay Mark A. , Nakai Hiroyuki 
Published: August 2007

ABSTRACT
A subset of cellular DNA hairpins at double-strand breaks is processed by DNA-dependent protein kinase catalytic subunit (DNA-PKcs)- and Artemis-associated endonuclease. DNA hairpin termini of adeno-associated virus (AAV) are processed by DNA repair machinery; however, how and what cellular factors are involved in the process remain elusive. Here, we show that DNA-PKcs and Artemis open AAV inverted terminal repeat (ITR) hairpin loops in a tissue-dependent manner. We investigated recombinant AAV (rAAV) genome metabolism in various tissues of DNA-PKcs- or Artemis-proficient or -deficient mice. In the absence of either factor, ITR hairpin opening was impaired, resulting in accumulation of double-stranded linear rAAV genomes capped with covalently closed hairpins at termini. The 5′ end of 3-base hairpin loops of the ITR was the primary target for DNA-PKcs- and Artemis-mediated cleavage. In the muscle, heart, and kidney, DNA-PKcs- and Artemis-dependent hairpin opening constituted a significant pathway, while in the liver, undefined alternative pathways effectively processed hairpins. In addition, our study revealed a Holliday junction resolvase-like activity in the liver that cleaved T-shaped ITR hairpin shoulders by making nicks at diametrically opposed sites. Thus, our approach furthers our understanding of not only rAAV biology but also fundamental DNA repair systems in various tissues of living animals.
Identification and Characterization of Interferon-Induced Proteins That Inhibit Alphavirus Replication
Authors: Zhang Yugen , Burke Crystal W. , Ryman Kate D. , Klimstra William B. 
Published: August 2007

ABSTRACT
Alpha/beta interferon (IFN-α/β) produces antiviral effects through upregulation of many interferon-stimulated genes (ISGs) whose protein products are effectors of the antiviral state. Previous data from our laboratory have shown that IFN-α/β can limit Sindbis virus (SB) replication through protein kinase R (PKR)-dependent and PKR-independent mechanisms and that one PKR-independent mechanism inhibits translation of the infecting virus genome (K. D. Ryman et al., J. Virol. 79:1487-1499, 2005). Further, using Affymetrix microarray technology, we identified 44 genes as candidates for PKR/RNase L-independent IFN-induced antiviral activities. In the current studies, we have begun analyzing these gene products for antialphavirus activity using three techniques: (i) overexpression of the protein from SB vectors and assessment of virulence attenuation in mice; (ii) overexpression of the proteins in a stable tetracycline-inducible murine fibroblast culture system and assessment of effects upon SB replication; and (iii) small interfering RNA-mediated knockdown of gene mRNA in fibroblast cultures followed by SB replication assessment as above. Tested proteins included those we hypothesized had potential to affect virus genome translation and included murine ISG20, ISG15, the zinc finger antiviral protein (ZAP), viperin, p56, p54, and p49. Interestingly, the pattern of antiviral activity for some gene products was different between in vitro and in vivo assays. Viperin and ZAP attenuated virulence most profoundly in mice. However, ISG20 and ZAP potently inhibited SB replication in vitro, whereas and viperin, p56, and ISG15 exhibited modest replication inhibition in vitro. In contrast, p54 and p49 had little to no effect in any assay.
Adjunctive Passive Immunotherapy in Human Immunodeficiency Virus Type 1-Infected Individuals Treated with Antiviral Therapy during Acute and Early Infection
Authors: Mehandru Saurabh , Vcelar Brigitta , Wrin Terri , Stiegler Gabriela , Joos Beda , Mohri Hiroshi , Boden Daniel , Galovich Justin , Tenner-Racz Klara , Racz Paul , Carrington Mary , Petropoulos Christos , Katinger Hermann , Markowitz Martin 
Published: August 2007

ABSTRACT

Three neutralizing monoclonal antibodies (MAbs), 2G12, 2F5, and 4E10, with activity in vitro and in vivo were administered in an open-label, nonrandomized, proof-of-concept study to attempt to prevent viral rebound after interruption of antiretroviral therapy (ART). Ten human immunodeficiency virus type 1-infected individuals identified and treated with ART during acute and early infection were enrolled. The first six patients were administered 1.0 g of each of the three MAbs per infusion. The remaining four patients received 2G12 at 1.0 g/infusion and 2.0 g/infusion of 2F5 and 4E10. The MAbs were well tolerated. Grade I post-partial thromboplastin time prolongations were noted. Viral rebound was observed in 8/10 subjects (28 to 73 days post-ART interruption), and 2/10 subjects remained aviremic over the course of the study. In seven of eight subjects with viral rebound, clear resistance to 2G12 emerged, whereas reductions in the susceptibilities of plasma-derived recombinant viruses to 2F5 and 4E10 were neither sustained nor consistently measured. Viral rebound was associated with a preferential depletion of CD4
+
T cells within the gastrointestinal tract. Though safe, the use of MAbs generally delayed, but did not prevent, virologic rebound. Consideration should be given to further pilot studies with alternative combinations of MAbs and perhaps additional novel treatment modalities.
Intracellular Trafficking and Maturation of Herpes Simplex Virus Type 1 gB and Virus Egress Require Functional Biogenesis of Multivesicular Bodies
Authors: Calistri Arianna , Sette Paola , Salata Cristiano , Cancellotti Enrico , Forghieri Cristina , Comin Alessandra , Göttlinger Heinrich , Campadelli-Fiume Gabriella , Palù Giorgio , Parolin Cristina 
Published: August 2007

ABSTRACTThe biogenesis of multivesicular bodies (MVBs) is topologically equivalent to virion budding. Hence, a number of viruses exploit the MVB pathway to build their envelope and exit from the cell. By expression of dominant negative forms of Vps4 and Vps24, two components of the MVB pathway, we observed an impairment in infectious herpes simplex virus (HSV) assembly/egress, in agreement with a recent report showing the involvement in HSV envelopment of Vps4, the MVB-specific ATPase (C. M. Crump, C. Yates, and T. Minson, J. Virol. 81:7380-7387). Furthermore, HSV infection resulted in morphological changes to MVBs. Glycoprotein B (gB), one of the most highly conserved glycoproteins across theHerpesviridaefamily, was sorted to MVB membranes. In cells expressing the dominant negative form of Vps4, the site of intracellular gB accumulation was altered; part of gB accumulated as an endoglycosidase H-sensitive immature form at a calreticulin-positive compartment, indicating that gB traffic was dependent on a functional MVB pathway. gB was ubiquitinated in both infected and transfected cells. Ubiquitination was in part dependent on ubiquitin lysine 63, a signal for cargo sorting to MVBs. Partial deletion of the gB cytoplasmic tail resulted in a dramatic reduction of ubiquitination, as well as of progeny virus assembly and release to the extracellular compartment. Thus, HSV envelopment/egress and gB intracellular trafficking are dependent on functional MVB biogenesis. Our data support the view that the sorting of gB to MVB membranes may represent a critical step in HSV envelopment and egress and that modified MVB membranes constitute a platform for HSV cytoplasmic envelopment or that MVB components are recruited to the site(s) of envelopment.
Proteolytic Processing of
Turnip Yellow Mosaic Virus
Replication Proteins and Functional Impact on Infectivity
Authors: Jakubiec Anna , Drugeon Gabrièle , Camborde Laurent , Jupin Isabelle 
Published: August 2007

ABSTRACT

Turnip yellow mosaic virus
(TYMV), a positive-strand RNA virus belonging to the alphavirus-like supergroup, encodes its nonstructural replication proteins as a 206K precursor with domains indicative of methyltransferase (MT), proteinase (PRO), NTPase/helicase (HEL), and polymerase (POL) activities. Subsequent processing of 206K generates a 66K protein encompassing the POL domain and uncharacterized 115K and 85K proteins. Here, we demonstrate that TYMV proteinase mediates an additional cleavage between the PRO and HEL domains of the polyprotein, generating the 115K protein and a 42K protein encompassing the HEL domain that can be detected in plant cells using a specific antiserum. Deletion and substitution mutagenesis experiments and sequence comparisons indicate that the scissile bond is located between residues Ser879 and Gln880. The 85K protein is generated by a host proteinase and is likely to result from nonspecific proteolytic degradation occurring during protein sample extraction or analysis. We also report that TYMV proteinase has the ability to process substrates in
trans
in vivo. Finally, we examined the processing of the 206K protein containing native, mutated, or shuffled cleavage sites and analyzed the effects of cleavage mutations on viral infectivity and RNA synthesis by performing reverse-genetics experiments. We present evidence that PRO/HEL cleavage is critical for productive virus infection and that the impaired infectivity of PRO/HEL cleavage mutants is due mainly to defective synthesis of positive-strand RNA.
A Palaeogeological Map of the Lower Palaeozoic Floor below the cover of Upper Devonian, Carboniferous and Later Formations : with inferred and speculative reconstructions of Lower Palaeozoic and Precambrian outcrops in adjacent areas
Authors: Wills Leonard Johnston 
Published: August 2007

Abstract
It is four years since Professor Wills produced his outstanding pre‐Permian Palaeogeological Map of England and Wales, published by this Society with an explanatory memoir and now to be found on the walls of many working offices across the country. He was then 89 and it was assumed that this was his final production, a remarkable achievement in the face of great physical frailty.
Nevertheless he immediately moved on to a map of a stratigraphically deeper level — a palaeogeological map of the rocks following the Caledonian movements and the subsequent erosion, the surface of which would be exposed by the removal of Upper Devonian and later strata. This was completed and printed in 1975, and Wills began the equally complex task of writing an accompanying memoir to explain the way he had interpreted and applied the varied evidence of the deep structure. This process however led him to undertake still another map, that of the pre‐Devonian rocks of a belt extending from East Anglia to South Wales, which has been completed this year. These two maps form the coloured plates accompanying this memoir.
The memoir is also illustrated by a map of the Basal Elements, and by three Phanerozoic Time Scale sections, which illustrate the point which Wills has made before — that in the dominantly shelf environment of Britain the stratigraphical record is largely incomplete, with the lacunae at least comparable in time terms to the periods represented by sediments.
This publication, then, represents the further remarkable achievement of a man of 93 (— “and a half”, as he emphasises — he feels that months count now), working in a country study without technical support, his activity sharply limited by eye trouble and by a heart condition. It would have been a notable production for a fit man half his age. Both economic and academic geologists are already deeply indebted to Wills for his map of the pre‐Permian surface; these further compilations add more organised data and more food for thought about the past history and deep structure of Britain.
Late Precambrian and Cambrian geological time-scale
Authors: Cowie J. W. , Johnson M. R. W. 
Published: August 2007

Summary
The suggestion by the Subcommission on Precambrian Stratigraphy (of the International Union of Geological Sciences) that the beginning of Late Proterozoic times should be defined in the geochronometric scale at 900 Ma is accepted; this probably correlates with the chronostratic scale at the Middle-Upper Riphean boundary. The Upper Riphean-Vendian boundary on the chronostratic scale seems to correlate with approximately 650 Ma. The chronostratic Precambrian-Cambrian boundary is poorly correlated with the chronometric scale on a global basis at present but may be more accurately related in the next decade or so. In the meantime a range of 530-600 Ma can be considered but no conclusions are offered here.
An attempt is made to give the present state of knowledge and techniques, with only a selection of radiometric data, especially those bearing more or less directly on the calibration of chrono-stratigraphic units. The geographic coverage is not intended to be complete.
Numerical calibration of the Palaeozoic time-scale; Ordovician, Silurian and Devonian periods
Authors: Gale N. H. 
Published: August 2007

Summary
Thirty-five reliable dates for rock units of well-defined biostratigraphy within the Ordovician, Silurian and Devonian periods are listed. Two alternative graphical presentations of the data show that all the data, including Rb-Sr whole rock ages of acid rocks, are internally consistent. Less precise fission track dates are consistent with the other data, but too imprecise sufficiently to constrain the time-scale. Estimates are given for the numerical calibration of the base of the Carboniferous, Frasnian, Eifelian, Gedinnian, Llandovery, Caradoc, Llandeilo and Arenig, by considering the sets of reliable ages for rock units near each boundary.
Oceanic magnetic lineaments and the calibration of the late Mesozoic — Cenozoic time-scale
Authors: Curry Dennis 
Published: August 2007

Summary
The pattern of magnetic reversals from mid-Cretaceous times onwards is now well-known from the study of ocean-floor spreading systems. Integration of the pattern of polarity reversals with the standard biostratigraphical time-scale is now well-advanced and, as a result, a series of recently proposed time-scales use the detailed pattern of magnetic lineaments, calibrated radio-metrically at a few points only, as their major control. The anomaly sequence generally accepted as standard is based on a single track across the South Atlantic and its representativeness of at least the greater part of the Cenozoic has never been seriously challenged. Assumption of a constant spreading rate with time has enabled detailed and apparently very accurate time-scales to be generated. However, spacings within anomaly sequences in the same oceanic area vary notably from track to track and oceanic areas themselves may exhibit characteristic patterns. Clearly, in detail, the rate of ocean-floor spreading with time is not constant, and the role of patterns of magnetic reversals in the construction of time-scales needs reevaluation in the light of this fact.
Processes and problems in the continental lithosphere: geological history and physical implications
Authors: Brown G. C. 
Published: August 2007

Summary
Systematic changes in surface continental patterns of geology, tectonics and magma types reflect the unidirectional non-uniformitarian evolution of the continental lithosphere upon which the dominant constraint has been progressively declining terrestrial heat production. Widespread shallow asthenospheric mantle precluded the early stabilization of continental lithosphere, and the subsequent rapid growth of late Archaean continental crust implies considerable differences in the long-term thermal histories of oceanic and continental lithospheres. Proterozoic continental lithosphere rapidly became thick and refractory, though internally ductile, whilst oceanic lithosphere, the focus of terrestrial heat flow, remained relatively thin and plastic. This physical contrast probably has decreased in more recent times, a trend which may be coupled with the increased evidence for continental fragmentation in the Phanerozoic record. Finally, it is argued from thermal considerations, coupled with freeboard, isotopic and geochemical data, that continental growth has continued at a decreased and decreasing rate throughout post-Archaean time.
Chapter 1 Svalbard
Authors: Harland W. Brian 
Published: August 2007

An introduction to Svalbard is as necessary for a geoscientist as for any other student of the archipelago. The section on geographical nomenclature is illustrated by maps which are designed to locate many of the commonly used names. These and others are listed at the end of the volume where additional names used later are referred to. The regional context of Svalbard is shown in Fig. 1.1.
The present-day physical environment is mentioned, but treated more fully in Chapters 21 and 22.
The section on the present-day Svalbard biota is not by a specialist for specialists, but is intended to list those organisms commonly encountered in the field and of interest to most workers.
The political and treaty considerations are interwoven and have sometimes left the Norwegian administration in an ambivalent position. Happily however the resources forthcoming from the petroleum industry to the nation has enabled the administration to fulfil its responsibility admirably and latterly without the pressures from the Cold War.
Svalbard for its size has a small population, less than 4000 concentrated in relatively few settlements, but numbers are augmented by summer arrivals of construction/maintenance staff, tourists, students and scientists, while the residents often take their summer holidays on the mainland. The environmental threat from this expanding seasonal population presents one of the most serious challenges, while at the same time tourism is replacing coal mining as the principal economic resource. Provision of shipping facilities supplemented by air travel is transforming the economy, which however still requires substantial
Chapter 8 Northwestern Spitsbergen
Authors: Harland W. Brian , Doubled Ay Paul A. 
Published: August 2007

Northwestern Spitsbergen is bounded by Billefjorden and Wijde-fjorden in the east and by the coastline in the north and west round to the southwest by Kongsfjorden (Fig. 8.1). The southern boundary overlaps with the Central Basin (Chapter 4) and central western sector of Spitsbergen (Chapter 9) along Kongsfjorden and Sveabreen. At this boundary Devonian and older rocks are uncon-formably overlain, and finally obscured to the south, by the cover of Carboniferous through Paleogene strata. This sector contains Andree Land, Albert I Land, Haakon VII Land, James I Land and northern Dickson Land. It is deeply penetrated by fjords and largely covered by ice.
Apart from Quaternary sediments and volcanics, Cenozoic plateau lavas and the overlying platform sequence (Carboniferous through Paleogene) to the south, the main consideration here is with Devonian sediments, mid-Paleozoic migmatites and granites, and Precambrian metasediments.
The Northwestern sector is bounded and divided by faults. The eastern boundary is delineated by the Billefjorden Fault Zone (BFZ) and the southwestern boundary is the postulated Kongs-fjorden-Hansbreen Fault Zone (KHFZ). These faults separate the Central Province respectively from the Eastern and Western provinces. Two main N-S oriented faults divide the sector into three terranes: the Raudfjorden Fault (RFF), and the Breibogen Fault (BBF) (Fig. 8.1) as noted by Holtedahl (1914). The three terranes are introduced below. (1) The Andree Land-Dickson Land Terrane is a large area of Devonian strata bounded by the Breibogen Fault Zone and the Billefjorden Fault Zone. (2) The Biskayerfonna-Holtedahlfonna Terrane is a N-S belt bounded to the
Chapter 13 Vendian History
Authors: Harland W. Brian 
Published: August 2007

The Vendian Period, the latest Precambrian division, and the earliest division in which several Phanerozoic methods of correlation can be applied, is a convenient time division for Svalbard. It is separated from the earlier history in which correlation has uncertainties of tens of millions of years if not more. The period is divided here into an early (Varanger) epoch and a late (Ediacara) epoch (Harland
et al
. 1990).

The Varanger Epoch is documented by remarkably rich sequences, correlated throughout (but limited in Prins Karls Forland and Bjornoya) by the two distinctive major glacial episodes: the earlier Smalfjord Stage and the Mortensnes Stage, with a substantial interglacial record between the diamictite horizons. The Vendian age of these glacigenic sediments is confirmed biostrati-graphically.
The Ediacara Epoch is only confirmed from the Scotia Group in Prins Karls Forland, identified by a microbiota. A number of conformable post-glacial successions are plausibly of Ediacara age: the Dracoisen and Klackbergbukta formations in the northeast; the Annabreen Formation in Oscar II Land; the Peachflya and Geikie as well as the Scotia Group in Prins Karls Forland; and the Bogstranda and Gashamna Formations in Hornsund. Nevertheless the second part of Vendian time is as yet poorly demonstrated in Svalbard.
According to the correlation followed here from Harland, Hambrey & Waddams (1993) based largely on the two glacial episodes, the outcrop area of Vendian strata is not small as shown in Fig. 13.1.
Vendian, as used here, is the latest Precambrian time-interval preceding the Cambrian Period. Whereas Cambrian and