bluuebunny/crossref_metadata_2025 huggingface dataset:
Finite Cohen–Macaulay Type and Smooth Non-Commutative Schemes
Authors: Jørgensen Peter
Published: November 2009

A commutative local Cohen–Macaulay ring R of finite Cohen–Macaulay type is known to be an isolated singularity; that is, Spec(R) \ ﹛m﹜ is smooth. This paper proves a non-commutative analogue. Namely, if A is a (non-commutative) graded Artin–Schelter Cohen–Macaulay algebra which is fully bounded Noetherian and has finite Cohen–Macaulay type, then the non-commutative projective scheme determined by A is smooth.
Heegner Points and the Rank of Elliptic Curves over Large Extensions of Global Fields
Authors: Breuer Florian , Im Bo-Hae
Published: November 2009

Letkbe a global field,a separable closure ofk, andGkthe absolute Galois groupofoverk. For everyσ ∈ Gk, letbe the fixed subfield ofunderσ. LetE/kbe an elliptic curve overk. It is known that the Mordell–Weil grouphas infinite rank. We present a new proof of this fact in the following two cases. First, when k is a global function field of odd characteristic andEis parametrized by a Drinfeld modular curve, and secondly whenkis a totally real number field andE/kis parametrized by a Shimura curve. In both cases our approach uses the non-triviality of a sequence of Heegner points onEdefined over ring class fields.
A Multi-Frey Approach to Some Multi-Parameter Families of Diophantine Equations
Authors: Bugeaud Yann , Mignotte Maurice , Siksek Samir
Published: November 2009

We solve several multi-parameter families of binomial Thue equations of arbitrary degree; for example, we solve the equation

5uxn − 2r3s yn = ±1,

in non-zero integers x, y and positive integers u, r, s and n ≥ 3. Our approach uses several Frey curves simultaneously, Galois representations and level-lowering, new lower bounds for linear forms in 3 logarithms due to Mignotte and a famous theorem of Bennett on binomial Thue equations.
Non-Selfadjoint Perturbations of Selfadjoint Operators in Two Dimensions IIIa. One Branching Point
Authors: Hitrik Michael , Sjöstrand Johannes
Published: November 2009

This is the third in a series of works devoted to spectral asymptotics for non-selfadjoint perturbations of selfadjointh-pseudodifferential operators in dimension 2, having a periodic classical flow. Assuming that the strength ॉ of the perturbation is in the rangeh2≪ ॉ ≪ h1/2(and may sometimes reach even smaller values), we get an asymptotic description of the eigenvalues in rectangles [−1/C, 1/C] +iॉ[F0− 1/C,F0 + 1/C],C≫ 1, when ॉF0is a saddle point value of the flow average of the leading perturbation.
Uniform Linear Bound in Chevalley’s Lemma
Authors: Adamus J. , Bierstone E. , Milman P. D.
Published: November 2009

We obtain a uniform linear bound for the Chevalley function at a point in the source of an analytic mapping that is regular in the sense of Gabrielov. There is a version of Chevalley’s lemma also along a fibre, or at a point of the image of a proper analytic mapping. We get a uniform linear bound for the Chevalley function of a closed Nash (or formally Nash) subanalytic set.
Genus 2 Curves with Quaternionic Multiplication
Authors: Baba Srinath , Granath Håkan
Published: November 2009

We explicitly construct the canonical rational models of Shimura curves, both analytically in terms of modular forms and algebraically in terms of coefficients of genus 2 curves, in the cases of quaternion algebras of discriminant 6 and 10. This emulates the classical construction in the elliptic curve case. We also give families of genus 2 QMcurves, whose Jacobians are the corresponding abelian surfaces on the Shimura curve, and with coefficients that are modular forms of weight 12. We apply these results to show that our j-functions are supported exactly at those primes where the genus 2 curve does not admit potentially good reduction, and construct fields where this potentially good reduction is attained. Finally, using j, we construct the fields ofmoduli and definition for somemoduli problems associated to the Atkin–Lehner group actions.
Maximum Principles for Subharmonic Functions Via Local Semi-Dirichlet Forms
Authors: Kuwae Kazuhiro
Published: November 2009

Maximum principles for subharmonic functions in the framework of quasi-regular local semi-Dirichlet forms admitting lower bounds are presented. As applications, we give weak and strong maximum principles for (local) subsolutions of a second order elliptic differential operator on the domain of Euclidean space under conditions on coefficients, which partially generalize the results by Stampacchia.
H∞ Functional Calculus and Mikhlin-Type Multiplier Conditions
Authors: Galé José E. , Miana Pedro J.
Published: November 2009

Let T be a sectorial operator. It is known that the existence of a bounded (suitably scaled) H∞ calculus for T, on every sector containing the positive half-line, is equivalent to the existence of a bounded functional calculus on the Besov algebra . Such an algebra includes functions defined byMikhlin-type conditions and so the Besov calculus can be seen as a result on multipliers for T. In this paper, we use fractional derivation to analyse in detail the relationship between and Banach algebras of Mikhlin-type. As a result, we obtain a new version of the quoted equivalence.
On Types for Unramified p-Adic Unitary Groups
Authors: Kariyama Kazutoshi
Published: November 2009

Let F be a non-archimedean local field of residue characteristic neither 2 nor 3 equipped with a galois involution with fixed field F0, and let G be a symplectic group over F or an unramified unitary group over F0. Following the methods of Bushnell–Kutzko for GL(N, F), we define an analogue of a simple type attached to a certain skew simple stratum, and realize a type in G. In particular, we obtain an irreducible supercuspidal representation of G like GL(N, F).
A Classification of Tsirelson Type Spaces
Authors: Lopez-Abad J. , Manoussakis A.
Published: November 2009

We give a complete classification of mixed Tsirelson spacesfor finitely many pairs of given compact and hereditary familiesof finite sets of integers and 0 <θi< 1 in terms of the Cantor–Bendixson indices of the families, andθi(1 ≤i≤r). We prove that there are unique countable ordinalαand 0 <θ< 1 such that every block sequence ofhas a subsequence equivalent to a subsequence of the natural basis of the. Finally, we give a complete criterion of comparison in between two of these mixed Tsirelson spaces.
Short Time Behavior of Solutions to Linear and Nonlinear Schrödinger Equations
Authors: Taylor Michael
Published: November 2009

We examine the fine structure of the short time behavior of solutions to various linear and nonlinear Schrödinger equations ut = iΔu+q(u) on I×ℝn, with initial data u(0, x) = f (x). Particular attention is paid to cases where f is piecewise smooth, with jump across an (n−1)-dimensional surface. We give detailed analyses of Gibbs-like phenomena and also focusing effects, including analogues of the Pinsky phenomenon. We give results for general n in the linear case. We also have detailed analyses for a broad class of nonlinear equations when n = 1 and 2, with emphasis on the analysis of the first order correction to the solution of the corresponding linear equation. This work complements estimates on the error in this approximation.
Remarks on Littlewood–Paley Analysis
Authors: Ho Kwok-Pun
Published: November 2009

Littlewood–Paley analysis is generalized in this article. We show that the compactness of the Fourier support imposed on the analyzing function can be removed. We also prove that the Littlewood–Paley decomposition of tempered distributions converges under a topology stronger than the weak-star topology, namely, the inductive limit topology. Finally, we construct a multiparameter Littlewood–Paley analysis and obtain the corresponding “renormalization” for the convergence of this multiparameter Littlewood–Paley analysis.
Case series of liver failure associated with rosiglitazone and pioglitazone
Authors: Floyd James S. , Barbehenn Elizabeth , Lurie Peter , Wolfe Sidney M.
Published: November 2009

Purpose

The thiazolidinedione drugs rosiglitazone and pioglitazone are not widely known to be hepatotoxic. We evaluated the FDA Adverse Event Reporting System (AERS) to determine the number of reported cases of liver failure associated with rosiglitazone and pioglitazone between 1997 and 2006, and described their clinical characteristics.

Methods

Adverse event reports spontaneously submitted to the FDA AERS from 1997 to 2006 were examined. Liver failure associated with rosiglitazone or pioglitazone was defined as liver injury accompanied by hepatic encephalopathy, liver transplantation, placement on a liver transplant list, or death in which all other likely etiologies were excluded. Using prescribing data, the number of reported cases of liver failure per million patient‐years of exposure was calculated for each drug.

Results

Twenty‐one cases met our case definition. Clinical characteristics, outcomes, and pathologic data were similar between cases of liver failure associated with rosiglitazone and with pioglitazone. The median duration of therapy was 9 weeks and 85% of cases were acute, defined as symptom onset to liver failure in less than 26 weeks. The case‐fatality rate was 81% (17/21), and only 14% (3/21) spontaneously recovered. Accounting for underreporting, the number needed to harm (NNH) for each case of liver failure was 44 000 patient‐years of exposure for rosiglitazone and 52 000 patient‐years of exposure for pioglitazone.

Conclusions

This is the largest case series of liver failure associated with rosiglitazone or pioglitazone reported to date, strengthening the evidence that these drugs can cause severe hepatotoxicity. Copyright © 2009 John Wiley & Sons, Ltd.
COSMOPEN: dynamic reverse engineering on a budget. How cheap observation techniques can be used to reconstruct complex multi‐level behaviour
Authors: Taïani François , Killijian Marc‐Olivier , Fabre Jean‐Charles
Published: November 2009

In this paper we present COSMOPEN, a reverse‐engineering tool optimized for the behavioural analysis of complex layered software. COSMOPENcombines cheap and non‐intrusive observation techniques with a versatile graph manipulation engine. By programming different graph manipulation scripts, the ‘focal length’ of our tool can be adapted to different abstraction levels. We illustrate how our tool can be used to extract high‐level behavioural models from a complex multi‐threaded platform (GNU/Linux, CORBA middleware). Copyright © 2009 John Wiley & Sons, Ltd.
In silico models of cancer
Authors: Edelman Lucas B. , Eddy James A. , Price Nathan D.
Published: November 2009

Cancer is a complex disease that involves multiple types of biological interactions across diverse physical, temporal, and biological scales. This complexity presents substantial challenges for the characterization of cancer biology, and motivates the study of cancer in the context of molecular, cellular, and physiological systems. Computational models of cancer are being developed to aid both biological discovery and clinical medicine. The development of these in silico models is facilitated by rapidly advancing experimental and analytical tools that generate information‐rich, high‐throughput biological data. Statistical models of cancer at the genomic, transcriptomic, and pathway levels have proven effective in developing diagnostic and prognostic molecular signatures, as well as in identifying perturbed pathways. Statistically inferred network models can prove useful in settings where data overfitting can be avoided, and provide an important means for biological discovery. Mechanistically based signaling and metabolic models that apply a priori knowledge of biochemical processes derived from experiments can also be reconstructed where data are available, and can provide insight and predictive ability regarding the behavior of these systems. At longer length scales, continuum and agent‐based models of the tumor microenvironment and other tissue‐level interactions enable modeling of cancer cell populations and tumor progression. Even though cancer has been among the most‐studied human diseases using systems approaches, significant challenges remain before the enormous potential of in silico cancer biology can be fully realized. Copyright © 2009 John Wiley & Sons, Inc.

This article is categorized under:

Models of Systems Properties and Processes > Cellular Models
Learning from SimCity: An empirical study of Turkish adolescents
Authors: Tanes Zeynep , Cemalcilar Zeynep
Published: November 2009

SimCity is a system simulation game frequently used in educational settings. This study investigates whether playing SimCity could change Turkish adolescents' perception of the city they live in. We hypothesized that playing the game would lead to perceptional changes in the players regarding their ideal and real cities. Two hundred forty eight 13‐year old Turkish adolescents attending 7th grade constituted the sample. Ninety adolescents played the game for six weeks. Their scores on various perception variables on city issues were compared to those of the control group's. Results showed that students in the experimental group changed their expectations of an ideal city to resemble the game, expected city authorities to pay greater attention to city issues, and reported higher level of distrust to city authorities at the post‐test compared to those in the control group. Findings are discussed in terms of the potential of SimCity in training informed citizens.
The role of brain‐derived neurotrophic factor in experimental inflammation of mouse gut
Authors: Yang Jing , Yu Yanbo , Yu Hui , Zuo Xiuli , Liu Chunxi , Gao Lijun , Chen Zhe‐Yu , Li Yanqing
Published: November 2009

Previous studies suggested that brain‐derived neurotrophic factor (BDNF) might act as an important modulator in chronic pain states. However, no systematic study has used knock‐out mice to clarify its effect on visceral sensitivity. In the present study, 2,4,6‐trinitrobenzene sulfonic acid (TNBS) was administered to heterozygous (BDNF+/−) knock‐out and wild‐type (BDNF+/+) mice to induce colitis. Visceral response to colorectal distension (CRD) and bladder reactivity were recorded. Results demonstrated that in normal state, BDNF+/−and BDNF+/+mice did not differ in the visceral response to CRD at <60 mm Hg pressure and the bladder reactivity; however, with ≥60 mm Hg pressure, BDNF+/−mice showed a weaker visceral response to CRD. In inflammatory state of colitis, TNBS induced upregulation of BDNF in dorsal root ganglia of both genotypes while BDNF+/−mice showing significantly lower sensitivity in the colon at ≥30 mm Hg and lower sensitivity in bladder than BDNF+/+mice. The two genotypes showed no significant difference in inflammatory severity. Thus, BDNF deficiency results in developmental changes in colonic nociception in both control and inflammatory states, which are more significant in inflammatory state. For bladder reactivity, BDNF deficiency leads to lower sensitization in inflammatory state but has no effect in control state.

Perspective:This article highlights the role of BDNF in colonic and referred bladder hyperalgesia in mice. The findings might help in determining novel pharmaceutical interventions targeted at BDNF to relieve abdominal pain.
Clinical signs, magnetic resonance imaging findings and outcome in 77 cats with vestibular disease: A retrospective study
Authors: Negrin Arianna , Cherubini Giunio B. , Lamb Chris , Benigni Livia , Adams Vicky , Platt Simon
Published: November 2009

Medical records of 77 cats that had clinical signs of vestibular disease and magnetic resonance imaging (MRI) of the head were reviewed retrospectively. The aetiological, clinical and MRI characteristics were described and evaluated for a relationship with patient outcome. Forty cats (52%) had signs of central vestibular dysfunction (CVD), which was part of a multifocal disease in 17 cats (43%). The most frequent causes of CVD were inflammatory conditions (18 cats; 45%), including bacterial inflammation as an intracranial extension of otitis interna (five cats; 13%), feline infectious peritonitis (three cats; 8%) and toxoplasmosis (two cats; 5%). Neoplasia (12 cats; 30%) and vascular disease (four cats; 10%) were respectively the second and the third most frequent causes of CVD. Thiamine deficiency was diagnosed in one cat based on MRI findings and improvement following vitamin B1supplementation. Of 37 cats (48%) with peripheral vestibular dysfunction (PVD), idiopathic vestibular syndrome (IVS) was suspected in 16 (43%) and otitis media/interna was suspected in 16 (43%). Within the group of cats with evident MRI lesions, the location of the imaged lesions agreed with the clinical classification of vestibular dysfunction in 52/55 (95%) cats. Most of the cats (nine cases; 56%) with presumed IVS had rapid and complete recovery of their clinical signs. As most of these cats presented with progressive clinical signs over 3 weeks they were classified as having ‘atypical’ IVS to differentiate them from cats with the typical non-progressive IVS. No underlying systemic diseases were documented in any of these cases. Statistically significant predictors of survival included neurolocalisation (central or peripheral vestibular system), age and gender. No difference in survival was observed between cats with presumed idiopathic peripheral syndrome and cats with otitis media/interna.
Spinal cord compression in a cat due to vertebral angiomatosis
Authors: Schur David , Rademacher Nathalie , Vasanjee Sunil , McLaughlin Leslie , Gaschen Lorrie
Published: November 2009

A 1-year-old cat was presented with general discomfort but no neurologic deficits on physical examination. An extradural spinal cord compression at the level of T10–11 and T11–12 was evident on myelography and computed tomography examination. Hemilaminectomy was performed to decompress the spinal cord. Histopathology of the abnormal pedicle and lamina revealed vertebral angiomatosis. This rare vascular malformation was the cause of the spinal cord compression in this cat. It is seen in cats less than 2 years of age and affected the thoracic spine in all four previously reported cases.
Evolution of electron fluxes in the outer radiation belt computed with the VERB code
Authors: Shprits Yuri Y. , Subbotin Dmitri , Ni Binbin
Published: November 2009

Three‐dimensional simulations of the dynamics of outer radiation belt electrons with the recently developed Versatile Electron Radiation Belt (VERB) code are presented. Simulations are preformed for an idealized storm with geomagnetic activity–dependent wave amplitudes that are parameterized as a function of the level of geomagnetic activity. Numerical experiments using the VERB code with various scattering processes (pitch angle diffusion, radial diffusion, and energy diffusion) indicate that diffusive processes are strongly coupled with each other and that they all should be included in realistic simulations of the radiation belts. We show that during storms, inward radial diffusion can produce significant accelerations to relativistic energies, while pitch angle scattering and energy diffusion produce a decrease and an increase in fluxes, respectively. We show that in the presence of high‐latitude and low‐latitude chorus, peaks in the radial profile of phase space density are formed between L of 4 and 6 during the recovery phase of a storm and are later smoothed by radial diffusion. Sensitivity experiments show that geomagnetic control of wave intensities plays a controlling role in the dynamics of radiation belt electrons. Numerical simulations indicate that electrons of 10–100 keV near geosynchronous orbit can reach MeV energies in the heart of the radiation belts by combined radial diffusion and in situ acceleration. We present two scenarios of acceleration of the plasma sheet electrons: (1) in the range of hundreds of keV by means of radial diffusion and (2) in the range of tens of keV by means of radial diffusion combined with local acceleration.
Watershed Allied Telemetry Experimental Research
Authors: Li Xin , Li Xiaowen , Li Zengyuan , Ma Mingguo , Wang Jian , Xiao Qing , Liu Qiang , Che Tao , Chen Erxue , Yan Guangjian , Hu Zeyong , Zhang Lixin , Chu Rongzhong , Su Peixi , Liu Qinhuo , Liu Shaomin , Wang Jindi , Niu Zheng , Chen Yan , Jin Rui , Wang Weizhen , Ran Youhua , Xin Xiaozhou , Ren Huazhong
Published: November 2009

The Watershed Allied Telemetry Experimental Research (WATER) is a simultaneous airborne, satellite‐borne, and ground‐based remote sensing experiment aiming to improve the observability, understanding, and predictability of hydrological and related ecological processes at a catchment scale. WATER consists of the cold region, forest, and arid region hydrological experiments as well as a hydrometeorology experiment and took place in the Heihe River Basin, a typical inland river basin in the northwest of China. The field campaigns have been completed, with an intensive observation period lasting from 7 March to 12 April, from 15 May to 22 July, and from 23 August to 5 September 2008: in total, 120 days. Twenty‐five airborne missions were flown. Airborne sensors including microwave radiometers at L, K, and Ka bands, imaging spectrometer, thermal imager, CCD, and lidar were used. Various satellite data were collected. Ground measurements were carried out at four scales, that is, key experimental area, foci experimental area, experiment site, and elementary sampling plot, using ground‐based remote sensing instruments, densified network of automatic meteorological stations, flux towers, and hydrological stations. On the basis of these measurements, the remote sensing retrieval models and algorithms of water cycle variables are to be developed or improved, and a catchment‐scale land/hydrological data assimilation system is being developed. This paper reviews the background, scientific objectives, experiment design, filed campaign implementation, and current status of WATER. The analysis of the data will continue over the next 2 years, and limited revisits to the field are anticipated.
Optimal management of wetlands: Quantifying trade‐offs between flood risks, recreation, and biodiversity conservation
Authors: Birol Ekin , Hanley Nick , Koundouri Phoebe , Kountouris Yiannis
Published: November 2009

This paper employs a simple choice experiment to estimate the value of management options for the Bobrek wetland in Poland. The local public's valuation of several wetland management attributes, including flood risk reduction, biodiversity conservation and improvement of recreational access, are investigated. A latent class model is estimated to account for heterogeneity in the wetland management choices of the local public. The results reveal that there is considerable heterogeneity among the local public as two distinct segments are identified. For both of the segments, flood risk reduction, in the ranges considered, is more important than the other two attributes. The results of this study are expected to assist policy makers in undertaking effective flood risk reduction measures and formulating efficient, equitable and sustainable wetland management policies in accordance with the European Union's Water Framework Directive (2000/60/EC).
Ocean surface wave evolvement in the Arctic Basin
Authors: Squire Vernon A. , Vaughan Gareth L. , Bennetts Luke G.
Published: November 2009

Recent basin‐scale changes to the compactness and thickness of Arctic sea ice foreshadow that encroaching swells and locally generated waves will exert more influence there in the future. Indeed, it is conceivable that waves may have already hastened the adjustments observed by breaking up ice floes. Yet waves advancing in sea ice attenuate due to being scattered from ice thickness variations and damped by ice inelasticity, turbulence and friction. While past research focuses on scattering by unnaturally perfect features in the ice, the model reported herein assimilates realistic basin‐scale swathes of heterogeneous ice and parameterizes damping. By way of example, we show how an ocean wave train evolves during its passage in an 1670‐km‐long Arctic sea ice profile obtained from submarine.
Cold decade (AD 1810–1819) caused by Tambora (1815) and another (1809) stratospheric volcanic eruption
Authors: Cole‐Dai Jihong , Ferris David , Lanciki Alyson , Savarino Joël , Baroni Mélanie , Thiemens Mark H.
Published: November 2009

Climate records indicate that the decade of AD 1810–1819 including “the year without a summer” (1816) is probably the coldest during the past 500 years or longer, and the cause of the climatic extreme has been attributed primarily to the 1815 cataclysmic Tambora eruption in Indonesia. But the cold temperatures in the early part of the decade and the timing of the Tambora eruption call into question the real climatic impact of volcanic eruptions. Here we present new evidence, based on sulfur isotope anomaly (Δ33S), a unique indicator of volcanic sulfuric acid produced in the stratosphere and preserved in polar snow, and on the precise timing of the volcanic deposition in both polar regions, that another large eruption in 1809 of a volcano is also stratospheric and occurred in the tropics. The Tambora eruption and the undocumented 1809 eruption are together responsible for the unusually cold decade.
A new approach to correct for absorbing aerosols in OMI UV
Authors: Arola A. , Kazadzis S. , Lindfors A. , Krotkov N. , Kujanpää J. , Tamminen J. , Bais A. , di Sarra A. , Villaplana J. M. , Brogniez C. , Siani A. M. , Janouch M. , Weihs P. , Webb A. , Koskela T. , Kouremeti N. , Meloni D. , Buchard V. , Auriol F. , Ialongo I. , Staneck M. , Simic S. , Smedley A. , Kinne S.
Published: November 2009

Several validation studies of surface UV irradiance based on the Ozone Monitoring Instrument (OMI) satellite data have shown a high correlation with ground‐based measurements but a positive bias in many locations. The main part of the bias can be attributed to the boundary layer aerosol absorption that is not accounted for in the current satellite UV algorithms. To correct for this shortfall, a post‐correction procedure was applied, based on global climatological fields of aerosol absorption optical depth. These fields were obtained by using global aerosol optical depth and aerosol single scattering albedo data assembled by combining global aerosol model data and ground‐based aerosol measurements from AERONET. The resulting improvements in the satellite‐based surface UV irradiance were evaluated by comparing satellite and ground‐based spectral irradiances at various European UV monitoring sites. The results generally showed a significantly reduced bias by 5–20%, a lower variability, and an unchanged, high correlation coefficient.
Stress transfer in the Lazufre volcanic area, central Andes
Authors: Ruch J. , Manconi A. , Zeni G. , Solaro G. , Pepe A. , Shirzaei M. , Walter T. R. , Lanari R.
Published: November 2009

We generated a 13‐year InSAR time series from 1995–2008 to investigate the spatiotemporal characteristics of two neighboring volcano's deformations for the Lazufre volcanic area, central Andes. The data reveal two scales of uplift initiating during the observation time: (1) a large‐scale uplift started in 1997 that shows an increase of the mean uplift rate of up to 3.2 cm/yr, now affecting several eruptive centers situated in an area larger than 1800 km2 and (2) a small‐scale uplift located at Lastarria volcano, which is the only volcano to show strong fumarolic activity in decades, with most of the clear deformation apparently not observed before 2000. Both the large and small uplift signals can be explained by magmatic or hydrothermal sources located at about 13 km and 1 km deep, respectively. To test a possible relationship, we use numerical modeling and estimate that the depth inflating source increased the tensile stress close to the shallow source. We discuss how the deep inflating source may have disturbed the shallow one and triggered the observed deformation at Lastarria.
Cloud condensation nucleation activity of biomass burning aerosol
Authors: Petters Markus D. , Carrico Christian M. , Kreidenweis Sonia M. , Prenni Anthony J. , DeMott Paul J. , Collett Jeffrey L. , Moosmüller Hans
Published: November 2009

We examine the hygroscopic properties of particles freshly emitted from laboratory biomass burning experiments conducted during the second Fire Lab At Missoula Experiment (FLAME‐II). Values of the hygroscopicity parameter, kappa, were derived from both hygroscopic growth measurements and size‐resolved (30–300 nm in diameter) cloud condensation nuclei (CCN) measurements for smokes emitted by the open combustion of 24 biomass fuels from the United States and Asia. To analyze the complex cloud condensation nuclei response curves we propose a new inversion scheme that corrects for multiple charge effects without the necessity of prior assumptions about the chemical composition and mixing state of the particles. Kappa varied between 0.02 (weakly hygroscopic) and 0.8 (highly hygroscopic). For individual smokes, kappa was a function of particle size, with 250 nm particles being generally weakly hygroscopic and sub‐100 nm particles being more hygroscopic. At any given size the emissions were often externally mixed, showing more and less hygroscopic growth modes and bimodal CCN activation spectra. Comparisons between growth factor‐derived and CCN‐derived hygroscopicities were consistent when taking this heterogeneity into account. A conceptual model of biomass burning emissions suggests that most particles are CCN active at the point of emission and do not require conversion in the atmosphere to more hygroscopic compositions before they can participate in cloud formation and undergo wet deposition.
A critical perspective on 1‐D modeling of river processes: Gravel load and aggradation in lower Fraser River
Authors: Ferguson Rob , Church Michael
Published: November 2009

We investigate how well a width‐averaged morphodynamic model can simulate gravel transport and aggradation along a highly irregular 38‐km reach of lower Fraser River and discuss critical issues in this type of modeling. Bed load equations with plausible parameter values predict a gravel input consistent with direct measurements and a sediment budget. Simulations using spatially varying channel width, and forced by dominant discharge or a 20‐year hydrograph, match the observed downstream fining well. They reproduce major qualitative features of a 47 year sediment budget and match maximum local rates of aggradation and degradation to well within a factor of 2. Locations and rates of aggradation and degradation are influenced by channel constrictions. Runs for single years of unusually high or low peak discharge suggest that the main transfers of gravel occur in different parts of the reach in different years. One‐dimensional morphodynamic modeling of highly nonuniform rivers has serious conceptual limitations but may be a valuable complement to empirical approaches.
Thermal stability and vibrational spectroscopy of N–O shallow donor centers in silicon
Authors: Alt Hans Christian , Wagner Hans Edwin
Published: November 2009

N–O-related shallow donors in nitrogen-doped Czochralski silicon have been studied by infrared spectroscopy. Quasithermal equilibrium states were established by long-term thermal annealing in the temperature range from 600to1000°C. By quantitative analysis of the 1s→2p± far-infrared electronic transitions between 230 and 250cm−1, it is found that the formation and decay characteristics of these centers do not correspond to theoretical predictions. All complexes investigated show a monotonic decrease for annealing temperatures above 600°C. In particular, the dominant NO2 complex exhibits a pronounced biexponential decay behavior. Based on the characteristic thermal fingerprint of the individual shallow donor species, associated local vibrational modes in the midinfrared were investigated. Two bands at 1070 and 860cm−1 can be assigned to NO2, the center with the highest concentration variation in the relevant temperature range between 600 and 800°C. These frequencies match favorably with recent calculations for this complex in the symmetrical O–N–O configuration.
Flux pinning properties in BaMO3 (M=Zr,Sn) nanorod-introduced ErBa2Cu3Ox films
Authors: Awaji Satoshi , Namba Masafumi , Watnabe Kazuo , Ito Shun , Aoyagi Eiji , Kai Hideki , Mukaida Masashi , Kita Ryusuke
Published: November 2009

Flux pinning properties on the ErBa2Ca3O7 films with the nanoscaled and columnar-shaped BaMO3 (BMO,M=Zr,Sn) precipitates, i.e., nanorods, were investigated systematically based on the microstructure, critical current density Jc and irreversibility field Bi properties in high magnetic fields. We found that the in-field Jc and Bi increase monotonically with increasing the nanorod density until 3.5 wt % BZO and 6 wt % BSO additions, respectively, although the critical temperature Tc is reduced. According to the flux pinning analysis assuming of the linear summation, the BSO doped samples have the higher performance of the flux pinning than the BZO doped samples quantitatively even after the reduction in the Tc and size of the nanorods. It is considered that those differences originate from the effective pinning length of the nanorods and/or the condensation energy due to the difference of the carrier density.
A method for evaluating the ground state excitonic band gaps of strained InxGa1−xN/GaN quantum wells
Authors: Sharma T. K. , Towe E.
Published: November 2009

A simple method for calculating the ground state excitonic band gaps of strained wurtzite InxGa1−xN/GaN quantum wells (QWs) for the entire composition range is proposed. The modification of the electronic band structure due to strain becomes significant for high values of indium concentration. It is observed that confinement effects become less important for electrons (due to a shallower well) while the opposite is true for holes (because of a deeper well) in InxGa1−xN/GaN QW with large residual strain. Following the proposed method, one can obtain a satisfactory agreement between the theoretical predictions and experimental observations for ground state excitonic band gaps in InGaN/GaN QWs and InN/GaN ultrathin QWs.
Von Kármán vortex streets on the sphere
Authors: Chamoun George , Kanso Eva , Newton Paul K.
Published: November 2009

We consider streamline patterns associated with single and double von Kármán point vortex streets on the surface of a nonrotating sphere, with and without pole vortices. The full family of streamline patterns are identified and the topological bifurcations from one pattern to another are depicted as a function of latitude and pole strength. The process involves first finding appropriate vortex strengths so that the configuration forms a relative equilibrium, then calculating the angular rotation of the configuration about the center-of-vorticity vector. We move in a rotating frame of reference so that the configuration is fixed, identify the separatrices in the flowfield, and plot the global streamline patterns as a function of the pole strengths and latitudinal positions of the rings. We carry the procedure out for single and double von Kármán vortex streets, with and without pole vortices. The single von Kármán street configurations are comprised of n evenly spaced vortices on each of two rings that symmetrically straddle the equator and are skewed with respect to each other by half a wavelength, while the double von Kármán ring configurations are made up of four rings of n evenly spaced vortices symmetrically straddling the equator.
Asymptotic behavior for logarithmic diffusion
Authors: Salvarani F.
Published: November 2009

In this paper we prove, via the entropy dissipation method, that the solutions of the d-dimensional logarithmic diffusion equation, with nonhomogeneous Dirichlet boundary data, decay exponentially in time toward its own steady state. The result is valid not only in L1-norm (as customary when applying entropy dissipation methods) but also in any Lp-norm with p∊[1,+∞).
Optical spectroscopy and upconversion luminescence in Nd3+ doped Ga10Ge25S65 glass
Authors: Rai Vineet Kumar , de Araújo Cid B. , Ledemi Y. , Bureau B. , Poulain M. , Messaddeq Y.
Published: November 2009

Optical properties of a neodymium (Nd3+) doped glass having composition based on the (Ga2S3)–(GeS2) system are reported. Transition probabilities, radiative lifetimes, and branching ratios related to Nd3+ levels were determined. Frequency upconversion (UC) luminescence due to nonresonant excitation at 1064 nm was observed at ≈535, ≈600, and ≈670 nm. The dependence of the UC intensity on the laser intensity and on the Nd3+ concentration as well as the dynamics of the luminescence process were studied. The results indicate that two-photon absorption by isolated Nd3+ ions and energy transfer among pairs of Nd3+ ions contribute to the UC luminescence.
The photon analysis, delivery, and reduction system at the FERMI@Elettra free electron laser user facility
Authors: Zangrando M. , Abrami A. , Bacescu D. , Cudin I. , Fava C. , Frassetto F. , Galimberti A. , Godnig R. , Giuressi D. , Poletto L. , Rumiz L. , Sergo R. , Svetina C. , Cocco D.
Published: November 2009

The FERMI@Elettra free electron laser (FEL) user facility is currently under construction at the Sincrotrone Trieste laboratory in Trieste (Italy). It will cover the wavelength range from 100 to about 5 nm in the fundamental and 3 or 1 nm using the third harmonic. We report the layout of the photon beam diagnostics section, the radiation transport system to the experimental area, and the photon beam distribution system. Due to the peculiar characteristics of the emitted FEL radiation (high peak power, short pulse length, and statistical variation of the emitted intensity and distribution), the realization of the diagnostics system is particularly challenging. The end users are interested in parameters such as the radiation pulse intensity and spectral distribution, as well as in the possibility to attenuate the intensity. In order to accomplish these tasks, a photon analysis, delivery, and reduction system is now under development and construction and is presented here. This system will work on-line producing pulse-resolved information and will let users keep track of the photon beam parameters during the experiments.
Dynamical estimates of chaotic systems from Poincaré recurrences
Authors: Baptista M. S. , Maranhão Dariel M. , Sartorelli J. C.
Published: November 2009

We show a function that fits well the probability density of return times between two consecutive visits of a chaotic trajectory to finite size regions in phase space. It deviates from the exponential statistics by a small power-law term, a term that represents the deterministic manifestation of the dynamics. We also show how one can quickly and easily estimate the Kolmogorov–Sinai entropy and the short-term correlation function by realizing observations of high probable returns. Our analyses are performed numerically in the Hénon map and experimentally in a Chua’s circuit. Finally, we discuss how our approach can be used to treat the data coming from experimental complex systems and for technological applications.
Single-molecule spectroscopy of the temperature-induced collapse of unfolded proteins
Authors: Nettels Daniel , Müller-Späth Sonja , Küster Frank , Hofmann Hagen , Haenni Dominik , Rüegger Stefan , Reymond Luc , Hoffmann Armin , Kubelka Jan , Heinz Benjamin , Gast Klaus , Best Robert B. , Schuler Benjamin
Published: November 2009

We used single-molecule FRET in combination with other biophysical methods and molecular simulations to investigate the effect of temperature on the dimensions of unfolded proteins. With single-molecule FRET, this question can be addressed even under near-native conditions, where most molecules are folded, allowing us to probe a wide range of denaturant concentrations and temperatures. We find a compaction of the unfolded state of a small cold shock protein with increasing temperature in both the presence and the absence of denaturant, with good agreement between the results from single-molecule FRET and dynamic light scattering. Although dissociation of denaturant from the polypeptide chain with increasing temperature accounts for part of the compaction, the results indicate an important role for additional temperature-dependent interactions within the unfolded chain. The observation of a collapse of a similar extent in the extremely hydrophilic, intrinsically disordered protein prothymosin α suggests that the hydrophobic effect is not the sole source of the underlying interactions. Circular dichroism spectroscopy and replica exchange molecular dynamics simulations in explicit water show changes in secondary structure content with increasing temperature and suggest a contribution of intramolecular hydrogen bonding to unfolded state collapse.
Biochemical and structural characterization of CYP124: A methyl-branched lipid ω-hydroxylase from
Mycobacterium tuberculosis
Authors: Johnston Jonathan B. , Kells Petrea M. , Podust Larissa M. , Ortiz de Montellano Paul R.
Published: November 2009

Mycobacterium tuberculosis
(
Mtb
) produces a variety of methyl-branched lipids that serve important functions, including modulating the immune response during pathogenesis and contributing to a robust cell wall that is impermeable to many chemical agents. Here, we report characterization of
Mtb
CYP124 (
Rv2266
) that includes demonstration of preferential oxidation of methyl-branched lipids. Spectrophotometric titrations and analysis of reaction products indicate that CYP124 tightly binds and hydroxylates these substrates at the chemically disfavored ω-position. We also report X-ray crystal structures of the ligand-free and phytanic acid-bound protein at a resolution of 1.5 Å and 2.1 Å, respectively, which provide structural insights into a cytochrome P450 with predominant ω-hydroxylase activity. The structures of ligand-free and substrate-bound CYP124 reveal several differences induced by substrate binding, including reorganization of the I helix and closure of the active site by elements of the F, G, and D helices that bind the substrate and exclude solvent from the hydrophobic active site cavity. The observed regiospecific catalytic activity suggests roles of CYP124 in the physiological oxidation of relevant
Mtb
methyl-branched lipids. The enzymatic specificity and structures reported here provide a scaffold for the design and testing of specific inhibitors of CYP124.
Multiple conformations of full-length p53 detected with single-molecule fluorescence resonance energy transfer
Authors: Huang Fang , Rajagopalan Sridharan , Settanni Giovanni , Marsh Richard J. , Armoogum Daven A. , Nicolaou Nick , Bain Angus J. , Lerner Eitan , Haas Elisha , Ying Liming , Fersht Alan R.
Published: November 2009

The tumor suppressor p53 is a member of the emerging class of proteins that have both folded and intrinsically disordered domains, which are a challenge to structural biology. Its N-terminal domain (NTD) is linked to a folded core domain, which has a disordered link to the folded tetramerization domain, which is followed by a disordered C-terminal domain. The quaternary structure of human p53 has been solved by a combination of NMR spectroscopy, electron microscopy, and small-angle X-ray scattering (SAXS), and the NTD ensemble structure has been solved by NMR and SAXS. The murine p53 is reported to have a different quaternary structure, with the N and C termini interacting. Here, we used single-molecule FRET (SM-FRET) and ensemble FRET to investigate the conformational dynamics of the NTD of p53 in isolation and in the context of tetrameric full-length p53 (flp53). Our results showed that the isolated NTD was extended in solution with a strong preference for residues 66–86 forming a polyproline II conformation. The NTD associated weakly with the DNA binding domain of p53, but not the C termini. We detected multiple conformations in flp53 that were likely to result from the interactions of NTD with the DNA binding domain of each monomeric p53. Overall, the SM-FRET results, in addition to corroborating the previous ensemble findings, enabled the identification of the existence of multiple conformations of p53, which are often averaged and neglected in conventional ensemble techniques. Our study exemplifies the usefulness of SM-FRET in exploring the dynamic landscape of multimeric proteins that contain regions of unstructured domains.
Mapping polypeptide interactions of the SecA ATPase during translocation
Authors: Bauer Benedikt W. , Rapoport Tom A.
Published: November 2009

Many bacterial proteins, including most secretory proteins, are translocated across the plasma membrane by the interplay of the cytoplasmic SecA ATPase and a protein-conducting channel formed by the SecY complex. SecA catalyzes the sequential movement of polypeptide segments through the SecY channel. How SecA interacts with a broad range of polypeptide segments is unclear, but structural data raise the possibility that translocation substrates bind into a “clamp” of SecA. Here, we have used disulfide bridge cross-linking to test this hypothesis. To analyze polypeptide interactions of SecA during translocation, two cysteines were introduced into a translocation intermediate: one that cross-links to the SecY channel and the other one for cross-linking to a cysteine placed at various positions in SecA. Our results show that a translocating polypeptide is indeed captured inside SecA's clamp and moves in an extended conformation through the clamp into the SecY channel. These results define the polypeptide path during SecA-mediated protein translocation and suggest a mechanism by which ATP hydrolysis by SecA is used to move a polypeptide chain through the SecY channel.
Activation of innate and humoral immunity in the peripheral nervous system of ALS transgenic mice
Authors: Chiu Isaac M. , Phatnani Hemali , Kuligowski Michael , Tapia Juan C. , Carrasco Monica A. , Zhang Ming , Maniatis Tom , Carroll Michael C.
Published: November 2009

During injury to the nervous system, innate immune cells mediate phagocytosis of debris, cytokine production, and axon regeneration. In the neuro-degenerative disease amyotrophic lateral sclerosis (ALS), innate immune cells in the CNS are activated. However, the role of innate immunity in the peripheral nervous system (PNS) has not been well defined. In this study, we characterized robust activation of CD169/CD68/Iba1+ macrophages throughout the PNS in mutant SOD1
G93A
and SOD1
G37R
transgenic mouse models of ALS. Macrophage activation occurred pre-symptomatically, and expanded from focal arrays within nerve bundles to a tissue-wide distribution following symptom onset. We found a striking dichotomy for immune cells within the spinal cord and PNS. Flow cytometry and GFP bone marrow chimeras showed that spinal cord microglia were mainly tissue resident derived, dendritic-like cells, whereas in peripheral nerves, the majority of activated macrophages infiltrated from the circulation. Humoral antibodies and complement localized to PNS tissue in tandem with macrophage recruitment, and deficiency in complement C4 led to decreased macrophage activation. Therefore, cross-talk between nervous and immune systems occurs throughout the PNS during ALS disease progression. These data reveal a progressive innate and humoral immune response in peripheral nerves that is separate and distinct from spinal cord immune activation in ALS transgenic mice.