bluuebunny/crossref_metadata_2025_split huggingface dataset:
Twisted sheaves and the period-index problem
Authors: Lieblich Max 
Published: January 2008

AbstractWe use twisted sheaves and their moduli spaces to study the Brauer group of a scheme. In particular, we (1) show how twisted methods can be efficiently used to re-prove the basic facts about the Brauer group and cohomological Brauer group (including Gabber’s theorem that they coincide for a separated union of two affine schemes), (2) give a new proof of de Jong’s period-index theorem for surfaces over algebraically closed fields, and (3) prove an analogous result for surfaces over finite fields. We also include a reduction of all period-index problems for Brauer groups of function fields over algebraically closed fields to characteristic zero, which (among other things) extends de Jong’s result to include classes of period divisible by the characteristic of the base field. Finally, we use the theory developed here to give counterexamples to a standard type of local-to-global conjecture for geometrically rational varieties over the function field of the projective plane.
On lattices in semi-stable representations: a proof of a conjecture of Breuil
Authors: Liu Tong 
Published: January 2008

AbstractFor p≥3 an odd prime and a nonnegative integer r≤p−2, we prove a conjecture of Breuil on lattices in semi-stable representations, that is, the anti-equivalence of categories between the category of strongly divisible lattices of weight r and the category of Galois stable $\mathbb {Z}_p$-lattices in semi-stable p-adic Galois representations with Hodge–Tate weights in {0,…,r}.
Genetic and Biochemical Characterization of OXA-63, a New Class D β-Lactamase fromBrachyspira pilosicoliBM4442
Authors: Meziane-Cherif Djalal , Lambert Thierry , Dupêchez Marine , Courvalin Patrice , Galimand Marc 
Published: January 2008

ABSTRACTBrachyspira pilosicoliBM4442, isolated from the feces of a patient with diarrhea at the Hospital Saint-Michel in Paris, was resistant to oxacillin (MIC > 256 μg/ml) but remained susceptible to cephalosporins and to the combination of amoxicillin and clavulanic acid. Cloning and sequencing of the corresponding resistance determinant revealed a coding sequence of 807 bp encoding a new class D β-lactamase named OXA-63. TheblaOXA-63gene was chromosomally located and not part of a transposon or of an integron. OXA-63 shared 54% identity with FUS-1 (OXA-85), an oxacillinase fromFusobacterium nucleatumsubsp.polymorphum, and 25 to 44% identity with other class D β-lactamases (DBLs) and contained all the conserved structural motifs of DBLs.Escherichia colicarrying theblaOXA-63gene exhibited resistance to benzylpenicillin and amoxicillin but remained susceptible to amoxicillin in combination with clavulanic acid. Mature OXA-63 consisted of a 31.5-kDa polypeptide and appeared to be dimeric. Kinetic analysis revealed that OXA-63 exhibited a narrow substrate profile, hydrolyzing oxacillin, benzylpenicillin, and ampicillin with catalytic efficiencies of 980, 250, and 150 mM−1s−1, respectively. The enzyme did not apparently interact with oxyimino-cephalosporins, imipenem, or aztreonam. Unlike FUS-1 and other DBLs, OXA-63 was strongly inhibited by clavulanic acid (50% inhibitory concentration [IC50] of 2 μM) and tazobactam (IC50of 0.16 μM) and exhibited low susceptibility to NaCl (IC50of >2 M). OXA-63 is the first DBL described for the anaerobic spirocheteB. pilosicoli.
Combination Echinocandin-Polyene Treatment of Murine Mucormycosis
Authors: Ibrahim Ashraf S. , Gebremariam Teclegiorgis , Fu Yue , Edwards John E. , Spellberg Brad 
Published: January 2008

ABSTRACT
We previously found that caspofungin synergized with amphotericin B lipid complex in treating murine mucormycosis. We now report a similarly enhanced activity of liposomal amphotericin combined with micafungin or anidulafungin in mice with disseminated mucormycosis. The efficacy of combination echinocandin-polyene therapy for mucormycosis is a class effect.
Induction of L1 and L2 β-Lactamase Production inStenotrophomonas maltophiliaIs Dependent on an AmpR-Type Regulator
Authors: Okazaki Aki , Avison Matthew B. 
Published: January 2008

ABSTRACTA divergently orientedampRhas been located upstream ofblaL2inStenotrophomonas maltophilia. AmpR is necessary for L1 and L2 β-lactamase induction in response to β-lactam challenge, and activation of AmpR is sufficient to induce L1 and L2 production. L1 induction requires more activation of AmpR than does L2 induction.
Clinical Response and Outcome of Infection with
Salmonella enterica
Serotype Typhi with Decreased Susceptibility to Fluoroquinolones: a United States FoodNet Multicenter Retrospective Cohort Study
Authors: Crump John A. , Kretsinger Katrina , Gay Kathryn , Hoekstra R. Michael , Vugia Duc J. , Hurd Sharon , Segler Susan D. , Megginson Melanie , Luedeman L. Jeffrey , Shiferaw Beletshachew , Hanna Samir S. , Joyce Kevin W. , Mintz Eric D. , Angulo Frederick J. 
Published: January 2008

ABSTRACT

Patients with typhoid fever due to
Salmonella enterica
serotype Typhi strains for which fluoroquinolones MICs are elevated yet that are classified as susceptible by the current interpretive criteria of the Clinical and Laboratory Standards Institute may not respond adequately to fluoroquinolone therapy. Patients from seven U.S. states with invasive
Salmonella
serotype Typhi infection between 1999 and 2002 were enrolled in a multicenter retrospective cohort study. Patients infected with
Salmonella
serotype Typhi isolates with ciprofloxacin MICs of 0.12 to 1 μg/ml (decreased ciprofloxacin susceptibility but not resistant to ciprofloxacin [DCS]) were compared with patients infected with isolates with ciprofloxacin MICs <0.12 μg/ml for fever clearance time and treatment failure. Of 71 patients, 30 (43%) were female and 24 (34%) were infected with
Salmonella
serotype Typhi with DCS; the median age was 14 years (range, 1 to 51 years). Twenty-one (88%) of 24 isolates with DCS were resistant to nalidixic acid. The median antimicrobial-related fever clearance times in the DCS and non-DCS groups were 92 h (range, 21 to 373 h) and 72 h (range, 19 to 264 h) (
P
= 0.010), respectively, and the fluoroquinolone-related fever clearance times in the DCS and non-DCS groups were 90 h (range, 9 to 373 h) and 64 h (range, 34 to 204 h) (
P
= 0.153), respectively. Four (17%) of 24 patients in the DCS group and 2 (4%) of 46 patients in the non-DCS group (relative risk, 2.5; 95% confidence interval, 1.2 to 5.1) experienced treatment failure. Associations persisted after adjustment for potential confounders. We demonstrate that patients infected with
Salmonella
serotype Typhi isolates with DCS show evidence of a longer time to fever clearance and more frequent treatment failure. Nalidixic acid screening does not detect all isolates with DCS.
Direct Binding of Human NK Cell Natural Cytotoxicity Receptor NKp44 to the Surfaces of Mycobacteria and Other Bacteria
Authors: Esin Semih , Batoni Giovanna , Counoupas Claudio , Stringaro Annarita , Brancatisano Franca Lisa , Colone Marisa , Maisetta Giuseppantonio , Florio Walter , Arancia Giuseppe , Campa Mario 
Published: January 2008

ABSTRACT

Our previous studies demonstrated that
Mycobacterium bovis
bacillus Calmette-Guérin (BCG) can directly interact with human NK cells and induce the proliferation, gamma interferon production, and cytotoxic activity of such cells without the need for accessory cells. Thus, the aim of the present study was to identify the putative receptor(s) responsible for the recognition of BCG by human NK cells and potentially involved in the activation of NK cells. To this end, we first investigated the surface expression of three NK cell-activating receptors belonging to the natural cytoxicity receptor (NCR) family on highly purified human NK cells upon in vitro direct stimulation with BCG. An induction of the surface expression of NKp44, but not of NKp30 or NKp46, was observed after 3 and 4 days of in vitro stimulation with live BCG. The NKp44 induction involved mainly a particular NK cell subset expressing the CD56 marker at high density, CD56
bright
. In order to establish whether NKp44 could directly bind to BCG, whole BCG cells were stained with soluble forms of the three NCRs chimeric for the human immunoglobulin G (IgG) Fc fragment (NKp30-Fc, NKp44-Fc, NKp46-Fc), followed by incubation with a phycoerythrin (PE)-conjugated goat anti-human IgG antibody. Analysis by flow cytometry of the complexes revealed a higher PE fluorescence intensity for BCG incubated with NKp44-Fc than for BCG incubated with NKp30-Fc, NKp46-Fc, or negative controls. The binding of NKp44-Fc to the BCG surface was confirmed with immunogold labeling using transmission electron microscopy, suggesting the presence of a putative ligand(s) for human NKp44 on the BCG cell wall. Similar binding assays performed on a number of gram-positive and gram-negative bacteria revealed a pattern of NKp44-Fc binding restricted to members of the genus
Mycobacterium
, to the mycobacterium-related species
Nocardia farcinica
, and to
Pseudomonas aeruginosa
. Altogether, the results obtained indicate, for the first time, that at least one member of the NCR family (NKp44) may be involved in the direct recognition of bacterial pathogens by human NK cells.
Fetal Responses during Placental Malaria Modify the Risk of Low Birth Weight
Authors: Kabyemela Edward R. , Fried Michal , Kurtis Jonathan D. , Mutabingwa Theonest K. , Duffy Patrick E. 
Published: January 2008

ABSTRACTInflammation during placental malaria (PM) is associated with low birth weight (LBW), especially during the first pregnancy, but the relative contribution of maternal or fetal factors that mediate this effect remains unclear and the role of gamma interferon (IFN-γ) has been controversial. We examined the relationship of maternal and cord plasma levels of IFN-γ, tumor necrosis factor alpha, interleukin-10, ferritin, and leptin to birth weight for Tanzanian women delivering in an area where there is a high rate of malaria transmission. The placental levels of inflammatory cytokines, including IFN-γ, increased significantly during PM in primigravid and multigravid women but not in secundigravid women. PM also increased maternal peripheral levels of all inflammatory markers except IFN-γ but had strikingly little effect on cord levels of these proteins. In a multivariate analysis, placental IFN-γ was negatively associated (P= 0.01) and cord ferritin was positively associated (P< 0.0001) with birth weight in infected (PM-positive [PM+]) first-time mothers. This relationship was not observed in other mothers, consistent with the epidemiology of PM and disease. Cord leptin had a strong positive relationship with birth weight in offspring of PM-negative women (P= 0.02 toP< 0.0001) but not in offspring of PM+women (all differences were not significant) in the three gravidity groups. The results confirmed that placental IFN-γ is related to LBW due to PM during first pregnancies and suggest that fetal ferritin plays a protective role. Because fetal cells are a source of placental IFN-γ and cord ferritin, the fetal response to PM may modify the risk of LBW.
Recent advances in Clostridium difficile-associated disease
Authors: Monaghan T , Boswell T , Mahida Y R 
Published: February 2008

Abstract
The main purpose of this article is to review recent developments in the management of acute and recurrent Clostridium difficile-associated disease, with consideration of existing and new antibiotic and non-antibiotic agents for treatment. Details of the current developmental stage of new agents are provided and the role of surgery in the management of severe disease is discussed. Infection control measures considered comprise prudent use of antimicrobials, prevention of cross-infection and surveillance. Other topics that are covered include the recent emergence of an epidemic hypervirulent strain, pathogenesis, clinical presentation and approaches to rapid diagnosis and assessment of the colonic disease.
Pioneers of cortical plasticity: six classic papers by Wiesel and Hubel
Authors: Constantine-Paton Martha 
Published: January 2008

This essay looks at six APS classic papers published by D. H. Hubel and T. N. Wiesel that first identified a developmental critical period for environment influenced receptive field plasticity in the visual pathway. These classic papers are freely available online. These are listed here, in chronological order. Wiesel TN, Hubel DH. Effects of visual deprivation on morphology and physiology of cells in the cat's lateral geniculate body. J Neurophysiol 26: 978–993, 1963 ( http://jn.physiology.org/cgi/reprint/26/6/978 ). Hubel DH, Wiesel TN. Receptive fields of cells in striate cortex of very young, visually inexperienced kittens. J Neurophysiol 26: 994–1002, 1963 ( http://jn.physiology.org/cgi/reprint/26/6/994 ). Wiesel TN, Hubel DH. Single-cell responses in striate cortex of kittens deprived of vision in one eye. J Neurophysiol 26: 1003–1017, 1963 ( http://jn.physiology.org/cgi/reprint/26/6/1003 ). Wiesel TN, Hubel DH. Comparison of the effects of unilateral and bilateral eye closure on cortical unit responses in kittens. J Neurophysiol 28: 1029–1040, 1965 ( http://jn.physiology.org/cgi/reprint/28/6/1029 ). Hubel DH, Wiesel TN. Binocular interaction in striate cortex of kittens reared with artificial squint. J Neurophysiol 28: 1041–1059, 1965 ( http://jn.physiology.org/cgi/reprint/28/6/1041 ). Wiesel TN, Hubel DH. Extent of recovery from the effects of visual deprivation in kittens. J Neurophysiol 28: 1060–1072, 1965 ( http://jn.physiology.org/cgi/reprint/28/6/1060 ).
Stochastic Backscatter for Cloud-Resolving Models. Part I: Implementation and Testing in a Dry Convective Boundary Layer
Authors: Weinbrecht Sonja , Mason Paul J. 
Published: January 2008

Abstract
In simulations of deep convection with cloud-resolving models the turbulence is often rather poorly resolved, and the influence of the subfilter-scale parameterization used in such circumstances is probably greater than in better-resolved simulations. Therefore a study to investigate the influence of stochastic backscatter was performed and presented in two papers. This first paper focuses on a description of the stochastic backscatter model and its effect on a neutral and a dry convective boundary layer. The second paper then deals with two cases of deep convection.
The dry convective boundary layer is typical of the subcloud layer in deep convection and this study allows for influences on this layer to be investigated separately. As a simple case of convection it also allows for general effects to be identified. The implementation of stochastic backscatter was improved to ensure an appropriate scale of backscatter that is independent of any mesh refinements and always spatially isotropic. It can also be applied in a deep atmosphere with use of the anelastic approximation.
Generally the backscatter is found to affect the velocity and scalar variances as well as the spatial structure and time development of the simulations. An additional issue is the marked influence of both varying resolution and backscatter on the near-surface temperature differences. This is an element of the complex issue of surface transfers under free convection conditions. Overall, the investigations show that the backscatter gives some beneficial changes to the simulations, which tend to keep results in less well- resolved cases closer to those in better-resolved simulations.
Axial Atmospheric Angular Momentum Budget at Diurnal and Subdiurnal Periodicities
Authors: Lott François , de Viron Olivier , Viterbo Pedro , Vial François 
Published: January 2008

Abstract
The diurnal and subdiurnal variations of the mass and wind terms of the axial atmospheric angular momentum (AAM) are explored using a 1-yr integration of the Laboratoire de Météorologie Dynamique (LMDz) GCM, twelve 10-day ECMWF forecasts, and some ECMWF analysis products. In these datasets, the wind and mass AAMs present diurnal and semidiurnal oscillations for which tendencies far exceed the total torque.
In the LMDz GCM, these diurnal and semidiurnal oscillations are associated with axisymmetric (s = 0) and barotropic circulation modes that resemble the second gravest (n = 2) eigensolution of Laplace’s tidal equations. This mode induces a Coriolis conversion from the wind AAM toward the mass AAM that far exceeds the total torque. At the semidiurnal period, this mode dominates the axisymmetric and barotropic circulation. At the diurnal period, this n = 2 mode is also present, but the barotropic circulation also presents a mode resembling the first gravest n = 1 eigensolution of the tidal equations. This last mode does not produce anomalies in the mass and wind AAMs.
A shallow-water axisymmetric model driven by zonal mean zonal forces, for which the vertical integral equals the zonal mean zonal stresses issued from the GCM, is then used to interpret these results. This model reproduces well the semidiurnal oscillations in mass and wind AAM, and the semidiurnal mode resembling the n = 2 eigensolution that produces them, when the forcing is distributed barotropically in the vertical direction. This model also reproduces diurnal modes resembling the n = 1 and n = 2 eigensolutions when the forcings are distributed more baroclinically. Among the dynamical forcings that produce these modes of motion, it is found that the mountain forcing and the divergence of the AAM flux are equally important and are more efficient than the boundary layer friction.
In geodesy, the large but opposite signals in the mass and wind AAM due to the n = 2 modes can lead to large errors in the evaluation of the AAM budget. The n = 2 responses in surface pressure can affect the earth ellipcity, and the n = 1 diurnal response can affect the geocenter position. For the surface pressure tide, the results suggest that the dynamical forcings of the zonal-mean zonal flow are a potential cause for its s = 0 component.
Limits, Variability, and General Behavior of Statistical Predictability of the Midlatitude Atmosphere
Authors: Kleeman Richard 
Published: January 2008

AbstractThe nature of statistical predictability is analyzed in a T42 global atmospheric model that is able to adequately capture the main features of the midlatitude atmosphere. Key novel features of the present study include very large prediction ensembles and information theoretic techniques. It is found globally that predictability declines in a quasi-linear fashion with time for short-term predictions (3–25 days), while for long ranges (30–45 days) there is an exponential tail. In general, beyond 45 days the prediction and climatological ensembles have essentially converged, which means that beyond that point, atmospheric initial conditions are irrelevant to atmospheric statistical prediction.Regional predictions show considerable variation in behavior. Both of the (northern) winter storm-track regions show a close-to-quasi-linear decline in predictability toward a cutoff at around 40 days. The (southern) summer storm track shows a much more exponential and considerably slower decline with a small amount of predictability still in evidence even at 90 days. Because the winter storm tracks dominate global variance the behavior of their predictability tends to dominate the global measure, except at longer lags. Variability in predictability with respect to initial conditions is also examined, and it is found that this is related more strongly to ensemble signal rather than ensemble spread. This result may serve to explain why the relation between weather forecast skill and ensemble spread is often observed to be significantly less than perfect. Results herein suggest that the ensemble signal as well as spread variations may be a major contributor to skill variations. Finally, it is found that the sensitivity of the calculated global predictability to changes in model horizontal resolution is not large; results from a T85 resolution model are not qualitatively all that different from the T42 case.
Emission of Inertial Waves by Baroclinically Unstable Flows: Laboratory Experiments with Altimetric Imaging Velocimetry
Authors: Afanasyev Y. D. , Rhines P. B. , Lindahl E. G. 
Published: January 2008

Abstract
Results from new experiments on baroclinic instability of a coastal jet demonstrate that this almost balanced flow spontaneously emits inertial waves when the Rossby radius of deformation is relatively small such that the characteristics of baroclinic meanders match the dispersion relation for the inertial waves. The energy of the waves is small compared to the energy of the flow. A single event of wave emission is identified in the experiment with larger radius of deformation and is interpreted in terms of vorticity dynamics. The flows are generated on a laboratory polar β plane where the Coriolis parameter varies quadratically with latitude. A new method for imaging the rotating flows, which the authors call “altimetric imaging velocimetry,” is employed. Optical color coding of slopes of the free-surface elevation field allows the authors to derive the fields of pressure, surface elevation, geostrophic velocity, or the “gradient wind” velocity with very high spatial resolution (typically several million vectors) limited largely by the pixel resolution of the available imaging sensors. The technique is particularly suited for the investigations of small-amplitude waves, which are often difficult to detect by other methods.
The Effect of Dynamics on Mixed-Phase Clouds: Theoretical Considerations
Authors: Korolev Alexei , Field Paul R. 
Published: January 2008

Abstract
A theoretical framework has been developed describing nonequilibrium formation and maintenance of mixed-phase clouds. The necessary and sufficient conditions required to activate liquid water within a preexisting ice cloud, and thus convert it to mixed phase, are considered for three scenarios: (i) uniform ascent, (ii) harmonic vertical oscillations, and (iii) turbulent fluctuations. The general conditions are the following:First necessary condition: The vertical velocity of an ice cloud parcel must exceed a threshold velocity to activate liquid water.Second necessary condition: The activation of liquid water within an ice cloud parcel, below water saturation, requires a vertical ascent above some threshold altitude to bring the vapor pressure of the parcel to water saturation.
Only when the first and second conditions are true do these conditions become sufficient for the activation of liquid water in ice clouds. These required conditions for the generation of mixed-phase cloud are supported by parcel modeling results and analogous conditions for a harmonic oscillation concerning the amplitude and tangential velocity of the parcel motion are proposed. The authors do not assume steady-state conditions, but demonstrate that nonequilibrium evolution of cloud parcels can lead to long-term steady existence of mixed-phase cloud.