bluuebunny/crossref_metadata_2025 huggingface dataset:
A Celebration of the Genome, Part IV
Authors: Jasny Barbara R. , Zahn Laura M.
Published: February 2011

The last installment of human genome anniversary “vignettes” covers topics ranging from the impact of this “big science” project on the rest of the research community, to the commonalities between art and science.
House Cuts to DOE National Labs Would Also Hamstring Industry
Authors: Cho Adrian
Published: February 2011

A spending bill passed by the House of Representatives last week would bring the Department of Energy's entire science program to a screeching halt and wreak havoc on research funded by other agencies and by private industry.
Schooling the
Jeopardy!
Champ: Far From Elementary
Authors: Frenkel Karen A.
Published: February 2011

Last week, Nico Schlaefer, a Ph.D. candidate in computer science at Carnegie Mellon University and an IBM Ph.D. Fellow, told
Science
about the algorithm he contributed to the now-world-famous Watson computer.
Induction of Immune Tolerance in Asthmatic Mice by Vaccination with DNA Encoding an Allergen–Cytotoxic T Lymphocyte-Associated Antigen 4 Combination
Authors: Zhang Fang , Huang Gang , Hu Bo , Song Yong , Shi Yi
Published: February 2011

Allergen-specific immunotherapy is a potential treatment for allergic diseases. We constructed an allergen–cytotoxic T lymphocyte-associated antigen 4 (CTLA-4)-encoding DNA vaccine, administered it directly to antigen-presenting cells (APCs), and investigated its ability and mechanisms to ameliorate allergic airway inflammation in an asthmatic mouse model. An allergen-CTLA-4 DNA plasmid (OVA-CTLA-4-pcDNA3.1) encoding an ovalbumin (OVA) and the mouse CTLA-4 extracellular domain was constructed and transfected into COS-7 cells to obtain the fusion protein OVA-CTLA-4, which was able to bind the B7 ligand on dendritic cells (DCs), and induced CD25+Foxp3+regulatory T (Treg) cells by the coculture of naive CD4+T cells with DCsin vitro. In an animal study, BALB/c mice were sensitized and challenged with OVA to establish the asthmatic model. Vaccination with a high dose of OVA-CTLA-4-pcDNA3.1significantly decreased interleukin-4 (IL-4) and IL-5 levels and eosinophil counts and prevented OVA-induced reduction of the gamma interferon level in the bronchoalveolar lavage fluid. In addition, these mice suffered less severe airway inflammation and had lower levels of OVA-specific IgE and IgG1 titers in serum. Also, high-dose OVA-CTLA-4-pcDNA3.1vaccination inhibited the development of airway hyperreactivity and prevented OVA-induced reduction of the percentages of Foxp3+Treg cells in the spleen. Our results indicate that a high dose of allergen-CTLA-4-encoding DNA vaccine was more effective in preventing an allergen-induced Th2-skewed immune response through the induction of Treg cells and may be a new alternative therapy for asthma.
Efficacy of the Canine Influenza Virus H3N8 Vaccine To Decrease Severity of Clinical Disease after Cochallenge with Canine Influenza Virus and Streptococcus equi subsp. zooepidemicus
Authors: Larson Laurie J. , Henningson Jamie , Sharp Patricia , Thiel Bliss , Deshpande Muralidhar S. , Davis Tamara , Jayappa Huchappa , Wasmoen Terri , Lakshmanan Nallakannu , Schultz Ronald D.
Published: February 2011

Since first emerging in the North American canine population in 2004, canine influenza virus (CIV) subtype H3N8 has shown horizontal transmission among dogs, with a high level of adaptation to this species. The severity of disease is variable, and coinfection by other respiratory pathogens is an important factor in the degree of morbidity and mortality. The first influenza vaccine for dogs, an inactivated vaccine containing CIV subtype H3N8, was conditionally approved by the U.S. Department of Agriculture (USDA) for licensure in May 2009 and fully licensed in June 2010. This study evaluates the efficacy of this vaccine to reduce the severity of illness in dogs cochallenged with virulent CIV andStreptococcus equisubsp.zooepidemicus.
Evaluation of Fluoromycobacteriophages for Detecting Drug Resistance in Mycobacterium tuberculosis
Authors: Rondón Liliana , Piuri Mariana , Jacobs William R. , de Waard Jacobus , Hatfull Graham F. , Takiff Howard E.
Published: February 2011

We tested a new method for detecting drug-resistant strains of
Mycobacterium tuberculosis
that uses a TM4 mycobacteriophage phAE87::
hsp60-EGFP
(
EGFP
-phage) engineered to contain the gene encoding enhanced green fluorescent protein (EGFP). After promising results in preliminary studies, the
EGFP
-phage was used to detect isoniazid (INH), rifampin (RIF), and streptomycin (STR) resistance in 155 strains of
M. tuberculosis
, and the results were compared to the resazurin microplate technique, with the proportion method serving as the reference standard. The resazurin technique yielded sensitivities of 94% for INH and RIF and 98% for STR and specificities of 97% for INH, 95% for RIF, and 98% for STR. The sensitivity of
EGFP
-phage was 94% for all three antibiotics, with specificities of 90% for INH, 93% for RIF, and 95% for STR. The
EGFP
-phage results were available in 2 days for RIF and STR and in 3 days for INH, with an estimated cost of ∼2$ to test the three antibiotics. Using a more stringent criterion for resistance improved the specificity of the
EGFP
-phage for INH and RIF without affecting the sensitivity. In preliminary studies, the
EGFP
-phage could also effectively detect resistance to the fluoroquinolones. The
EGFP
-phage method has the potential to be a valuable rapid and economic screen for detecting drug-resistant tuberculosis if the procedure can be simplified, if it can be adapted to clinical material, and if its sensitivity can be improved.
Role of Helicobacter Species in Chinese Patients with Inflammatory Bowel Disease
Authors: Zhang Shenghong , Zhong Bihui , Chao Kang , Xiao Yingliang , Cui Yi , Gao Xiang , Chen Baili , He Yao , Hu Pinjin , Chen Minhu , Mitchell Hazel M.
Published: February 2011

Based on 16S rRNA gene PCR, no significant difference was observed in rates of detection of
Helicobacter
species in intestinal biopsy specimens from 160 Chinese inflammatory bowel disease (IBD) patients (10%) and 80 controls (6.3%). By using a [
13
C]urea breath test, the
H. pylori
infection rate in 208 Chinese IBD patients (19.7%) was found to be significantly lower than that in 416 controls (48.8%).
Clinical Isolates of Trichomonas vaginalis Concurrently Infected by Strains of Up to Four Trichomonasvirus Species (Family Totiviridae)
Authors: Goodman Russell P. , Freret Taylor S. , Kula Tomasz , Geller Alexander M. , Talkington Megan W. T. , Tang-Fernandez Vanessa , Suciu Olimpia , Demidenko Aleksander A. , Ghabrial Said A. , Beach David H. , Singh Bibhuti N. , Fichorova Raina N. , Nibert Max L.
Published: February 2011

Trichomonas vaginalis
, which causes the most common nonviral sexually transmitted disease worldwide, is itself commonly infected by nonsegmented double-stranded RNA (dsRNA) viruses from the genus
Trichomonasvirus
, family
Totiviridae
. To date, cDNA sequences of one or more strains of each of three trichomonasvirus species have been reported, and gel electrophoresis showing several different dsRNA molecules obtained from a few
T. vaginalis
isolates has suggested that more than one virus strain might concurrently infect the same parasite cell. Here, we report the complete cDNA sequences of 3 trichomonasvirus strains, one from each of the 3 known species, infecting a single, agar-cloned clinical isolate of
T. vaginalis
, confirming the natural capacity for concurrent (in this case, triple) infections in this system. We furthermore report the complete cDNA sequences of 11 additional trichomonasvirus strains, from 4 other clinical isolates of
T. vaginalis
. These additional strains represent the three known trichomonasvirus species, as well as a newly identified fourth species. Moreover, 2 of these other
T. vaginalis
isolates are concurrently infected by strains of all 4 trichomonasvirus species (i.e., quadruple infections). In sum, the full-length cDNA sequences of these 14 new trichomonasviruses greatly expand the existing data set for members of this genus and substantiate our understanding of their genome organizations, protein-coding and replication signals, diversity, and phylogenetics. The complexity of this virus-host system is greater than has been previously well recognized and suggests a number of important questions relating to the pathogenesis and disease outcomes of
T. vaginalis
infections of the human genital mucosa.
A Tryptophan-Rich Motif in the Human Parainfluenza Virus Type 2 V Protein Is Critical for the Blockade of Toll-Like Receptor 7 (TLR7)- and TLR9-Dependent Signaling
Authors: Kitagawa Yoshinori , Yamaguchi Mayu , Zhou Min , Komatsu Takayuki , Nishio Machiko , Sugiyama Tsuyoshi , Takeuchi Kenji , Itoh Masae , Gotoh Bin
Published: February 2011

Plasmacytoid dendritic cells (pDCs) do not produce alpha interferon (IFN-α) unless viruses cause a systemic infection or overcome the first-line defense provided by conventional DCs and macrophages. We show here that even paramyxoviruses, whose infections are restricted to the respiratory tract, have a V protein able to prevent Toll-like receptor 7 (TLR7)- and TLR9-dependent IFN-α induction specific to pDCs. Mutational analysis of human parainfluenza virus type 2 demonstrates that the second Trp residue of the Trp-rich motif (Trp-X
3
-Trp-X
9
-Trp) in the C-terminal domain unique to V, a determinant for IRF7 binding, is critical for the blockade of TLR7/9-dependent signaling.
TRIM22 Inhibits HIV-1 Transcription Independently of Its E3 Ubiquitin Ligase Activity, Tat, and NF-κB-Responsive Long Terminal Repeat Elements
Authors: Kajaste-Rudnitski Anna , Marelli Sara S. , Pultrone Cinzia , Pertel Thomas , Uchil Pradeep D. , Mechti Nadir , Mothes Walther , Poli Guido , Luban Jeremy , Vicenzi Elisa
Published: February 2011

Previous studies identified clones of the U937 promonocytic cell line that were either permissive or nonpermissive for human immunodeficiency virus type 1 (HIV-1) replication. These clones were investigated further in the search for host restriction factors that could explain their differential capacity to support HIV-1 replication. Among known HIV-1 restriction factors screened,tripartitemotif-containing protein 22 (TRIM22) was the only factor constitutively expressed in nonpermissive and absent in permissive U937 cells. Stable TRIM22 knockdown (KD) rescued HIV-1 long-terminal-repeat (LTR)-driven transcription in KD-nonpermissive cells to the levels observed in permissive cells. Conversely, transduction-mediated expression of TRIM22 in permissive cells reduced LTR-driven luciferase expression by ∼7-fold, supporting a negative role of TRIM22 in HIV-1 transcription. This finding was further confirmed in the human T cell line A3.01 expressing TRIM22. Moreover, overexpression of TRIM22 in 293T cells significantly impaired basal and phorbol myristate acetate-ionomycin-induced HIV-1 LTR-driven gene expression, whereas inhibition of tumor necrosis factor alpha-induced viral transcription was a consequence of lower basal expression. In agreement, TRIM22 equally inhibited an LTR construct lacking the tandem NF-κB binding sites. In addition, TRIM22 did not affect Tat-mediated LTR transactivation. Finally, these effects were independent of TRIM22 E3 ubiquitin-ligase activity. In the context of replication-competent virus, significantly higher levels of HIV-1 production were observed in KD-nonpermissive versus control nonpermissive U937 cells after infection. In contrast, lower peak levels of HIV-1 replication characterized U937 and A3.01 cells expressing TRIM22 versus their control transduced counterpart. Thus, nuclear TRIM22 significantly impairs HIV-1 replication, likely by interfering with Tat- and NF-κB-independent LTR-driven transcription.
Evaluation of human papillomavirus testing for squamous cell carcinoma of the tonsil in clinical practice
Authors: Thavaraj Selvam , Stokes Angela , Guerra Eliete , Bible Jon , Halligan Eugene , Long Anna , Okpokam Atuora , Sloan Philip , Odell Edward , Robinson Max
Published: February 2011

Background

Oncogenic human papillomavirus (HPV)-associated oropharyngeal squamous cell carcinoma (SCC) is a subtype of head-and-neck cancer with a distinct clinical and prognostic profile. While there are calls to undertake HPV testing for oropharyngeal SCCs within the diagnostic setting and for clinical trials, there are currently no internationally accepted standards.

Methods

142 tonsil SCCs were tested using p16 immunohistochemistry (IHC), high-risk HPV DNA in situ hybridisation (ISH) and HPV DNA polymerase chain reaction (PCR; GP5+/6+ primers).

Results

There were high levels of agreement between pathologists for p16 IHC and HPV ISH scoring; however, around 10% of HPV ISH cases showed some interobserver discrepancy that was resolved by slide review. The combination of p16 IHC and HPV ISH classified 53% of the samples as HPV-positive, whereas the combination of p16 IHC and HPV PCR classified 61% of the samples as HPV-positive. By employing a three-tiered, staged algorithm (p16 IHC/HPV ISH/HPV PCR), the authors were able to classify 98% of the cases as either HPV-positive (p16 IHC+/HPV DNA+; 62%) or HPV-negative (p16 IHC−/HPV DNA−; 35%).

Conclusions

The current study suggests that using a combination of p16 IHC/HPV ISH/HPV PCR, in a three-tiered, staged algorithm, in conjunction with consensus reporting of HPV ISH, leads to less equivocal molecular classification. In order to ensure consistent reporting of this emerging disease, it is increasingly important for the head-and-neck oncology community to define the minimum requirements for assigning a diagnosis of ‘HPV-related’ oropharyngeal SCC in order to inform prognosis and for stratification in clinical trials.
CASIMIR EFFECT FOR THE ROBIN SURFACES IN STATIC ROBERTSON–WALKER SPACE–TIME
Authors: SETARE MOHAMMAD R. , DEHGHANI M.
Published: February 2011

We investigate the energy–momentum tensor for a massless conformally coupled scalar field in the region between two curved surfaces in k = -1 static Robertson–Walker space–time. We assume that the scalar field satisfies the Robin boundary condition on the surfaces. Robertson–Walker space–time space is conformally related to Rindler space; as a result we can obtain vacuum expectation values of the energy–momentum tensor for a conformally invariant field in Robertson–Walker space–time space from the corresponding Rindler counterpart by the conformal transformation.
Enhancing tectonic and provenance information from detrital zircon studies: assessing terrane-scale sampling and grain-scale characterization
Authors: Hietpas Jack , Samson Scott , Moecher David , Chakraborty Suvankar
Published: February 2011

Determining detrital zircon U–Pb ages has become the method of choice for single- mineral-based provenance studies focused on the identification of potential source regions of siliciclastic sediments. Advances in microanalytical methods have significantly accelerated the acquisition rate of U–Pb ages, thus allowing for more statistically significant zircon age datasets to be acquired than previously. However, several studies have demonstrated limitations of relying solely on detrital zircon as a provenance proxy. To further assess the utility of this provenance indicator we measured U–Pb ages of detrital zircon derived from modern sediment collected from the French Broad River and its tributaries that drain portions of the Appalachian Orogen in southeastern USA. The results demonstrate that significant detrital zircon age variations occur along the length of the river. The age variations suggest that characterization of entire sedimentary formations by analysis of single samples may be misleading and that a multiple-sample approach is required. In addition, by incorporating high-magnification cathodoluminescence images with Th/U for each detrital grain, a more robust interpretation can be made regarding zircon source.

Supplementary material:

Global positioning system coordinates for each sampling location and complete zircon data are available at
http:/www.geolsoc.org.uk/SUP18445
.
Late Cretaceous to Recent deformation related to inherited structures and subsequent compression within the Persian Gulf: a 2D seismic case study
Authors: Burberry C.M. , Jackson C.A.-L. , Cosgrove J.W.
Published: February 2011

The Persian Gulf is part of an asymmetric foreland basin related to the Zagros Orogen. Few published studies of this basin and associated onshore areas include seismic reflection data. We present a seismic-stratigraphic interpretation based on marine 2D seismic data, which reveals the presence of two types of compressional structures within the basin: (1) faulted domes related to salt movement and the offshore trace of a NNE–SSW-trending dextral basement fault (the Kazerun Fault); (2) long-wavelength (16 km), low-amplitude (60 ms two-way travel time) folds relating to the advancing deformation front associated with the orogen. Thinning of age-constrained stratal units across structures related to the offshore trace of the Kazerun Fault implies a distinct pulse of uplift on this fault during the Maastrichtian. The geometry of growth strata across other intra-basin structures suggests a second, later stage of deformation, which began in the Middle Miocene. Thickening and folding of post-Middle Miocene stratal units towards the NE (i.e. towards the Zagros Orogen) is interpreted to reflect rapid loading, subsidence and compression related to southwestwards advance of the orogen. The results of this study have implications for the interaction between pre-existing structures and later compressional events both within the Persian Gulf and elsewhere.
Sedimentation in deep-sea lobe-elements: implications for the origin of thickening-upward sequences
Authors: Macdonald Heather A. , Peakall Jeff , Wignall Paul B. , Best Jim
Published: February 2011

The frequency and origin of thickening-upward packages in the sediments of deep-sea environments has been a topic of much recent debate. Excellent bed-scale exposures in the Carboniferous Ross Formation, western Ireland, allow single surfaces to be traced laterally and the detailed architecture of whole packages to be evaluated using multiple vertical logs. The deposits comprise architectural elements including bed-sets, lobe-elements and composite lobes, with the lobe-elements being arranged in thickening-upward depositional packages. Results show that these packages are the result of the progradation of each lobe-element, whereby each package records a vertical trend from distal to proximal deposits accompanied by an increasing frequency of megaflutes and ultimately the development of broad erosional surfaces. We propose a six-stage model for lobe-element evolution that documents successive phases of deposition, sediment bypass, erosion and lobe abandonment. This new model provides a mechanism for lobe-element switching and explains the development of thickening-upward successions. This allows the re-examination of existing process models for these sedimentary packages in deep-sea sediments.
Late Devonian transpressional tectonics in Spitsbergen, Svalbard, and implications for basement uplift of the Sørkapp–Hornsund High
Authors: Bergh S.G. , Maher H.D. , Braathen A.
Published: February 2011

The Late Devonian Svalbardian event relates to the final activity in the Caledonian Orogen, and affected Devonian strata in Spitsbergen by major folding, oblique thrusting and basement uplift. In southern Spitsbergen, the Devonian deformation and the complementary, presumed Mid-Carboniferous Adriabukta event deformation caused uplift of the Sørkapp–Hornsund basement high or horst. This high is fault-bounded by Devonian sandstones and a questionably aged Early or Mid-Carboniferous mudstone unit (Adriabukta Formation). The Adriabukta Formation at Hornsund occurs in the core of a major syncline, with underlying Devonian strata in the west limb, all truncated in the footwall by a steep, east-side-up oblique-reverse fault. Mid- to Late Carboniferous rifting reversed the motion and produced rift-fill deposits, and these strata overlie the deformed Devonian rocks and the Adriabukta Formation with an angular unconformity. A similar basin architecture and major syncline bounded by a reverse fault with lateral movement characterize the Svalbardian deformation in the Mimerdalen–Pyramiden area at Billefjorden farther north. Similarity also exists between a Late Devonian unit (Plantekløfta Formation) at Mimerdalen and the Adriabukta Formation at Hornsund, and we question the previous interpretation of the Adriabukta Formation as Carboniferous. Rather, we suggest that the Adriabukta and Svalbardian deformation events may have been part of the same event.
The age of the Mesoproterozoic Stoer Group sedimentary and impact deposits, NW Scotland
Authors: Parnell John , Mark Darren , Fallick Anthony E. , Boyce Adrian , Thackrey Scott
Published: February 2011

The Mesoproterozoic Stoer Group of the ‘Torridonian' has been dated at 1177 ± 5 Ma (2σ), based on
40
Ar/
39
Ar dating of authigenic K-feldspars precipitated in degassing structures within the Stac Fada Member, interpreted previously as an impact ejecta deposit. Fluid inclusion analysis of the K-feldspar shows that it precipitated from hot fluids, and so must immediately post-date emplacement of the ejecta blanket. The oxygen isotopic composition of K-feldspar is remarkably constant at 9.7 ± 0.2‰ (V-SMOW) and is consistent with derivation from evaporated lake water. The new age supports previous determinations of 1199 ± 70 Ma from Pb–Pb dating of limestone and 1180 Ma from palaeomagnetic data, but provides much higher precision.

Supplementary material:

The raw
40
Ar/
39
Ar data, J-parameters, correction factors, air calibrations and blank data are available at
http://www.geolsoc.org.uk/SUP18453
.
Provenance of Cenozoic sedimentary rocks from the Sulaiman fold and thrust belt, Pakistan: implications for the palaeogeography of the Indus drainage system
Authors: Roddaz Martin , Said Aymen , Guillot Stéphane , Antoine Pierre-Olivier , Montel Jean-Marc , Martin François , Darrozes José
Published: February 2011

The provenance of middle Eocene to early Miocene sedimentary rocks cropping out in the Sulaiman fold and thrust belt has been determined examining the mineralogy, bulk-rock major and trace elements, and Nd–Sr isotopes. The older (50–30 Ma) deposits are characterized by a mixed orogenic provenance with a major contribution from the Karakorum and the Tethyan belt (
c
. 80%). As the 50–30 Ma deposits have a provenance distinct from that of coeval Subathu, Khojak and Ghazij shallow marine formations of India and Pakistan, we propose that they were deposited as a distinct delta system that once fed the Palaeo-Indus fan. We document a major change in provenance that occurred before the early–late Oligocene transition at
c
. 30 Ma. This change in provenance is marked by the appearance of chlorite and monazite and a shift toward more radiogenic Nd–Sr isotopic compositions. We interpret this change as the result of the exhumation and erosion of the proto-Higher Himalaya. The 30–15 Ma sampled rocks are characterized by a major contribution from the Tethyan belt and the Higher Himalayan Crystallines (70–90%) and a subordinate contribution (10–30%) from the Karakorum, Ophiolitic Suture and Trans-Himalaya. As the εNd(0) values of our 30–15 Ma samples are similar to those of the Palaeo-Indus fan deposits, we suggest that the 30–15 Ma sedimentary rocks of the Sulaiman fold and thrust belt were the fluvial onshore record of the Indus fan. Other coeval deposits of India and Pakistan recorded similar increasing exhumation of the Higher Himalaya range, so that we postulate that these sedimentary rocks all derived from the Palaeo-Indus drainage basin. This would suggest that the modern Indus drainage basin is no younger than 30 Ma.
Pennsylvanian ‘fossil forests' in growth position (T
0
assemblages): origin, taphonomic bias and palaeoecological insights
Authors: DiMichele William A. , Falcon-Lang Howard J.
Published: February 2011

Fossil forests, buried in growth position in a geological instant (T
0
assemblages) are far more abundant in Pennsylvanian successions than in any other part of the geological record. In this review paper, we evaluate the fundamental controls on the origin of these phenomena, investigate the taphonomic biases that influence their composition, and summarize their palaeoecological significance. Following earlier workers, we highlight that high rates of burial and accommodation are essential for the formation and preservation of T
0
assemblages. Contexts especially favourable for their origin include ashfalls proximal to volcanic centres, coastal plains drowned by relative sea-level rise, and fluvial environments such as channel bars, crevasse splays, and distributary lobes. Long-term preservation requires high rates of subsidence. Consequently, the vast majority of Palaeozoic T
0
assemblages are confined to wetland settings at, or close to, sea level, whereas drylands are poorly represented and uplands rarely sampled, if ever. However, this is not the only major bias in the fossil record; taphonomic processes selectively preserve plants dependent on their anatomy and stature, and on groundwater chemistry. Thus, although T
0
assemblages offer unrivalled insights into the nature of ancient forests (whole-plant reconstructions, tree density, canopy height, productivity, plant hydraulics, cohort dynamics, spatial heterogeneity, ecological gradients, tree–sediment interactions, and animal–plant interactions, to name but a few), it is naive to believe they provide ‘photographic snapshots' of palaeoecosystems. None the less, careful taphonomic analysis of T
0
assemblages offers the potential for a nuanced understanding of these evocative phenomena, and much remains to be learned from these important palaeoecological resources.
The possible role of extensional faults in localizing magmatic activity: a crustal model for the Campanian Volcanic Zone (eastern Tyrrhenian Sea, Italy)
Authors: Milia A. , Torrente M.M.
Published: February 2011

Three crustal geological sections of the Campanian Volcanic Zone (Italy) were reconstructed by integrating basin architecture and deep well stratigraphies. In addition, mapping of the fault system and of large-volume ignimbrites was carried out. A linked fault system has been identified, which was responsible for asymmetric subsidence contemporaneous with the eruption of ignimbrites. Late Quaternary extension is characterized by a WNW–ESE stretching axis, NNE–SSW normal faults and reactivation of inherited structures. Structural, stratigraphic and palaeogeographical analyses reveal evidence for up to 750 m of subsidence, which has occurred at a mean rate of up to 4.9 mm a
−1
over the past 154 ka. These rates suggest that extensional tectonics was responsible for the regional subsidence. A 6 km deep seismic reflector was associated with a magmatic reservoir underlying Campi Flegrei. By matching the structural and stratigraphic architecture with published geophysical and geochemical data a crustal tectonomagmatic model was constructed that displays high-angle faults that root into a low-angle detachment, which in turn roots into a deep sill-like magma reservoir. This model suggests the possible role of extensional faults in localizing magmatic activity, as faults controlled magma rise from deep to shallow reservoirs and to the surface during ignimbrite eruptions.

Supplementary material:

Seismic reflection profiles and interpretations are available at
http://www.geolsoc.org.uk/SUP18451
.
Deformation partitioning during transpressional emplacement of a ‘mantle extrusion wedge': the Ronda peridotites, western Betic Cordillera, Spain
Authors: Mazzoli S. , Algarra A. Martín
Published: February 2011

Composite tectonic emplacement of the world's largest outcropping body of subcontinental mantle rocks, the Ronda peridotites, occurred during Early Miocene continental subduction and as a result of oblique plate convergence. Partitioning of transpressional deformation between coeval orogen-parallel wrenching and orogen-perpendicular, pure thrusting components is recorded by shear zone kinematics and dynamothermal metamorphism in the footwall to the ultramafic rocks. Left-lateral shear, characterizing the deeper, high-pressure (eclogitic) portions of the continental subduction system, propagated through the mantle into the overlying continental crust of the overriding plate, whereas top-to-the-foreland frontal thrusting dominated at the leading edge of the hot peridotite body. Top-to-the-hinterland shear along the upper contact of the peridotites is consistent with the kinematics expected for an extrusion wedge consisting of subcontinental mantle rocks. On the other hand, coeval strike-parallel extension and thinning of the crustal rocks overlying the peridotites confirms that, similarly to other Alpine–Mediterranean examples, partitioned transpression resulted in the development of a complex deformation pattern, with kinematically linked shear zones aiding exhumation. The proposed model provides a new, coherent scenario for syn-convergence peridotite emplacement and exhumation in the western Betic Cordillera.
Quantifying creep behaviour of clay-bearing rocks below the critical stress state for rapid failure: Mam Tor landslide, Derbyshire, England
Authors: Rutter E.H. , Green S.
Published: February 2011

The Mam Tor landslide (Derbyshire, England) slips downhill at up to 0.5 m a
−1
, and offers an excellent opportunity to study time-dependent creep in mudstones under
in situ
conditions. Annual surveys show that creep rates increase following heavy rainfall, but to establish detailed correlation between creep and pore water pressure required spatially and temporally higher resolution monitoring. We acquired 3 years of such data, at 3 h intervals, from wire creep meters, borehole piezometers and rainfall monitoring, showing that creep is strongly focused into the winter months and correlates well with pore water pressure. Summer grass and fern growth strongly influence rainfall infiltration, recycling much of the rainfall back to the atmosphere, explaining the seasonal variability of creep. The dependence of creep rate on pore pressure can be recast as a rheological model relating shear strain rate to shear stress using the friction angle for the creeping mudstone to link effective normal stress to shear stress. The creep is very non-linear, following a power law with a stress exponent of 48. This flow law may apply also to shear failure in poorly consolidated mudrocks under high pore pressure conditions; for example, within some landslides, subglacial sediments, tectonic fault zones, tectonic mélanges and accretionary complexes.
Etch Behavior of ALD Al2O3 on HfSiO and HfSiON Stacks in Acidic and Basic Etchants
Authors: Oh Jisook , Myoung Jihyun , Bae Jin Sung , Lim Sangwoo
Published: February 2011

For the integration of advance gate stacks, selective wet etching of an Al2O3 capping layer on top of high-k dielectrics was studied. From the fundamental etch study on the single-layer Al2O3, HfSiO and HfSiON thin films were prepared by atomic layer deposition (ALD). Using the etch rate information of each single layer, several optimized etch conditions in acidic and basic etchants including H3PO4, NH4OH, and TMAH resulted in wet etch selectivities of Al2O3 to high-k materials higher than 50:1. As a result, the Al2O3 capping layer on Si/SiO2/high-k multi-layer gate stack could be completely removed without thinning of the underlying high-k thin films. Finally, the etch mechanisms of Al2O3 in acidic and basic etchants were studied and the etch rates of Al2O3 were determined as functions of [H+] and [OH−].
Redistribution of the tight junction protein ZO-1 during physiological shedding of mouse intestinal epithelial cells
Authors: Guan Yanfang , Watson Alastair J. M. , Marchiando Amanda M. , Bradford Emily , Shen Le , Turner Jerrold R. , Montrose Marshall H.
Published: February 2011

We questioned how tight junctions contribute to intestinal barrier function during the cell shedding that is part of physiological cell renewal. Intravital confocal microscopy studied the jejunal villus epithelium of mice expressing a fluorescent zonula occludens 1 (ZO-1) fusion protein. Vital staining also visualized the cell nucleus (Hoechst staining) or local permeability to luminal constituents (Lucifer Yellow; LY). In a cell fated to be shed, ZO-1 redistributes from the tight junction toward the apical and then basolateral cell region. ZO-1 rearrangement occurs 15 ± 6 min ( n = 28) before movement of the cell nucleus from the epithelial layer. During cell extrusion, permeation of luminal LY extends along the lateral intercellular spaces of the shedding cell only as far as the location of ZO-1. Within 3 min after detachment from the epithelial layer, nuclear chromatin condenses. After cell loss, a residual patch of ZO-1 remains in the space previously occupied by the departed cell, and the size of the patch shrinks to 14 ± 2% ( n = 15) of the original cell space over 20 min. The duration of cell shedding measured by nucleus movement (14 ± 1 min) is much less than the total duration of ZO-1 redistribution at the same sites (45 ± 2 min). In about 15% of cell shedding cases, neighboring epithelial cells also undergo extrusion with a delay of 5–10 min. With the use of normal mice, ZO-1 immunofluorescent staining of fixed tissue confirmed ZO-1 redistribution and the presence of ZO-1 patches beneath shedding cells. Immunostaining also showed that redistribution of ZO-1 occurred without corresponding mixing of apical and basolateral membrane domains as marked by ezrin or E-cadherin. ZO-1 redistribution is the earliest cellular event yet identified as a herald of physiological cell shedding, and redistribution of tight junction function along the lateral plasma membrane sustains epithelial barrier during cell shedding.
Acute-phase responses vary with pathogen identity in house sparrows (Passer domesticus)
Authors: Coon Courtney A. C. , Warne Robin W. , Martin Lynn B.
Published: February 2011

Pathogens may induce different immune responses in hosts contingent on pathogen characteristics, host characteristics, or interactions between the two. We investigated whether the broadly effective acute-phase response (APR), a whole body immune response that occurs in response to constitutive immune receptor activation and includes fever, secretion of immune peptides, and sickness behaviors such as anorexia and lethargy, varies with pathogen identity in the house sparrow ( Passer domesticus ). Birds were challenged with a subcutaneous injection of either a glucan at 0.7 mg/kg (to simulate fungal infection), a synthetic double-stranded RNA at 25 mg/kg (to simulate viral infection), or LPS at 1 mg/kg (to simulate a gram-negative bacterial infection), and then body mass, core body temperature changes, sickness behaviors, and secretion of an acute-phase protein, haptoglobin, were compared. Despite using what are moderate-to-high pyrogen doses for other vertebrates, only house sparrows challenged with LPS showed measurable APRs. Febrile, behavioral, and physiological responses to fungal and viral mimetics had minimal effects.
Regulation of mitochondrial morphology and function by O-GlcNAcylation in neonatal cardiac myocytes
Authors: Makino Ayako , Suarez Jorge , Gawlowski Thomas , Han Wenlong , Wang Hong , Scott Brian T. , Dillmann Wolfgang H.
Published: February 2011

Mitochondria are crucial organelles in cell life serving as a source of energy production and as regulators of Ca2+ homeostasis, apoptosis, and development. Mitochondria frequently change their shape by fusion and fission, and recent research on these morphological dynamics of mitochondria has highlighted their role in normal cell physiology and disease. In this study, we investigated the effect of high glucose on mitochondrial dynamics in neonatal cardiac myocytes (NCMs). High-glucose treatment of NCMs significantly decreased the level of optical atrophy 1 (OPA1) (mitochondrial fusion-related protein) protein expression. NCMs exhibit two different kinds of mitochondrial structure: round shape around the nuclear area and elongated tubular structures in the pseudopod area. High-glucose-treated NCMs exhibited augmented mitochondrial fragmentation in the pseudopod area. This effect was significantly decreased by OPA1 overexpression. High-glucose exposure also led to increased O-GlcNAcylation of OPA1 in NCMs. GlcNAcase (GCA) overexpression in high-glucose-treated NCMs decreased OPA1 protein O-GlcNAcylation and significantly increased mitochondrial elongation. In addition to the morphological change caused by high glucose, we observed that high glucose decreased mitochondrial membrane potential and complex IV activity and that OPA1 overexpression increased both levels to the control level. These data suggest that decreased OPA1 protein level and increased O-GlcNAcylation of OPA1 protein by high glucose lead to mitochondrial dysfunction by increasing mitochondrial fragmentation, decreasing mitochondrial membrane potential, and attenuating the activity of mitochondrial complex IV, and that overexpression of OPA1 and GCA in cardiac myocytes may help improve the cardiac dysfunction in diabetes.
Excitatory synaptic transmission and network activity are depressed following mechanical injury in cortical neurons
Authors: Goforth Paulette B. , Ren Jianhua , Schwartz Benjamin S. , Satin Leslie S.
Published: February 2011

In vitro and in vivo traumatic brain injury (TBI) alter the function and expression of glutamate receptors, yet the combined effect of these alterations on cortical excitatory synaptic transmission is unclear. We examined the effect of in vitro mechanical injury on excitatory synaptic function in cultured cortical neurons by assaying synaptically driven intracellular free calcium ([Ca2+]i) oscillations in small neuronal networks as well as spontaneous and miniature excitatory postsynaptic currents (mEPSCs). We show that injury decreased the incidence and frequency of spontaneous neuronal [Ca2+]i oscillations for at least 2 days post-injury. The amplitude of the oscillations was reduced immediately and 2 days post-injury, although a transient rebound at 4 h post-injury was observed due to increased activity of N-methyl-d-aspartate (NMDARs) and calcium-permeable α-amino-3-hydroxyl-5-methyl-4-isoxazole-propionate receptors (CP-AMPARs). Increased CP-AMPAR function was abolished by the inhibition of protein synthesis. In parallel, mEPSC amplitude decreased immediately, 4 h, and 2 days post-injury, with a transient increase in the contribution of synaptic CP-AMPARs observed at 4 h post-injury. Decreased mEPSC amplitude was evident after injury, even if NMDARs and CP-AMPARs were blocked pharmacologically, suggesting the decrease reflected alterations in synaptic Glur2-containing, calcium-impermeable AMPARs. Despite the transient increase in CP-AMPAR activity that we observed, the overriding effect of mechanical injury was long-term depression of excitatory neurotransmission that would be expected to contribute to the cognitive deficits of TBI.
Deficits in task-specific modulation of anticipatory postural adjustments in individuals with spastic diplegic cerebral palsy
Authors: Tomita Hidehito , Fukaya Yoshiki , Ueda Tomomi , Honma Shota , Yamashita Eriya , Yamamoto Yoshiji , Mori Etsuko , Shionoya Katsuyoshi
Published: February 2011

We examined whether individuals with spastic diplegic cerebral palsy (SDCP) have the ability to utilize lower leg muscles in anticipatory postural adjustments (APAs) associated with voluntary arm movement while standing, as well as the ability to modulate APAs with changes in the degree of postural perturbation caused by arm movement. Seven individuals with spastic diplegia (SDCP group, 12–22 yr of age) and seven age- and sex-matched individuals without disability (control group) participated in this study. Participants flexed both shoulders and lifted a load under two different load conditions, during which electromyographic activities of focal and postural muscles were recorded. Although the timing of anticipatory activation of the erector spinae and medial hamstring (MH) muscles was similar in the two participant groups, that of the gastrocnemius (GcM) muscle was significantly later in the SDCP group than in the control group. An increase in anticipatory postural muscle activity with an increase in load was observed in MH and GcM in the control group but not in GcM in the SDCP group. The degree of modulation in MH was significantly smaller in the SDCP group than in the control group. An additional experiment confirmed that these differences in APAs between the two participant groups were unlikely to be attributable to their differences in initial standing posture before load lift. The present findings suggest that lower leg muscles play a minor role in APAs in individuals with spastic diplegia. In addition, it is likely that these individuals have difficulty modulating anticipatory postural muscle activity with changes in the degree of postural perturbation.
Neural correlates of inter- and intra-individual saccadic reaction time differences in the gap/overlap paradigm
Authors: Özyurt Jale , Greenlee Mark W.
Published: February 2011

To examine the neural correlates of contextually differing control mechanisms in saccade initiation, we studied 18 subjects who performed two saccade paradigms in a pseudo-random order, while their eye movements were recorded in the MRI scanner (1.5 T). In the gap task the fixation point was extinguished 200 ms before target onset, and in the overlap task the fixation point vanished 500 ms after target onset. Subjects were asked to maintain stable fixation in the fixation period and to quickly saccade to peripherally presented targets. Inter-individual activation differences were assessed using regression analyses at the second level, with mean saccadic reaction time (SRT) of subjects as a covariate. To identify brain regions varying with trial-by-trial changes in SRTs, we included SRTs as a parametric modulation regressor in the general linear model. All analyses were regions of interest based and were performed separately for the gap and overlap conditions. For the gap paradigm, we did not obtain activation in regions previously shown to be involved in preparatory processes with much longer gap periods. Interestingly, both inter- and intra-individual variability analyses revealed a positive correlation of activation in frontal and parietal eye-movement regions with SRTs, indicating that slower saccade performance is possibly associated with higher cortical control. For the overlap paradigm, the trial-by-trial variability analysis revealed a positive correlation of activation in the right opercular inferior frontal gyrus with SRTs, possibly linked to fixation-related processes that have to be overcome to perform a speeded saccade in presence of a fixation point.
Modulation of motor cortex neuronal networks by rTMS: comparison of local and remote effects of six different protocols of stimulation
Authors: Di Lazzaro V. , Dileone M. , Pilato F. , Capone F. , Musumeci G. , Ranieri F. , Ricci V. , Bria P. , Di Iorio R. , de Waure C. , Pasqualetti P. , Profice P.
Published: February 2011

Repetitive transcranial magnetic stimulation (rTMS) of human motor cortex can produce long-lasting changes in the excitability of excitatory and inhibitory neuronal networks. The effects of rTMS depend critically on stimulus frequency. The aim of our present study was to compare the effects of different rTMS protocols. We compared the aftereffects of 6 different rTMS protocols [paired associative stimulation at interstimulus intervals of 25 (PAS25) and 10 ms (PAS10); theta burst stimulation delivered as continuous (cTBS) or intermittent delivery pattern (iTBS); 1- and 5-Hz rTMS] on the excitability of stimulated and contralateral motor cortex in 10 healthy subjects. A pronounced increase of cortical excitability, evaluated by measuring the amplitude of motor evoked potentials (MEPs), was produced by iTBS (+56%) and PAS25 (+45%). Five-hertz rTMS did not produce a significant increase of MEPs. A pronounced decrease of cortical excitability was produced by PAS10 (−31%), cTBS (−29%), and 1-Hz rTMS (−20%). Short-interval intracortical inhibition was suppressed by PAS10. Cortical silent period duration was increased by 1-Hz stimulation. No significant effect was observed in the contralateral hemisphere. Head-to-head comparison of the different protocols enabled us to identify the most effective paradigms for modulating the excitatory and inhibitory circuits activated by TMS.
Measurement of passive ankle stiffness in subjects with chronic hemiparesis using a novel ankle robot
Authors: Roy Anindo , Krebs Hermano I. , Bever Christopher T. , Forrester Larry W. , Macko Richard F. , Hogan Neville
Published: February 2011

Our objective in this study was to assess passive mechanical stiffness in the ankle of chronic hemiparetic stroke survivors and to compare it with those of healthy young and older (age-matched) individuals. Given the importance of the ankle during locomotion, an accurate estimate of passive ankle stiffness would be valuable for locomotor rehabilitation, potentially providing a measure of recovery and a quantitative basis to design treatment protocols. Using a novel ankle robot, we characterized passive ankle stiffness both in sagittal and in frontal planes by applying perturbations to the ankle joint over the entire range of motion with subjects in a relaxed state. We found that passive stiffness of the affected ankle joint was significantly higher in chronic stroke survivors than in healthy adults of a similar cohort, both in the sagittal as well as frontal plane of movement, in three out of four directions tested with indistinguishable stiffness values in plantarflexion direction. Our findings are comparable to the literature, thus indicating its plausibility, and, to our knowledge, report for the first time passive stiffness in the frontal plane for persons with chronic stroke and older healthy adults.
Activation of group I metabotropic glutamate receptors modulates locomotor-related motoneuron output in mice
Authors: Iwagaki Noboru , Miles Gareth B.
Published: February 2011

Fast glutamatergic transmission via ionotropic receptors is critical for the generation of locomotion by spinal motor networks. In addition, glutamate can act via metabotropic glutamate receptors (mGluRs) to modulate the timing of ongoing locomotor activity. In the present study, we investigated whether mGluRs also modulate the intensity of motor output generated by spinal motor networks. Application of the group I mGluR agonist ( S)-3,5-dihydroxyphenylglycine (DHPG) reduced the amplitude and increased the frequency of locomotor-related motoneuron output recorded from the lumbar ventral roots of isolated mouse spinal cord preparations. Whole cell patch-clamp recordings of spinal motoneurons revealed multiple mechanisms by which group I mGluRs modulate motoneuron output. Although DHPG depolarized the resting membrane potential and reduced the voltage threshold for action potential generation, the activation of group I mGluRs had a net inhibitory effect on motoneuron output that appeared to reflect the modulation of fast, inactivating Na+ currents and action potential parameters. In addition, group I mGluR activation decreased the amplitude of locomotor-related excitatory input to motoneurons. Analyses of miniature excitatory postsynaptic currents indicated that mGluRs modulate synaptic drive to motoneurons via both pre- and postsynaptic mechanisms. These data highlight group I mGluRs as a potentially important source of neuromodulation within the spinal cord that, in addition to modulating components of the central pattern generator for locomotion, can modulate the intensity of motoneuron output during motor behavior. Given that group I mGluR activation reduces motoneuron excitability, mGluRs may provide negative feedback control of motoneuron output, particularly during high levels of glutamatergic stimulation.