bluuebunny/crossref_metadata_2025_split huggingface dataset:
Marked Epitope- and Allele-Specific Differences in Rates of Mutation in Human Immunodeficiency Type 1 (HIV-1) Gag, Pol, and Nef Cytotoxic T-Lymphocyte Epitopes in Acute/Early HIV-1 Infection
Authors: Brumme Zabrina L. , Brumme Chanson J. , Carlson Jonathan , Streeck Hendrik , John Mina , Eichbaum Quentin , Block Brian L. , Baker Brett , Kadie Carl , Markowitz Martin , Jessen Heiko , Kelleher Anthony D. , Rosenberg Eric , Kaldor John , Yuki Yuko , Carrington Mary , Allen Todd M. , Mallal Simon , Altfeld Marcus , Heckerman David , Walker Bruce D. 
Published: July 2008

ABSTRACT

During acute human immunodeficiency virus type 1 (HIV-1) infection, early host cellular immune responses drive viral evolution. The rates and extent of these mutations, however, remain incompletely characterized. In a cohort of 98 individuals newly infected with HIV-1 subtype B, we longitudinally characterized the rates and extent of HLA-mediated escape and reversion in Gag, Pol, and Nef using a rational definition of HLA-attributable mutation based on the analysis of a large independent subtype B data set. We demonstrate rapid and dramatic HIV evolution in response to immune pressures that in general reflect established cytotoxic T-lymphocyte (CTL) response hierarchies in early infection. On a population level, HLA-driven evolution was observed in ∼80% of published CTL epitopes. Five of the 10 most rapidly evolving epitopes were restricted by protective HLA alleles (HLA-B*13/B*51/B*57/B*5801;
P
= 0.01), supporting the importance of a strong early CTL response in HIV control. Consistent with known fitness costs of escape, B*57-associated mutations in Gag were among the most rapidly reverting positions upon transmission to non-B*57-expressing individuals, whereas many other HLA-associated polymorphisms displayed slow or negligible reversion. Overall, an estimated minimum of 30% of observed substitutions in Gag/Pol and 60% in Nef were attributable to HLA-associated escape and reversion events. Results underscore the dominant role of immune pressures in driving early within-host HIV evolution. Dramatic differences in escape and reversion rates across codons, genes, and HLA restrictions are observed, highlighting the complexity of viral adaptation to the host immune response.
Nontemplated Terminal Nucleotidyltransferase Activity of Double-Stranded RNA Bacteriophage φ6 RNA-Dependent RNA Polymerase
Authors: Poranen Minna M. , Koivunen Minni R. L. , Bamford Dennis H. 
Published: July 2008

ABSTRACT
The replication and transcription of double-stranded RNA (dsRNA) viruses occur within a polymerase complex particle in which the viral genome is enclosed throughout the entire life cycle of the virus. A single protein subunit in the polymerase complex is responsible for the template-dependent RNA polymerization activity. The isolated polymerase subunit of the dsRNA bacteriophage φ6 was previously shown to replicate and transcribe given RNA molecules. In this study, we show that this enzyme also catalyzes nontemplated nucleotide additions to single-stranded and double-stranded nucleic acid molecules. This terminal nucleotidyltransferase activity not only is a property of the isolated enzyme but also is detected to take place within the viral nucleocapsid. This is the first time terminal nucleotidyltransferase activity has been reported for a dsRNA virus as well as for a viral particle. The results obtained together with previous high-resolution structural data on the φ6 RNA-dependent RNA polymerase suggest a mechanism for terminal nucleotidyl addition. We propose that the activity is involved in the termination of the template-dependent RNA polymerization reaction on the linear φ6 genome.
An Insect Virus-Encoded MicroRNA Regulates Viral Replication
Authors: Hussain Mazhar , Taft Ryan J. , Asgari Sassan 
Published: July 2008

ABSTRACT

MicroRNAs (miRNAs) are small (∼22 nucleotides) noncoding RNAs which play an essential role in gene regulation and affect a wide range of processes, including development, differentiation, and oncogenesis. Here we report the identification of the first miRNA from an insect virus, derived from the major capsid protein (MCP) gene in
Heliothis virescens
ascovirus (HvAV) (HvAV-miR-1). Although MCP was abundantly expressed at all time points 24 h after infection, HvAV-miR-1 expression was strictly regulated and specifically detected from 96 h postinfection. HvAV-miR-1 expression coincided with a marked reduction of the expression of HvAV DNA polymerase I, which is a predicted target. Ectopic expression of full-length and truncated versions of MCP retaining the miRNA sequence significantly reduced DNA polymerase I transcript levels and inhibited viral replication. Our results indicate that HvAV-miR-1 directs transcriptional degradation of DNA polymerase I and regulates HvAV replication. These findings are congruent with recent reports that miR-BART-2 regulates Epstein-Barr virus DNA polymerase expression and suggest that virus-encoded miRNA regulation of virus replication may be a general phenomenon.
Comparing the risk of work-related injuries between immigrants to Canada and Canadian-born labour market participants
Authors: Smith P M , Mustard C A 
Published: July 2008

Objectives:To examine the burden of work-related injuries among immigrants to Canada compared to Canadian-born labour force participants.Methods:Using data from the 2003 and 2005 Canadian Community Health Surveys (n = 99 115), two nationally representative population samples, we examined the risk of self-reported, activity limiting work-related injuries among immigrants with varying time periods since arrival in Canada. Models were adjusted for hours of work in the last 12 months as well as various demographic and work-related variables.Results:Immigrant men in their first 5 years in Canada reported lower rates of activity limiting injuries compared to Canadian-born respondents. Surprisingly, the percentage of injuries that required medical attention was much higher among recent immigrants compared to Canadian-born respondents, resulting in an increased risk of activity limiting injuries requiring medical attention among immigrant men compared to Canadian-born labour force participants. No excess risk was found among female immigrants compared to Canadian-born female labour market participants.Conclusions:Immigrant men in their first 5 years in Canada are at increased risk of work-related injuries that require medical attention. A similar risk is not present among immigrant women. Further, given differences in the number of activity limiting injuries requiring medical attention across immigrant groups, we believe this excess risk among immigrant men may be underestimated in the current data source. Future research should attempt to fully capture the barriers faced by immigrants in obtaining safe employment, the number of injuries that are sustained by immigrants while working, and the consequences of these injuries.
The western termination of the SEMP Fault (eastern Alps) and its bearing on the exhumation of the Tauern Window
Authors: Rosenberg Claudio L. , Schneider Susanne 
Published: July 2008

Abstract
The SEMP (Salzach–Ennstal–Mariazell–Puchberg) Fault strikes along more than 300 km from the southern margin of the Vienna Basin to the northern Tauern Window accommodating a sinistral displacement of 60 km during Tertiary time. We present new structural data, showing that the SEMP Fault continues into the Tauern Window within a 50 km long mylonitic belt of approximately 2 km width, which we term the Ahorn shear zone. This sinistral shear zone, which marks the northern boundary of the Zentral Gneiss, strikes E to ENE, dips subvertically, and is characterized by gently W-dipping to subhorizontal stretching lineations. S-side-up kinematic indicators in the Y–Z fabric plane and a pronounced southward increase in the inferred temperature of sinistral shearing are observed within the shear zone. Microstructural observations indicate that deformation of quartz at the northernmost boundary of the Zentral Gneiss occurred by dislocation glide with only incipient dynamic recrystallization, suggesting a temperature of approximately 300 °C. Further south, temperatures greater than 300 °C are inferred because all samples are affected by dynamic recrystallization of quartz, and dynamic recrystallization of feldspars also occurred in the southernmost part of the shear zone. These findings point to transpressive deformation accommodating a significant component of south-side-up displacement in addition to sinistral shearing. The sinistral mylonitic foliation forms the axial-plane foliation of the large-scale, ENE-striking upright folds of the western Tauern Window. From east to west, deformation becomes increasingly distributed, passing from an area of interconnected shear zones in the east to a homogeneously deformed mylonitic belt in the west, which terminates into a belt of WNW-striking, upright folds. From the above, we suggest the following: (1) the SEMP Fault extended beyond the brittle-ductile transition to a depth where temperatures exceeded 500 °C (>20 km depth?). These mylonites should be included in the seismic interpretation profiles as a major crustal discontinuity; (2) the large-amplitude, upright folds of the Tauern Window formed at the same time as the sinistral mylonites, and hence during south-side-up differential displacement; and (3) part of the 60 km lateral displacement of the SEMP fault is transferred into a vertical displacement at the western end of the Ahorn shear zone and into a fold belt accommodating NNE-oriented shortening, west of the Ahorn shear zone.
On the role and importance of orogen-parallel and -perpendicular extension, transcurrent shearing, and backthrusting in the Monte Rosa nappe and the Southern Steep Belt of the Alps (Penninic zone, Switzerland and Italy)
Authors: Pleuger Jan , Nagel Thorsten J. , Walter Jens M. , Jansen Ekkehard , Froitzheim Nikolaus 
Published: July 2008

Abstract

During Europe–Adria collision in Tertiary times, the Monte Rosa nappe was penetratively deformed in several stages after an eclogite-facies pressure peak: (1) top-to-the-NW thrust shearing (Mattmark phase, after 40 Ma); (2) orogen-parallel, top-to-the-SW extensional shearing and folding (Malfatta phase); (3) orogen-perpendicular, top-to-the-SE extensional shearing and folding (Mischabel phase, before 30 Ma); and (4) large-scale, upright, SE-vergent folding (Vanzone phase,
c
. 29–28 Ma). Structural analysis and neutron texture goniometry of quartz mylonites show that the Stellihorn shear zone in the Monte Rosa nappe accommodated a complex and multidirectional sequence of shearing movements during the Mattmark, Malfatta and Mischabel phases, and was folded in the Vanzone phase. In the tail-shaped eastward prolongation of the Monte Rosa nappe in the Southern Steep Belt of the Alps, both dextral and sinistral mylonites (Olino phase) were formed during and after the formation of the Vanzone fold, reflecting renewed orogen-parallel (SW–NE) extension contemporaneous with NW–SE shortening from
c
. 29 Ma onward. A similar sequence of deformation stages was identified in the Adula nappe at the eastern border of the Lepontine metamorphic dome. Important consequences arise for the Insubric fault at the southern border of the Lepontine dome: (1) the NW- to N-dipping orientation of the Insubric fault is not a primary feature but resulted from rotation of an originally SE-dipping shear zone after
c
. 30 Ma; and (2), the strong contrast in metamorphic grade across this fault (upper amphibolite facies to the north versus anchizone to the south) results from north-side-up faulting coupled with orogen-parallel extension of the northern block (Lepontine dome), while no such extension occurred in the southern block (Southern Alps). Extension in the northern block started in the Malfatta phase and continued in the Mischabel phase when the foliation in the area which later became the Southern Steep Belt still dipped towards south. During Vanzone/Olino deformation, further unroofing and uplift of the Lepontine dome relative to the South Alpine block took place while the Southern Steep Belt was progressively rotated into its present, overturned position, changing its character from a normal fault into a backthrust. Complex deformation paths in the Southern Steep Belt resulted from the combination of extension of the northern block with strike-slip motion along the Insubric fault.
Metamorphic evolution of a very low- to low-grade metamorphic core complex (Danubian window) in the South Carpathians
Authors: Ciulavu Magda , Mählmann Rafael Ferreiro , Schmid Stefan M. , Hofmann Heiko , Seghedi Antoneta , Frey Martin 
Published: July 2008

Abstract
The Danubian window, characterized by diagenetic to low greenschist facies conditions at a high thermal gradient, is evidently of great interest for methodological studies, because high metamorphic thermal gradient conditions during low grade metamorphism have received little attention so far. The general increase in metamorphic grade from SW to NE in the Danubian window is indicated by mineral Parageneses studies, as well as by illite Kübler index (KI) measurements and organic matter reflectance (OMR). For the first time, this study distinguishes between metamorphic conditions related to Jurassic ocean floor, Cretaceous nappe stacking, post-collisional accommodation and syn-kinematic Getic detachment metamorphism and cooling after Oligocene exhumation.
The occurrence of the prehnite–pumpellyite facies in the Severin–Cosustea units in the southeastern area is the result of Cretaceous metamorphism. Remnants of ocean floor metamorphism prevailed. The highest pressure is constrained by the upper stability limit of prehnite to be at around 4.0 kbar. The Danubian units situated within the diagenetic zone were not below 200 °C, due to epidote formation. The KI, OMR and mineral data, indicate diagenetic conditions. Assuming temperatures between >200 and <250 °C, pressures between 1.8 and 2.6 kbar were calculated using kinetic and numerical maturity models.
Orogenic collisional Cretaceous peak pressure conditions of 4.0±1.0 kbar are found in the Danubian nappes not altered by a subsequent syn-detachment metamorphic overprint. Highest temperatures in chloritoid schists and epidote–hornblende-bearing mylonites have been inferred for samples from the northern border of the Danubian window (between >300 and <400 °C). Along a syn- to post-detachment retrograde pressure path, post-dating the chloritoid formation, the occurrence of clinozoisite+chlorite+quartz suggests temperatures >300 °C in the northwest, while the association andalusite+quartz and biotite+muscovite indicates temperatures between 370 and 400 °C at <3.5 kbar in the northeast.
It is demonstrated that the slope of the regression lines between KI and OMR data gives valuable qualitative information about the relative magnitudes of P and T: the slope of the regression line for the Danubian window samples indicates normal heat flow conditions during nappe stacking and hyperthermal conditions during the formation of the Getic detachment.
High thermal gradient conditions can easily be explained by partly isothermal decompression during the Getic detachment event, the elevation of the geotherm being caused by crustal thinning and rapid exhumation of the Danubian units. Probably, also a higher heat-flux prevailed at the end of the Getic detachment, at a time when the retrograde chloritoid decomposition reactions took place, documenting late-stage HT greenschist facies metamorphism.
Calcareous nannofossil age constraints on Miocene flysch sedimentation in the Outer Dinarides (Slovenia, Croatia, Bosnia-Herzegovina and Montenegro)
Authors: Mikes Tamás , Báldi-Beke Mária , Kázmér Miklós , Dunkl István , von Eynatten Hilmar 
Published: July 2008

Abstract
Flysch deposits are associated with the Outer Dinaride nappe front. They overlie Eocene platform carbonate to bathyal marl successions that subsequently cover Cretaceous platform carbonates of Apulia and the Dinaride nappes. Planktonic foraminifer biostratigraphy indicates Eocene age of flysch sedimentation. New calcareous nannofossil data reveal that several assemblages are present; besides the dominant Mid-Eocene species, Cretaceous, Paleocene, Oligocene and Miocene taxa were also identified throughout the entire flysch belt. Widespread occurrence of nannofossil species of zone NN4-6 indicates that flysch deposition lasted up to at least the Mid-Miocene. Ubiquitous occurrence of various pre-Miocene taxa demonstrates that extensive, possibly submarine, sediment recycling has occurred in the Cenozoic. As flysch remnants are typically sandwiched between thrust sheets, these new stratigraphic ages give a lower bracket on deformation age of the coastal range. The data provide a link between Cretaceous compression in the Bosnian Flysch and recent deformation in the Adriatic offshore area.
Tertiary subduction, collision and exhumation recorded in the Adula nappe, central Alps
Authors: Nagel Thorsten J. 
Published: July 2008

Abstract
The Adula nappe in the Central Alps represents a lithospheric mélange assembled in a south-dipping subduction zone during the Tertiary orogenic cycle. It consists of several heterogeneous lobes which are stacked in a forward-dipping duplex geometry. Eclogites, garnet peridotites and garnet-white-mica schists record southward-increasing peak pressure conditions which culminate at 12–17 kbar/500–600 °C in the north and 30 kbar/800–850 °C in the south. Some studies infer even higher peak pressures for the garnet peridotite body of Alpe Arami. The present-day metamorphic field gradient for peak pressures exceeds the lithostatic pressure gradient. So far, only eclogites and garnet peridotites from the Cima Lunga complex in the south and the adjacent Southern Steep Belt have yielded Tertiary metamorphic ages for the peak-pressure stage. Some recent studies propose that the Adula nappe got assembled after the formation of high-pressure assemblages in eclogites and garnet peridotites and reject regional high-pressure conditions in Tertiary times. This scenario, however, is in conflict with the observed continuity of metamorphic field gradients and post-peak-pressure structures. Amphibolite facies conditions post-date formation of the Central Alpine nappe stack. In this paper, the associated field gradient is explained through southward-increasing temperatures during near-isothermal decompression.
The main mylonitic foliation in the Adula nappe post-dates peak-pressure conditions. It is associated with top-to-the-north shearing and southward-increasing amounts of decompression from eclogite facies to amphibolite facies conditions. Also, the present-day supra-lithostatic field gradient for peak pressures probably results from this deformation phase and is here related to substantial vertical flattening during northward shearing. All subsequent structures affect established nappe boundaries. Pervasive Oligocene deformation events in the Adula nappe are coeval with intense shearing along the so-called Insubric mylonites and occur during ongoing isothermal decompression to around 5 kbar. They are associated with orogen-oblique to orogen-parallel stretching of unspecified amount which may considerably contribute to the exhumation of the Lepontine dome already before the onset of the well-known Miocene extension.
Geodynamic evolution of an Alpine terrane—the Austroalpine basement to the south of the Tauern Window as a part of the Adriatic Plate (eastern Alps)
Authors: Schulz Bernhard , Steenken André , Siegesmund Siegfried 
Published: July 2008

Abstract
The Austroalpine basement underwent a multistage Precambrian to Tertiary evolution. Meta-magmatic rocks occur in pre-Early Ordovician and post-Early Ordovician units. Protolith zircon ages and whole-rock trace element data define two magmatic evolution lines. An older trend with Th/Yb typical of subduction-related metamorphism, started by 590 Ma N-MORB-type and 550–530 Ma volcanic arc basalt-type basic suites which mainly involved depleted mantle sources, and was continued by mainly crustal-source 470–450 Ma acid magmatic suites. A presumably younger evolution by tholeiitic MORB-type and 430 Ma alkaline within-plate basalt-type suites is characterized by an intraplate mantle metasomatism and multicomponent sources. These magmatic trends can be related to a Neoproterozoic to Ordovician active margin and a subsequent Palaeo-Tethys passive margin along the north-Gondwanan periphery. During Variscan collision, the Austroalpine basement underwent multiphase deformation and metamorphism. Early deformation involved non-coaxial shearing with formation of sheath folds and calcsilicategneiss bodies in some regions. Syndeformational clockwise P–T paths in lower basement parts passed high-pressure and high-temperature amphibolite-facies stages and are interpreted by a Devonian to Carboniferous crustal stacking. A post-collisional Permian thermal event is documented by pegmatite intrusions, LP-HT assemblages and monazite ages. Ductile overprinting under greenschist-facies conditions during the Cretaceous is indicated by foliated pegmatites and monazite ages in samples with retrogressed garnet. The emplacement of the Oligocene Rieserferner pluton was controlled by sinistral shear zone deformation along the Defereggen–Antholz–Vals line. Shear zone activity ceased at 15 Ma and was superseded by brittle strike-slip movements along NW and SE trending faults.