bluuebunny/crossref_metadata_2025 huggingface dataset:
Divergent Evolution of Norovirus GII/4 by Genome Recombination from May 2006 to February 2009 in Japan
Authors: Motomura Kazushi , Yokoyama Masaru , Ode Hirotaka , Nakamura Hiromi , Mori Hiromi , Kanda Tadahito , Oka Tomoichiro , Katayama Kazuhiko , Noda Mamoru , Tanaka Tomoyuki , Takeda Naokazu , Sato Hironori
Published: June 2010

Norovirus GII/4 is a leading cause of acute viral gastroenteritis in humans. We examined here how the GII/4 virus evolves to generate and sustain new epidemics in humans, using 199 near-full-length GII/4 genome sequences and 11 genome segment clones from human stool specimens collected at 19 sites in Japan between May 2006 and February 2009. Phylogenetic studies demonstrated outbreaks of 7 monophyletic GII/4 subtypes, among which a single subtype, termed 2006b, had continually predominated. Phylogenetic-tree, bootscanning-plot, and informative-site analyses revealed that 4 of the 7 GII/4 subtypes were mosaics of recently prevalent GII/4 subtypes and 1 was made up of the GII/4 and GII/12 genotypes. Notably, single putative recombination breakpoints with the highest statistical significance were constantly located around the border of open reading frame 1 (ORF1) and ORF2 (
P
≤ 0.000001), suggesting outgrowth of specific recombinant viruses in the outbreaks. The GII/4 subtypes had many unique amino acids at the time of their outbreaks, especially in the N-term, 3A-like, and capsid proteins. Unique amino acids in the capsids were preferentially positioned on the outer surface loops of the protruding P2 domain and more abundant in the dominant subtypes. These findings suggest that intersubtype genome recombination at the ORF1/2 boundary region is a common mechanism that realizes independent and concurrent changes on the virion surface and in viral replication proteins for the persistence of norovirus GII/4 in human populations.
Poliovirus Polymerase Residue 5 Plays a Critical Role in Elongation Complex Stability
Authors: Hobdey Sarah E. , Kempf Brian J. , Steil Benjamin P. , Barton David J. , Peersen Olve B.
Published: June 2010

The structures of polio-, coxsackie-, and rhinovirus polymerases have revealed a conserved yet unusual protein conformation surrounding their buried N termini where a β-strand distortion results in a solvent-exposed hydrophobic amino acid at residue 5. In a previous study, we found that coxsackievirus polymerase activity increased or decreased depending on the size of the amino acid at residue 5 and proposed that this residue becomes buried during the catalytic cycle. In this work, we extend our studies to show that poliovirus polymerase activity is also dependent on the nature of residue 5 and further elucidate which aspects of polymerase function are affected. Poliovirus polymerases with mutations of tryptophan 5 retain wild-type elongation rates, RNA binding affinities, and elongation complex formation rates but form unstable elongation complexes. A large hydrophobic residue is required to maintain the polymerase in an elongation-competent conformation, and smaller hydrophobic residues at position 5 progressively decrease the stability of elongation complexes and their processivity on genome-length templates. Consistent with this, the mutations also reduced viral RNA production in a cell-free replication system.
In vivo
, viruses containing residue 5 mutants produce viable virus, and an aromatic phenylalanine was maintained with only a slightly decreased virus growth rate. However, nonaromatic amino acids resulted in slow-growing viruses that reverted to wild type. The structural basis for this polymerase phenotype is yet to be determined, and we speculate that amino acid residue 5 interacts directly with template RNA or is involved in a protein structural interaction that stabilizes the elongation complex.
Identification of Five Interferon-Induced Cellular Proteins That Inhibit West Nile Virus and Dengue Virus Infections
Authors: Jiang Dong , Weidner Jessica M. , Qing Min , Pan Xiao-Ben , Guo Haitao , Xu Chunxiao , Zhang Xianchao , Birk Alex , Chang Jinhong , Shi Pei-Yong , Block Timothy M. , Guo Ju-Tao
Published: June 2010

Interferons (IFNs) are key mediators of the host innate antiviral immune response. To identify IFN-stimulated genes (ISGs) that instigate an antiviral state against two medically important flaviviruses, West Nile virus (WNV) and dengue virus (DENV), we tested 36 ISGs that are commonly induced by IFN-α for antiviral activity against the two viruses. We discovered that five ISGs efficiently suppressed WNV and/or DENV infection when they were individually expressed in HEK293 cells. Mechanistic analyses revealed that two structurally related cell plasma membrane proteins, IFITM2 and IFITM3, disrupted early steps (entry and/or uncoating) of the viral infection. In contrast, three IFN-induced cellular enzymes, viperin, ISG20, and double-stranded-RNA-activated protein kinase, inhibited steps in viral proteins and/or RNA biosynthesis. Our results thus imply that the antiviral activity of IFN-α is collectively mediated by a panel of ISGs that disrupt multiple steps of the DENV and WNV life cycles.
Informatics, evidence-based care, and research; implications for national policy: a report of an American Medical Informatics Association health policy conference
Authors: Bloomrosen Meryl , Detmer Don E
Published: June 2010

There is an increased level of activity in the biomedical and health informatics world (e-prescribing, electronic health records, personal health records) that, in the near future, will yield a wealth of available data that we can exploit meaningfully to strengthen knowledge building and evidence creation, and ultimately improve clinical and preventive care. The American Medical Informatics Association (AMIA) 2008 Health Policy Conference was convened to focus and propel discussions about informatics-enabled evidence-based care, clinical research, and knowledge management. Conference participants explored the potential of informatics tools and technologies to improve the evidence base on which providers and patients can draw to diagnose and treat health problems. The paper presents a model of an evidence continuum that is dynamic, collaborative, and powered by health informatics technologies. The conference's findings are described, and recommendations on terminology harmonization, facilitation of the evidence continuum in a “wired” world, development and dissemination of clinical practice guidelines and other knowledge support strategies, and the role of diverse stakeholders in the generation and adoption of evidence are presented.
VOLUME FORMS AND MINIMAL SURFACES OF ROTATION IN FINSLER SPACES WITH (α, β)-METRICS
Authors: HE QUN , YANG WEI
Published: June 2010

In this paper, the relation between the volume form of (α, β)-metric [Formula: see text] and that of Riemannian metric α is given. Minimal submanifolds in Finsler spaces with (α, β)-metrics are studied. Finally, an ordinary differential equation that characterizes minimal surfaces of revolution and an example of minimal surface of rotation are given.
LATERAL DIFFUSION OF MEMBRANE PROTEINS AT CELL MEMBRANE
Authors: FAN LEI , FAN TIAN YOU
Published: June 2010

The cell membrane is an important organ of living cells, which has a complex structure influenced by the interaction between membrane proteins and cell membrane. On the basis of fluid motion and diffusion interaction, a simple model is proposed to evaluate quantitatively the effects of the protein size and membrane fluid velocity on the lateral diffusion of membrane proteins at the cell membrane. The study shows that the diffusion coefficient is a dominant factor on the lateral diffusion.
WEAKLY MIXING IMPLIES DISTRIBUTIONAL CHAOS IN A SEQUENCE
Authors: WANG LIDONG , YANG YU'E , CHU ZHENYAN , LIAO GONGFU
Published: June 2010

Let X be a separable metric space containing at least two points, and f:X→X be continuous. In this paper, we consider dynamical systems on X, and prove that topologically weakly mixing implies distributional chaos in a sequence.
OPTICAL SPIN INJECTION IN SEMICONDUCTORS
Authors: MENDOZA BERNARDO S. , SALAZAR CUAUHTÉMOC , CABELLOS J. L.
Published: June 2010

A theoretical review of optical spin injection for bulk semiconductors is presented. As an example, we calculated such response in bulk Si , GaAs and CdSe . For each of these systems the computation of the electronic wavefunctions and energies are obtained under the density functional theory (DFT) within the local density approximation (LDA).
ON THE SIMULATION OF UNIAXIAL, COMPRESSIVE BEHAVIOR OF AMORPHOUS, GLASSY POLYMERS WITH MOLECULAR DYNAMICS
Authors: MAHAJAN DHIRAJ K. , BASU SUMIT
Published: June 2010

Molecular dynamics (MD) simulations offer an interesting route to simulating deformation and fracture behavior of amorphous glassy polymers. However, MD simulations are performed at extremely high rates and on very small samples (though periodic boundary conditions are routinely used) containing at most hundreds of chains which are much shorter than in real life. In this work, we try to assess the extent to which MD simulations produce physically realistic stress–strain responses and identify aspects of the simulation procedure that can be controlled closely in order to avoid numerical artifacts. We show that, when an appropriate protocol for sample generation and simulation of deformation is followed, in spite of the obvious constraints imposed by the simulation technique, MD simulations have the capability to generate realistic stress–strain curves and reproduce many experimental trends pertaining to them.
Ammonite jaw apparatuses from the Sinemurian (Lower Jurassic) of Dorset and their taphonomic relevance
Authors: Cope John C. W. , Sole David T. C.
Published: June 2010

The occurrence of ammonite jaw apparatuses
in situ
within concretions from the Sinemurian (Lower Jurassic) of Black Ven Cliff, Charmouth, Dorset, provides evidence of burial of the ammonites with soft parts intact and this is of importance in considering the origin of the concretions. The lower jaws (anaptychi) of arietitid and eoderoceratid ammonites are preserved and three examples of upper jaws are recorded in the species
Asteroceras stellare.
Although usually accepted as being entirely of organic composition, the anaptychi of
A. stellare
have an outer calcareous layer.
Facies changes across the Triassic–Jurassic boundary in Nevada, USA
Authors: HALLAM A. , WIGNALL P. B.
Published: June 2010

A combination of data from litho‐ and biofacies and gamma‐ray spectrometry indicates an upward marine shallowing in the late Rhaetian succession of Nevada followed by deepening in the early Hettangian, which conforms well to a regression–transgression couplet of the sort associated with many marine mass extinctions. This pattern can be discerned widely across the world, most notably in North and South America and in Europe, suggesting the operation of eustatic control of sea level, a global fall being followed by a rise.
Macrofabric fingerprints of Late Devonian–Early Carboniferous subduction in the Polish Variscides, the Kaczawa complex, Sudetes
Authors: COLLINS ALAN S. , KRYZA RYSZARD , ZALASIEWICZ JAN
Published: June 2010

We describe a remarkably preserved assemblage of sedimentary and tectonic fabrics in cores from the Kaczawa complex, Sudetes, SW Poland. These fabrics indicate a continuum of process from repeated remobilization of Upper Devonian–Lower Carboniferous muddy flysch and volcaniclastic sediments as debris flows and olistostromes, to fracturing, fluid‐streaming and soft‐sediment injection triggered by high pore‐water pressures during the initial stages of tectonic deformation, to contractional cleavage formation and local cataclasis while the sediment was still only partially consolidated. These structures are similar to those described from ODP cores through the toes of active accretionary prisms. They indicate active subduction of oceanic crust during the Late Devonian, suggesting that ophiolite obduction and significant overthrusting in the Sudetes occurred as an integral part of the Variscan orogeny.
Isotopic evidence for temperature variation during the early Cretaceous (late Ryazanian–mid‐Hauterivian)
Authors: PRICE GREGORY D. , RUFFELL ALASTAIR H. , JONES CHARLES E. , KALIN ROBERT M. , MUTTERLOSE JÖRG
Published: June 2010

Oxygen and carbon isotopic compositions have been determined from the belemnite genera
Acroteuthis
and
Hibolites
sampled from the early Cretaceous (Ryazanian–Hauterivian) interval of the Speeton Clay Formation, Filey Bay, England. The Speeton Clay Formation consists of a series of claystones and calcareous mudrocks deposited in an epicontinental sea. δ
18
O values from belemnites, which met petrographic and chemical criteria for well preserved skeletal carbonate, indicate warm marine palaeotemperatures (c. 12–15°C) for much of the early Valanginian whilst cool temperatures (<9°C) are inferred for the earliest Hauterivian. During the remainder of the Hauterivian, temperatures fluctuated considerably and rose to a maximum of 15.5°C. Changes in kaolinite and smectite abundances, considered to reflect humid and arid phases of climate, correlate with warm and cool episodes. The palaeotemperature record, appears to contradict evidence from cephalopod faunas, which show a Tethyan influx during the inferred early Hauterivian cool period. However, this was a transgressive phase and thus the cephalopods could have been less sensitive to temperature than to water column stability and to land barriers. A positive shift in the carbon isotope profile obtained from the Speeton belemnites appears correlatable with carbon isotope profiles recorded from pelagic Tethyan successions, albeit with somewhat differing absolute values. The data support earlier models of carbon isotope variation, in that positive excursions are associated with an inferred global rise in sea level.
Ordovician arc collision and foredeep evolution in the Gaspé Peninsula, Québec: the Taconic Orogeny in Canada and its bearing on the Grampian Orogeny in Scotland
Authors: PRAVE A. R. , KESSLER L. G. , MALO M. , BLOECHL W. V. , RIVA J.
Published: June 2010

The Middle to Upper Ordovician Deslandes, Cloridorme and Garin Formations in the eastern Gaspé Peninsula, Québec, are some of the most extensively exposed foredeep successions along the northern Appalachian portion of the Taconic–Caledonian orogen. Their depositional and biostratigraphic frameworks (
N. gracilis
to
C. spiniferus
Zones, approximate correlatives to the
N. gracilis
to
D. clingani
British Zones) indicate that foredeep evolution spanned
c.
 10 Ma and was essentially synchronous with the convergence and accretion of the Popelogan arc to the Laurentian margin during the Caradoc (
c.
 458–449 Ma). These results, when combined with metamorphic and radiometric age data synthesized from across the Laurentian segments of the northern Appalachian and northwestern Ireland Taconic–Caledonian orogen, further substantiate that orogenesis consisted of several short‐lived (
c.
 10–20 Ma) deformational episodes confined to Arenig through Ashgill time (
c.
 485–440 Ma). This indicates that the total duration of orogeny, as recorded by arc magmatism, metamorphism and Laurentian foredeep development, spanned no more than
c.
 45 Ma. In that the Scottish Caledonides are a consanguineous part of this orogen, their tectonostratigraphic evolution, i.e., Grampian Orogeny, should be similar. Accordingly, the results detailed above are geodynamically compatible with and thereby support tectonic models that define the Grampian Orogeny in Scotland as a mostly Early to Mid‐Ordovician (
c.
 480–460 Ma) tectonic episode of short, rather than long duration.
Sequence stratigraphy of a tidally dominated carbonate–siliciclastic ramp; the Tithonian–Early Berriasian of the Southern Neuquén Basin, Argentina
Authors: SPALLETTI LUIS A. , FRANZESE JUAN R. , MATHEOS SERGIO D. , SCHWARZ ERNESTO
Published: June 2010

The Tithonian–Berriasian Vaca Muerta, Carrín Curá and Picún Leufú formations in the southern Neuquén Basin were deposited on a tidally dominated, mixed carbonate–siliciclastic ramp. Basinal, outer, middle, shallow and back ramp facies associations are recognized and a sequence stratigraphic analysis reveals that the ramp record consists of three shallowing‐upwards sequences (Ti1, Ti2 and Ti3) set within a lower‐order progradational cycle. A higher order of cyclicity is superimposed on to the middle (Ti2) sequence. The majority of the ramp facies belong to the transgressive and highstand systems tracts; however, at the base of Ti2, a lowstand systems tract is identified, characterized by a basal unconformity and an abrupt basinward shift of the shallow marine lithofacies. Transgressive systems tracts were characterized by slow sedimentation rates and rapid sea‐level rises that affected carbonate productivity. Highstand systems tracts show the greatest carbonate productivity and an increased progradation rate on account of a reduction in accommodation space generation. Palaeogeography played a major role in the development of the depositional systems. Partial isolation from the Pacific Ocean reflecting the growth of the Andean magmatic arc and geographic restriction due to tectonic inversion in the central part of the basin resulted in a meso‐macrotidal regime that produced a tidally dominated sedimentary record in the shallow and back ramp environments. Coeval anoxic conditions in the central part of the Neuquén Basin favoured distal ramp and basinal black shale deposition during episodes of relative sea‐level rise.
Late Cretaceous sea‐level changes in Tunisia: a multi‐disciplinary approach
Authors: Li Liangquan , Keller Gerta , Adatte Thierry , Stinnesbeck Wolfgang
Published: June 2010

A multi‐disciplinary study of sea‐level and climate proxies, including bulk rock and clay mineral compositions, carbon isotopes, total organic carbon (TOC), Sr/Ca ratios, and macro‐ and microfaunal associations, reveals seven major sea‐level regressions in the southwestern Tethys during the last 10 million years of the Cretaceous: late Campanian (
c.
 74.2 Ma, 73.4–72.5 Ma and 72.2–71.7 Ma), early Maastrichtian (70.7–70.3 Ma, 69.6–69.3 Ma, and 68.9–68.3 Ma), and late Maastrichtian (65.45–65.3 Ma). Low sea levels are generally associated with increased terrigenous influx, low kaolinite/chlorite + mica ratios, high TOC and high Sr/Ca ratios, whereas high sea levels are generally associated with the reverse conditions. These sea‐level changes may be interpreted as eustatic as suggested by the global recognition of at least four of the seven major regressions identified (74.2 Ma, 70.7–70.3 Ma, 68.9–68.3 Ma and 65.45–65.3 Ma). Climatic changes inferred from clay mineral contents correlate with sea‐level changes: warm or humid climates accompany high sea levels and cooler or arid climates generally accompany low sea levels.
Structural evolution of the Li Basin, northern Thailand
Authors: MORLEY C. K. , SANGKUMARN N. , HOON T. B. , CHONGLAKMANI C. , LAMBIASE J.
Published: June 2010

Exposures in the Oligocene to Miocene section of coal mines in the Li Basin of northern Thailand show a complex structural evolution. The basins formed under approximately east–west extension. NW to north–south‐striking normal faults are dominant with some east–west normal faults also being present, but much less frequently. Episodically compressional and/or strike‐slip events affected the basin creating new east–west to NE–SW‐striking thrusts and folds and inverting some normal faults. The latest episode of compression formed NW‐SE to north–south striking thrusts and folds. Cross‐cutting structures, reactivation of structures, syn‐sedimentary deformation and unconformites help to constrain the relative timing of structural events. At least five episodes of predominantly NNW–SSE to NE–SW oriented compression interrupted the extensional development of the basin. The compression was probably related to the escape tectonics of the Himalayan orogeny. The episodic nature of the compression and extension is inconsistent with either simple strike‐slip related opening of the rift basins or simple extension. The data from the Li Basin indicate a reappraisal of current tectonic models for the region is necessary.
The isotopic signature of planktonic foraminifera from NE Atlantic surface sediments: implications for the reconstruction of past oceanic conditions
Authors: GANSSEN G. M. , KROON D.
Published: June 2010

The stable isotope compositions of the planktonic foraminifera
Globigerina bulloides, Globigerinoides ruber
(white and pink varieties),
Globigerinoides trilobus, Globorotalia inflata
and
Globorotalia truncatulinoides
(right‐ and left‐coiling types) were examined as recorders of North Atlantic surface water properties based on 40 box‐core surface sediments between 60° and 30°N. While
G. ruber
(white and pink varieties) and
G. trilobus
mainly reflect summer surface water conditions in their oxygen isotope composition,
G. bulloides
reflects temperatures of the northward‐migrating spring bloom, February–March in the south to May–June in the north. Our data show that
G. bulloides
cannot be regarded as an indicator for summer temperatures as deduced from Duplessy
et al.
’s data.
Gt. inflata
and
Gt. truncatulinoides
(right‐ and left‐coiling) build their shells in the coldest waters compared with the other species and reflect temperatures between 100 and 400 m water depth. The difference in oxygen isotope composition between
G. bulloides
and
G. inflata
serves as a proxy for water mass stratification.
G. bulloides
is the only species that gives a distinct pattern in its carbon isotopic composition showing a high correlation with the surface water phosphate values along the transect and may serve as a proxy for palaeonutrients and/or productivity.
Marine biodiversity through the Late Cenomanian–Early Turonian: palaeoceanographic controls and sequence stratigraphic biases
Authors: GALE A. S. , SMITH A. B. , MONKS N. E. A. , YOUNG J. A. , HOWARD A. , WRAY D. S. , HUGGETT J. M.
Published: June 2010

Changes in the marine macro- and microfauna, sedimentary geochemistry and surface-water palaeoproductivity through the last 500 000 years of the Cenomanian and first 300 000 years of the Turonian are documented. These are based on the succession at Eastbourne, the thickest and most complete section through the Late Cenomanian and Early Turonian in the Anglo–Paris Basin. Two levels of rapid faunal and geochemical change are identified, one coincident with a significant increase in siliciclastic input at the base of the Plenus Marls Member, and the other with a marked drop in surface water productivity near the top of the same unit. Faunal change is demonstrated to be largely a pattern of immigration–emigration rather than true extinction, and our sequence stratigraphical analysis shows that it was coincident with major sea-level changes. No evidence is found to support the hypothesis that reduced bottom water oxygenation developed and was responsible for extinctions amongst the benthos in mid-shelf environments. The onset of pure chalk facies is interpreted to mark the breakdown of shelf-break fronts and the spread of oligotrophic oceanic waters over much of the continental shelf, initiated by rising sea-level. The Cenomanian–Turonian event, far from recording a mass extinction of shelf fauna, is most probably an artifact caused by a significant switch in the nature of the surviving sedimentary record as a result of a major, but perfectly ordinary, oceanographic change.
Environmental geochemistry at the global scale
Authors: PLANT JANE , SMITH DAVID , SMITH BARRY , WILLIAMS LORRAINE
Published: June 2010

Land degradation and pollution caused by population pressure and economic development pose a threat to the sustainability of the Earth’s surface, especially in tropical regions where a long history of chemical weathering has made the surface environment particularly fragile.

Systematic baseline geochemical data provide a means of monitoring the state of the environment and identifying problem areas. Regional surveys have already been carried out in some countries, and with increased national and international funding they can be extended to cover the rest of the land surface of the globe. Preparations have been made, under the auspices of the IUGS, for the establishment of just such an integrated global database.
Environmental fate and toxicology of organophosphate pesticides
Authors: RAGNARSDOTTIR K. VALA
Published: June 2010

Organophosphate pesticides (OPs) are generally regarded as safe for use on crops and animals due to their relatively fast degradation rates. Their degradation varies as a function of microbial composition, pH, temperature, and availability of sunlight. Under laboratory conditions (25°C and pH 7) biodegradation is about one order of magnitude faster than chemical hydrolysis, which in turn is roughly ten times faster than photolysis. Microbial biomass often needs a lengthy adaptation period in which soil bacteria mutate to be able to metabolize OPs. Biodegradation is thus in general an order of magnitude faster in soils that have had repeated applications of OPs compared to control soils which have never had OP applications. Because OPs are relatively soluble, they often enter surface and groundwaters. In the latter OPs are primarily broken down through chemical hydrolysis, which is pH dependent. Hydrolysis half-life of an OP pesticide of 10 days in the laboratory increases to one year if the pH of the water is 6 and the temperature 5°C, suggesting that OPs can persist in the environment for long periods of time. Indeed, OPs are detected in soils years after application. Why this environmental persistence occurs is not clear, but it may be due to sorption of the OPs to soil particles, making them unavailable for microbial metabolism. Example calculations and literature data show that conditions can occur in soil where OPs are preserved and transferred to humans through food. A review of the literature shows that OPs are highly toxic and that human exposure is undesirable. Evidence suggests that OPs are mutagenic and teratogenic and that a large number of modern-day diseases of the nervous and immune system of mammals can be linked to these pesticides. These include BSE (mad cows disease), CJD, Gulf War syndrome, Parkinson’s disease and multiple sclerosis, arguing for a thorough examination of the environmental fate and toxicology of OPs as well as their use.
The bioaccessibility of essential and potentially toxic trace elements in tropical soils from Mukono District, Uganda
Authors: SMITH B. , RAWLINS B. G. , CORDEIRO M. J. A. R. , HUTCHINS M. G. , TIBERINDWA J. V. , SSERUNJOGI L. , TOMKINS A. M.
Published: June 2010

It has been postulated that endomyocardial fibrosis (EMF), a common cardiac disease in certain tropical communities including parts of Uganda, may be related to the presence of elevated levels of dietary Ce, and deficient levels of dietary Mg. In Uganda, significant variation in dietary exposure to both elements is likely due to variations in local soil geochemistry and dietary habits, including geophagia (the deliberate consumption of soil). This paper reports the concentration and bioaccessibility (determined from a physiologically based extraction test—PBET) of Ce and other essential (Mg and Fe) and trace elements in soils from the Mukono district of Uganda. Trace element concentrations varied markedly between soil samples (ground soils) and soils eaten deliberately, such as termite nest soils and traditional herbal–soil remedies. The highest bioaccessibility values were reported for the chelate-rich, intestinal phase of the PBET. Median percentage bioaccessibility values for Ce (1–15%), Mg (7–33%), Fe (0.1–2.9%) and other trace elements varied considerably, but were generally higher in geophagic (herbal–soil remedies and terminte nest soils) than common (ground) soil samples. Only in the case of Fe does the ingestion of soil account for a major proportion of recommended daily intake (RDI). The revised estimates of Ce and Mg dietary intake (based on bioaccessibility data rather than an assumption of 100% bioavailability) significantly reduced the importance of geophagia relative to exposure through the ingestion of food and water.
The Australian Stress Map
Authors: HILLIS R. R. , REYNOLDS S. D.
Published: June 2010

Knowledge of the
in situ
stress field of the Australian continent has increased greatly since compilation of the World Stress Map in 1992, principally by analysis of borehole breakouts and drilling-induced tensile fractures in petroleum wells. Stress orientations are variable across the Australian continent as a whole. However, within 15 of 16 individual stress provinces defined in the Australian continent (of one to a few hundred kilometres scale), mean stress orientations are statistically significant. The stress provinces, and stress trajectory mapping, reveal that there are systematic, continental-scale rotations of stress orientation within Australia. Unlike many other continental areas, stress orientations do not parallel the direction of absolute plate motion. Nonetheless, the regional pattern of stress orientation is consistent with control by plate boundary forces, if the complex nature of the convergent northeastern boundary of the Indo-Australian plate, and stress focusing by collisional segments of the boundary, is recognized.
Celebration and consideration of citations
Authors: FAIRCHILD IAN J.
Published: June 2010

The recent editorial policies of the
Journal of the Geological Society
are described in relation to an 18 year record of its citation statistics. Differences in citation patterns between types of papers are analysed and the use of the impact factor discussed. The
Journal
has now reached a long-term high in its impact factor.
Extensional folding in the Alaşehir (Gediz) graben, western Turkey
Authors: SEYITOĞLU GÜROL , ÇEMEN İBRAHIM , TEKELI OKAN
Published: June 2010

The broad folds exposed in the syn-extensional sedimentary rocks of the Alaşehir graben, western Turkey, have been recently interpreted as contractional in origin. Our field mapping of these folds suggests that they are the products of extensional tectonics. The field evidence includes the presence of several longitudinal extensional folds such as a rollover anticline and drag folds that are related to normal faults in the area. The extensional nature of these folds negates the previous interpretation and consequently suggests extensional tectonics in the region was not interrupted by short-lived contractional tectonics.
Large clockwise rotations in an extensional allochthon, Alboran Domain (southern Spain)
Authors: PLATZMAN E. , PLATT J. P. , KELLEY S. P. , ALLERTON S.
Published: June 2010

Palaeomagnetic, structural and geochronological analysis of a suite of Oligocene mafic dykes intruded into the Malaguide allochthon in the Internal Zone of the Betic Cordillera demonstrate that at least 134° clockwise vertical-axis rotation of a large region occurred, probably during early Miocene thrusting onto the External Zones. Initial results from Ar/Ar whole rock analysis suggests that the dykes were probably intruded over a period of time between 23 Ma and 30 Ma. Results of demagnetization experiments demonstrate that the remanence in many of the dykes is composed of one to three components. The lowest temperature component is poorly defined. The intermediate temperature (IT) component, carried by pyrrhotite, has reversed polarity, a declination of 314° and an inclination of −48°. This component was probably acquired during cooling after greenschist-facies metamorphism. The high temperature (HT) component is carried by magnetite and was probably acquired at or shortly after intrusion. This component has both reversed and normal polarity, with an average declination of 320° and an inclination of −13°. Rotation of approximately 35° about a horizontal NNE-trending axis, in present-day coordinates, brings the inclination of the HT component into statistical agreement with both the IT component and the expected inclination for the Oligocene. This rotation leaves the dykes in a near-vertical orientation but brings the foliation in the surrounding schists to approximately horizontal.

We suggest that the original regional foliation may have been sub-horizontal and related to the ductile phase of late-orogenic extension in the Betic Cordillera. The dykes were intruded sub-vertically into the schists with an original NW–SE trend. The region was then tilted and rotated clockwise by 23°±15 before acquiring the IT component after which it underwent 134°±10° of clockwise rotation about a vertical axis.
The Kennack Gneiss of the Lizard Peninsula, Cornwall, SW England: commingling and mixing of mafic and felsic magmas accompanying Givetian continental incorporation of the Lizard ophiolite
Authors: SANDEMAN HAMISH A. I. , CLARK ALAN H. , SCOTT DAVID J. , MALPAS JOHN G.
Published: June 2010

The Kennack Gneiss comprises a suite of interlayered mafic and felsic igneous rocks that intruded the 397 Ma Lizard Ophiolite Complex, Cornwall, at 376.4±1.7 Ma (U–Pb single-zircon date) and were shortly thereafter (
c.
 370 Ma) metamorphosed to the amphibolite facies. Weakly deformed examples at the type-locality of Kennack Sands reveal net-veining of the mafic by the felsic component, dispersed enclaves of the former in the latter and flame-like interfingering of the two, features indicative of magmatic commingling and mixing.

The silicic components of the Kennack Gneiss range from granodiorite to syenogranite and from metaluminous to peraluminous, the least silicic rocks being the most peraluminous. They were generated through anatexis of a predominantly metasedimentary crustal source having trace element and isotopic compositions comparable to those of the Devonian Gramscatho Group of South Cornwall. The mafic component of the gneiss includes members (group 1) which are weakly enriched in light REE, have minor negative Ta, Nb, P and Ti anomalies in extended trace element plots, and display primitive, time-corrected
143
Nd/
144
Nd and
87
Sr/
86
Sr values, and others (group 2) which are more strongly enriched in all incompatible trace elements, exhibit more prominent negative Ta, Nb, P and Ti anomalies, and have isotopic ratios intermediate between group 1 mafic components and the associated felsic gneiss. Group 2 represents mixtures of group 1 and granitic melts, whereas group 1 rocks are comparable to EMORB and were probably generated through partial melting of a weakly enriched mantle source. Emplacement of two commingled magmas into the base of the Lizard ophiolite, one representing the products of crustal anatexis, implies that the ophiolite was removed from its oceanic setting and was in the process of obduction in the Givetian.
Northward sediment transport from the late Carboniferous Variscan Mountains: zircon evidence from the Oslo Rift, Norway
Authors: DAHLGREN SVEN , CORFU FERNANDO
Published: June 2010

Proto-rift, late Carboniferous fluvial and deltaic sandstones from the Asker Group are locally preserved in the upper Palaeozoic Oslo Rift. High-precision U–Pb ages of single detrital zircon grains from a Moscovian (late Westphalian to early Stephanian) sandstone and overlying tuffaceous sediments, that predated initial basaltic volcanism, have been used to study the provenance of the detritus and to evaluate the tectonic significance of the deposits. We find late Neoproterozoic (of Avalonian affinity), Cambro-Ordovician and early Carboniferous detrital zircons requiring that one of the source regions was located along, or south of, the axis between southern England and northeastern Germany and implying sediment transport from the south, probably as a consequence of uplift during the Asturic compressional phase of the Variscan Orogeny. Other age groups reflect typical Baltic sources, possibly from the Ringkøbing–Fyn High. Detrital zircons (and monazite) from underlying Silurian sandstone (Wenlock–Ludlow) yield Svecofennian to Sveconorwegian as well as late Ordovician ages but lack late Neopoterozoic (Avalonian) ages. It is thus unlikely that the bulk of the Carboniferous detritus could have been derived by recycling of preexisting Silurian sandstones. These data imply that the rivers feeding the Asker Group originated in the Variscan mountains and entered the Oslo proto-rift from the south, possibly via the Horn Graben or along the Sorgenfrei–Tornquist Zone.
Recognition of tectonic events in undeformed regions: contrasting results from the Midland Platform and East Midlands Shelf, Central England
Authors: GREEN PAUL F. , THOMSON KEN , HUDSON JOHN D.
Published: June 2010

Apatite fission-track and vitrinite reflectance data from Central England demonstrate how these techniques can reveal otherwise unrecognized tectonic and/or palaeothermal episodes in apparently tectonically stable areas. The results document the transition from an inverted basinal region in the north (East Midlands Shelf), to a tectonically stable platform in the south (Midland Platform). AFTA data from the region reveal two discrete cooling episodes, in the Early and Late Tertiary. Maximum palaeotemperatures from AFTA and VR data in outcrop samples define a consistent increase from ≤50°C in Lower Cretaceous and Upper Jurassic units in the SE to around 80–90°C in Triassic and older units in the NW. These Early Tertiary palaeotemperatures reflect a combination of deeper burial and elevated basal heat flow. Results from the Rufford-1 well define an Early Tertiary palaeogeothermal gradient of 40.5°C km
−1
(32–50°C km
−1
at ±95% confidence limits), corresponding to deeper burial by 1450 m of additional section (1.1–2.2 km at ±95% confidence limits), subsequently removed by Tertiary erosion. In contrast, geological considerations suggest a maximum overburden of 800–900 m above the base of the Lower Jurassic in the vicinity of Rugby where palaeotemperatures at outcrop are similar to those near the Rufford-1 location. The discrepancy between stratigraphic and palaeo-thermal reconstruction of former burial depths, often noted in earlier studies, remains unresolved. The Late Tertiary episode is much less well-constrained, but results from Rufford- 1 may require between 910 and 1650 m of eroded section. Thus much of the total amount of removed overburden may have been removed during the Late Tertiary. Results from the Apley Barn Borehole (Oxfordshire) reveal a Late Tertiary palaeothermal episode characterized by a highly non-linear palaeotemperature profile which probably reflects local heating due to passage of hot fluids. Despite stratigraphic evidence for some Early Tertiary erosion results from this borehole show no evidence of Early Tertiary effects. Major Early and Late Tertiary exhumation was limited to regions underlain by older Palaeozoic basins while regions overlying Palaeozoic basement were more stable, experiencing significantly less exhumation. We suggest this reflects the preferential reactivation of the weaker basinal regions as a result of compressional events at plate margins. Our results emphasize the importance of incorporating results from both ‘inverted’ and ‘non-inverted’ areas in understanding the causal mechanisms of uplift and inversion, and highlight the importance of testing apparent stability using palaeo-thermal methods.
Biogenic alteration of volcanic glass from the Troodos ophiolite, Cyprus
Authors: FURNES H. , MUEHLENBACHS K. , TUMYR O. , TORSVIK T. , XENOPHONTOS C.
Published: June 2010

Alteration of basaltic glass through the entire volcanic sequence of the Troodos ophiolite is partly bio-mediated. The following observations support this conclusion: alteration textures resembling microbes in form and size; altered glass locally shows high carbon concentrations at the alteration front and organic remains. The absence of DNA suggests that the bio-alteration is a fossil process. Temperatures calculated from δ
18
O of carbonate, assumed to have been in equilibrium with seawater, yield 27–65°C, and δ
18
O
silicate
versus H
2
O relationships indicate seawater alteration. These data are consistent with biogenic alteration during an early stage of ocean-floor alteration of the Troodos oceanic crust some 70–90 Ma ago.
Dome and basin refolding and transpressive inversion along the Karatau Fault System, southern Kazakstan
Authors: ALLEN M. B. , ALSOP G. I. , ZHEMCHUZHNIKOV V. G.
Published: June 2010

The Karatau Fault System of southern Kazakstan forms a crustal-scale zone of strike-slip dominated transpressional tectonics which has undergone multiple phases and styles of deformation during a protracted history of reactivation from the Neoproterozoic to the Cenozoic. Ductile fabrics associated with dextral kinematic indicators are present in amphibolites along the Main Karatau Fault. The ages of the (possibly ophiolitic) protoliths and the ductile fabrics are not well constrained, but they are plausibly pre-late Riphean. Late Ordovician granites stitch thrusts and folds which deform late Riphean to Llanvirn clastics, preserved beneath a regional Late Devonian angular unconformity. This deformation may be related to a contemporary continental collision NE of the Karatau. Two phases of late Palaeozoic deformation affected the Upper Devonian and Carboniferous carbonate succession. The first phase is related to sinistral transpression along the Karatau Fault System, the second to dextral transpressional reactivation. The combination of these events produced a regional-scale dome-and-basin fold interference pattern. Similar polyphase deformation appears to have affected large areas of Central Asia and was possibly caused by the late Palaeozoic orogenies at Asia’s margins, such as the accretion of Tarim and the East European Craton to Asia, and the closure of the Kazakstan Orocline. Normal faults in the Karatau are related to the formation of the Leontiev Graben, South Turgay Basin and the Yarkand–Fergana Basin in the Early to Mid-Jurassic, during renewed dextral slip along the Karatau/Talas–Fergana Fault. Late Cenozoic deformation is minor, and resulted in the uplift and incision of a Cretaceous–Palaeogene peneplain without a major tectonic overprint. Reversals in the sense of strike-slip dominated transpressive deformation across major fault systems results in
transpressive inversion
. This represents an ideal process with which to generate overprinting orthogonal fold systems, resulting in classic dome and basin interference patterns on a regional scale.
Kinematics of the Alpine–West Carpathian orogen and palaeogeographic implications
Authors: NEUGEBAUER JOACHIM , GREINER BERND , APPEL ERWIN
Published: June 2010

We present the Euler rotations of the plates involved in the Alpine–West Carpathian orogen. The rotations are defined to a large extent by the magnetic anomalies of the Atlantic Ocean. A few extra rotations occurred during two collisions and a Mid-Cretaceous event. At variance with earlier reconstructions, we additionally control the rotations by the orientation of palaeomagnetic declinations. The plate rotations are integrated into a model illustrated by palaeogeographical maps. Special features of the model are: (1) subdivision of the northern margin of Adria into the two plates, Pelso and Austroalpine–West Carpathia, on the basis of palaeomagnetic data; (2) Eohellenic obduction of Meliata units onto the eastern margins of Pelso and Austroalpine–West Carpathia from the Tethys side; (3) first (Eoalpine) collision of the marginal plates of Adria with Tisza far off the West European plate margin; (4) a 80–90° rotation of Austroalpine–West Carpathia during the Eoalpine collision; (5) subdivision of the Neoalpine collision into a Palaeogene stage of predominantly strong SE–NW shortening and a Neogene stage of predominantly lateral extrusion westward and eastward. In principle, the maps show quantitative ocean spreading, subduction, and plate rotations. However, possible modifications of the model discussed in this paper limit the quantitative evaluation.
Ordovician and Silurian global geography
Authors: COCKS L. R. M.
Published: June 2010

The main palaeocontinents during the early Ordovician were Gondwana, Laurentia, Baltica, and Siberia, and a brief survey is made of their limits in the Ordovician and Silurian. In particular Gondwana, by far the largest continent, is analysed as including a core of South America, Antarctica, Africa, Australia and peninsular India, and also the marginal terranes, all of which show faunal links with, but which may not have been attached, to the core, of Avalonia, Ibero-Armorica and other European fragments, Turkey, Arabia, and terranes from the Far East including South China, Sibumasu and parts of Australasia. Changes within the benthic faunas reveal that Baltica, whilst isolated in the early Ordovician, became united with Avalonia by the end Ordovician and the two with Laurentia by the mid-Silurian to form the new supercontinent of Laurussia. Island arcs had distinctive faunas during the Ordovician, in particular those in the Iapetus between Laurentia, Baltica and Gondwana and the huge Kipchak Arc which ran from Baltica to Siberia. As the period progressed, the Iapetus arcs became subducted beneath or accreted to their neighbouring cratons, and the Kipchak Arc gradually collapsed to form the core of the new Kazakhstania terrane. Gondwana drifted over the South Pole and this movement is reflected in the cratonic benthic faunas, particularly brachiopods and trilobites, which in the early Ordovician had formed a cline between the high-latitude faunas of North Africa and the equatorial faunas of the Far East and Australia, but by the Devonian lived in much warmer seas in southern Europe and cooler waters in Antarctica. The faunas also reflect the global palaeoclimates, which were warm in the early to mid Ordovician and mid to late Silurian but which were much colder in the half million year period of the late Ordovician and early Silurian, particularly in the latest Ordovician Hirnantian ice age with its attendant widespread
Hirnantia
brachiopod Fauna. The relative closeness of the chief palaeocontinents by the early Silurian enabled brachiopod and trilobite larvae to cross the narrower oceans, enabling a relatively cosmopolitan benthic fauna to be established over much of the globe, apart from the cooler-water higher latitude
Clarkeia
Fauna to the south and the
Tuvaella
Fauna to the north.
Latest Neoproterozoic to Mid-Cambrian age for the main deformation phases of the Transantarctic Mountains: new stratigraphic and isotopic constraints from the Pensacola Mountains, Antarctica
Authors: ROWELL A. J. , VAN SCHMUS W. R. , STOREY B. C. , FETTER A. H. , EVANS K. R.
Published: June 2010

New isotopic ages and a fresh understanding of stratigraphic relations among siliciclastic strata in the Pensacola Mountains along the northern margin of the East Antarctic craton result in removal of some constraints for the Proterozoic break-up of Rodinia and necessitate revision of the subsequent history of the East Antarctic margin. These rocks, formerly all included in the Patuxent Formation, were thought to be of mid-Neoproterozoic age, to have formed as a consequence of Rodinia rifting, and to have been deformed during a Neoproterozoic orogenic event. Our data show, in contrast, that these siliciclastic strata were deposited in two chronologically distinct basins. The older basin, in which the Hannah Ridge Formation (new name) accumulated, received sediment that contains detrital zircons of latest Neoproterozoic or Early Cambrian age. It was deformed and its contents uplifted and eroded prior to the late Mid-Cambrian in an orogenic event that we interpret as the early stage(s) of the Ross orogeny. The second basin formed later, accumulated turbidite-rich sediments of the redefined Patuxent Formation of Mid- and probably Late Cambrian age, and was subsequently deformed, possibly in Ordovician time. Review of both biostratigraphic and isotopic ages along the length of the Transantarctic Mountains indicates that almost everywhere the main episodes of deformation predate 500 Ma and are thus older than latest Mid-Cambrian, rather than Ordovician, as they are commonly considered to be. Only in the accreted Bowers and Robertson Bay terranes of northern Victoria land, which reveal no clear record of pre-latest Mid-Cambrian or older folding, is the principal episode of Ross orogenic deformation demonstrably younger than Late Cambrian.