bluuebunny/crossref_metadata_2025 huggingface dataset:
On the jump in the frequency of acoustic oscillations in supersonic flows over rectangular cavity
Authors: Handa Taro , Masuda Mitsuharu
Published: February 2009

In this study, we analyze the jump in the frequency of acoustic oscillations that is observed in supersonic flows over a rectangular cavity. Frequency jumps have previously been observed in experiments when the length-to-depth ratio of a cavity is gradually varied. However, the reason for their occurrence has not been well understood. In order to explain the occurrence of the frequency jump, we improved the classical acoustic oscillation model by taking the acoustic reflections at the cavity walls into account. The results obtained using our analytical model are found to agree with experimental results with respect to both the frequency jump and the variation in frequency with the length-to-depth ratio. On the basis of the analytical model, a simple model is also proposed; in the simple model, it is assumed that the acoustic waves in the cavity are one-dimensional waves. This simple model can provide clearly the fundamental reason for the occurrence of the jump in the frequency of acoustic oscillations in the cavity.
Migration of a turbulent patch through a high-pressure turbine cascade
Authors: Wu Xiaohua , Li Lu Ting , St. Hilaire Matthew
Published: February 2009

We report two flow physics phenomena observed from direct numerical simulations on the migration and distortion of a turbulent patch inside a representative high-pressure turbine cascade. In the nonimpinging flow design, the upstream turbulent patch is on a trajectory offset from the blade leading edge, whereas in the impinging design the introduced turbulence impacts the stagnation. We found that in the nonimpinging flow, the original spanwisely continuous turbulent patch develops into long vortex tubes. They are quite persistent and are also nearly parallel to the blade pressure surface. In the impinging flow, slightly downstream of the leading edge, short vortex tubes form on the pressure side but not parallel to the local blade pressure surface, and they decay and fade away rapidly. Physical mechanisms responsible for these observed flow features are addressed. An additional simulation in which the turbulent patch migrates through a simple straight passage without the cascade is also reported.
How much exergy one can obtain from incident solar radiation?
Authors: Zamfirescu C. , Dincer I.
Published: February 2009

A thermodynamic model is proposed to study the exergetic content of incident solar radiation reaching on the Earth’s surface which can be used to produce work through a dually cascaded thermodynamic cycle. The “topping” cycle is an ad hoc engine created by nature that connects the outer shell of the terrestrial atmosphere (which is in equilibrium with the extraterrestrial solar radiation) to the collector of a solar heat engine operating on the Earth’s surface. The work produced by the topping cycle is dissipated in form of scattering, absorption, heat, movement of air masses (wind), etc. The “bottoming” cycle is a heat engine operating between the collector and surrounding temperatures, and delivers useful work. It is shown that the maximum work extractable from this system as exergy is obtained when both cycles operate reversibly. An expression for this maximum work, which represents the exergy of incident solar radiation on the Earth’s surface, is proposed. The application of the present model is illustrated and validated by calculating the exergy of solar radiation based on some measurements. The results obtained by the present model are compared to the ones obtained through other models available in the open literature.
Glass forming abilities of binary Cu100−xZrx (34, 35.5, and 38.2 at. %) metallic glasses: A LAMMPS study
Authors: Sha Z. D. , Wu R. Q. , Lu Y. H. , Shen L. , Yang M. , Cai Y. Q. , Feng Y. P. , Li Y.
Published: February 2009

Using large-scale atomic/molecular massively parallel simulator (LAMMPS), we have studied the liquid behaviors of Cu61.8Zr38.2, Cu64.5Zr35.5, and Cu66Zr34 amorphous alloys including their pair distribution functions, distributions of Voronoi clusters with different coordination numbers, and mean square displacements of Cu and Zr atoms. Compared to Cu61.8Zr38.2 and Cu66Zr34, we found high concentrations of distorted icosahedra with indices of ⟨0,2,8,2⟩ and ⟨0,4,4,4⟩, high numbers of Cu-centered Cu8Zr5 and Cu9Zr4 clusters, and reduced atomic diffusivity of Cu and Zr atoms in molten Cu64.5Zr35.5 alloy. These effects would benefit glass formation in Cu64.5Zr35.5 alloy. Meanwhile, from the viewpoints of local cluster structure, the majority of the glue atoms are Cu atoms in Cu64.5Zr35.5 amorphous alloy, which leads to denser packing and better glass forming ability.
Resputtering of zinc oxide films prepared by radical assisted sputtering
Authors: Song Qiuming , Wu Bingjun , Xie Bin , Huang Feng , Li Ming , Wang Haiqian , Jiang Yousong , Song Yizhou
Published: February 2009

Sputtering losses of zinc oxide films prepared by radical assisted sputtering were studied. It was found that the sputtering loss can be very severe in oxygenous sputtering processes of zinc oxide films. In general, resputtering caused by negative oxygen ions dominates the sputtering loss, while diffuse deposition plays a minor role. Resputtering is strongly correlated with the sputtering threshold energy of the deposited films and the concentration of O− in the sputtering zone. The balance between the oxygen concentration in the sputtering zone and the oxidation degree of the growing films depends on the sputtering rate. Our research suggests that a lower oxygen concentration in the sputtering zone and a higher oxidation degree of the growing films are favorable for reducing the resputtering losses. The sputtering loss mechanisms discussed in this work are also helpful for understanding the deposition processes of other magnetron sputtering systems.
Liouvillian quasinormal modes of Reissner–Nordstrom black holes
Authors: Couch W. E. , Holder C. L.
Published: February 2009

We identify a countable infinity of new exact, closed-form, quasinormal mode perturbations of Reissner–Nordstrom black holes. We obtain a finite number of these modes explicitly, together with the values of the quasinormal frequency and the black hole charge for which the modes are valid. These modes are contained in the Liouvillian perturbations obtained from the application of Kovacic’s well-known algorithm to Chandrasekhar’s radial equations. Our results suggest that the set of quasinormal modes found in this paper, plus the known algebraically special perturbations, are the only Liouvillian quasinormal modes of Reissner–Nordstrom.
A dilogarithmic integral arising in quantum field theory
Authors: Cvijović Djurdje
Published: February 2009

Recently, an interesting dilogarithmic integral arising in quantum field theory has been closed-form evaluated in terms of the Clausen function Cl2(θ) by Coffey [J. Math. Phys. 49, 093508 (2008)]. It represents the volume of an ideal tetrahedron in hyperbolic space and is involved in two intriguing equivalent conjectures of Borwein and Broadhurst. It is shown here by simple and direct arguments that this integral can be expressed by the triplet of the Clausen function values which are involved in one of the two above-mentioned conjectures.
Temperature-stable and high Q-factor TiO2 Bragg reflector resonator
Authors: Breeze Jonathan , Krupka Jerzy , Centeno Anthony , Alford Neil McN
Published: February 2009

The highest Q-factor resonators employ whispering gallery modes in single-crystal sapphire but have poor temperature stability. Rutile was the first dielectric material used to construct a microwave dielectric resonator. However, its very high temperature coefficient of permittivity made it unsuitable for practical applications. This paper reports a high Q-factor (50 000) and temperature-stable spherical Bragg reflector resonator based on polycrystalline rutile operating at 29.9 GHz. Temperature stability is achieved by adjusting the electric filling factor of a spherical shell so that in combination with its highly negative temperature coefficient of permittivity, the effect of thermal expansion is exactly cancelled out.
Contact resistance instability in pentacene thin film transistors induced by ambient gases
Authors: Wang S. D. , Minari T. , Miyadera T. , Tsukagoshi K. , Tang J. X.
Published: February 2009

Top-contact pentacene thin film transistors show the strong susceptibility of the contact resistance to ambient gases. Moisture and oxygen lead to the increase and decrease in the contact resistance, respectively. The phenomenon is interpreted by the local conductivity change in the contact region induced by the adsorption/desorption of ambient gases. The present works suggest that the current injection in the pentacene thin film transistors is strongly correlated with the charge transport property in the contact region, where the contact resistance is mainly controlled by the charge trap states.
Internal field engineering in CdZnO/MgZnO quantum well structures
Authors: Park Seoung-Hwan , Ahn Doyeol
Published: February 2009

Electronic and optical properties of CdZnO/MgZnO quantum well (QW) structures with the depolarization of an internal field are investigated by using the non-Markovian gain model. The Mg composition is selected to give zero internal field for a given Cd composition. The Mg content to give zero internal field is found to increase with increasing Cd content. The peak gain is improved with increasing Cd composition in a range of Cd<0.07 because a quasi-Fermi-level separation rapidly increases with the Cd composition. However, it begins to decrease when the Cd composition exceeds 0.07.
Nanophotonic energy up conversion using ZnO nanorod double-quantum-well structures
Authors: Yatsui T. , Sangu S. , Kobayashi K. , Kawazoe T. , Ohtsu M. , Yoo J. , Yi G.-C.
Published: February 2009

We report on near-field spectroscopy of ZnO/ZnMgO nanorod double-quantum-well structures (DQWs) for a nanometer-scale photonic device. We observed energy up conversion assisted by the absorption of phonons generated in the ZnO nanorod DQWs. Theoretical calculation of the coherent excitonic excitation of the population with incoherent phonon coupling agrees well with the obtained experimental power dependence of the up conversion efficiency. It should result in an increase in the efficiency of devices, such as photodetectors, solar cells, and so on.
Long-range-corrected hybrids including random phase approximation correlation
Authors: Janesko Benjamin G. , Henderson Thomas M. , Scuseria Gustavo E.
Published: February 2009

We recently demonstrated a connection between the random phase approximation (RPA) and coupled cluster theory [G. E. Scuseria et al., J. Chem. Phys. 129, 231101 (2008)]. Based on this result, we here propose and test a simple scheme for introducing long-range RPA correlation into density functional theory. Our method provides good thermochemical results and models van der Waals interactions accurately.
A conceptual framework for improving the P efficiency of organic farming without inputs of soluble P fertiliser
Authors: Conyers M. K. , Moody P. W.
Published: February 2009

The issues for P availability to agricultural plants are 3-fold: the solution concentration of P during early growth (intensity factor); the quantity of P in the soil ‘bank’ to meet plant and animal needs (capacity or quantity factor); and the rate at which P becomes available from mineral and organic sources (kinetic factor). These three needs can be met by: (1) applying traditional (manure, compost) and novel (biosuper) sources; (2) modifying or selecting plants for their root architecture, phytase activity, carboxylate excretion, and P translocation inefficiency; (3) encouraging rhizosphere conditions which favour phytase and carboxylase activity; (4) developing symbioses with mycorrhiza and Penicillium species; (5) developing exoenzyme products which release inositol P; (6) adjusting soil pH to 6–7 for maximum availability of native mineral P sources or lowering pH for maximum availability of reactive rock P; (7) developing rotations which maximise organic P cycling. These 7 broad groupings of strategies to improve P nutrition each operate by 1 or more of the 3 mechanisms of quantity, intensity, and kinetic factors. The possible application of these strategies to ‘organic’ farming is outlined in this review. However, a successful application of these strategies might also improve the P efficiency of conventional agriculture.
Site-directed nanoparticle labeling of cytochrome
c
Authors: Aubin-Tam Marie-Eve , Hwang Wonmuk , Hamad-Schifferli Kimberly
Published: February 2009

Although nanoparticle-protein conjugates have been synthesized for numerous applications, bioconjugation remains a challenge, often resulting in denaturation or loss of protein function. This is partly because the protein–nanoparticle interface is poorly understood, which impedes the use of nanoparticles in nanomedicine. Although the effects of nanoparticle ligand and material on protein structure have been explored, the choice of the labeling site on the protein has not yet been systematically studied. To address this issue, we label cytochrome
c
site-specifically with a negatively charged Au nanoparticle via a covalent thiol–Au bond. The attachment site is controlled by cysteine mutations of surface residues. The effect of labeling on protein structure is probed by circular dichroism. Protein unfolding is the most severe when the nanoparticle is attached to the N- and C-terminal foldon, the core motif of cytochrome
c
. Also, when the nanoparticle is attached in the vicinity of charged residues, the amount of structural damage is greater because of salt-dependent electrostatic interactions with charged ligand bis(
p
-sulfonatophenyl) phenylphosphine on the nanoparticle. Molecular dynamics simulations also elucidate local to global structural perturbation depending on labeling site. These results suggest that the labeling site must be considered as one of the main design criteria for nanoparticle–protein conjugates.
Site-specific C-functionalization of free-(NH) peptides and glycine derivatives via direct C–H bond functionalization
Authors: Zhao Liang , Baslé Oliver , Li Chao-Jun
Published: February 2009

A copper-catalyzed α-functionalization of glycine derivatives and short peptides with nucleophiles is described. The present method provides ways to introduce functionalities such as aryl, vinyl, alkynyl, or indolyl specifically to the terminal glycine moieties of small peptides, which are normally difficult in peptide modifications. Furthermore, on functionalization, the configurations of other stereocenters in the peptides could be maintained. Because the functionalized peptides could easily be deprotected and carried onto the next coupling process, our approach provides a useful tool for the peptide-based biological research.
Apoptosis-stimulating protein of p53 (ASPP2) heterozygous mice are tumor-prone and have attenuated cellular damage–response thresholds
Authors: Kampa Kerstin M. , Acoba Jared D. , Chen Dexi , Gay Joel , Lee Hunjoo , Beemer Kelly , Padiernos Emerson , Boonmark Nataya , Zhu Zhiyi , Fan Alice C. , Bailey Alexis S. , Fleming William H. , Corless Christopher , Felsher Dean W. , Naumovski Louie , Lopez Charles D.
Published: February 2009

The expression of ASPP2 (53BP2L), a proapoptotic member of a family of p53-binding proteins, is frequently suppressed in many human cancers. Accumulating evidence suggests that ASPP2 inhibits tumor growth; however, the mechanisms by which ASPP2 suppresses tumor formation remain to be clarified. To study this, we targeted the
ASPP2
allele in a mouse by replacing exons 10–17 with a
neoR
gene.
ASPP2
−/−
mice were not viable because of an early embryonic lethal event. Although
ASPP2
+/−
mice appeared developmentally normal, they displayed an increased incidence of a variety of spontaneous tumors as they aged. Moreover, γ-irradiated 6-week-old
ASPP2
+/−
mice developed an increased incidence of high-grade T cell lymphomas of thymic origin compared with
ASPP2
+/+
mice. Primary thymocytes derived from
ASPP2
+/−
mice exhibited an attenuated apoptotic response to γ-irradiation compared with
ASPP2
+/+
thymocytes. Additionally,
ASPP2
+/−
primary mouse embryonic fibroblasts demonstrated a defective G
0
/G
1
cell cycle checkpoint after γ-irradiation. Our results demonstrate that ASPP2 is a haploinsufficient tumor suppressor and, importantly, open new avenues for investigation into the mechanisms by which disruption of ASPP2 pathways could play a role in tumorigenesis and response to therapy.
Broad spectrum O-linked protein glycosylation in the human pathogen
Neisseria gonorrhoeae
Authors: Vik Åshild , Aas Finn Erik , Anonsen Jan Haug , Bilsborough Shaun , Schneider Andrea , Egge-Jacobsen Wolfgang , Koomey Michael
Published: February 2009

Protein glycosylation is an important element of biologic systems because of its significant effects on protein properties and functions. Although prominent within all domains of life, O-linked glycosylation systems modifying serine and threonine residues within bacteria and eukaryotes differ substantially in target protein selectivity. In particular, well-characterized bacterial systems have been invariably dedicated to modification of individual proteins or related subsets thereof. Here we characterize a general O-linked glycosylation system that targets structurally and functionally diverse groups of membrane-associated proteins in the Gram-negative bacterium
Neisseria gonorrhoeae
, the etiologic agent of the human disease gonorrhea. The 11 glycoproteins identified here are implicated in activities as varied as protein folding, disulfide bond formation, and solute uptake, as well as both aerobic and anaerobic respiration. Along with their common trafficking within the periplasmic compartment, the protein substrates share quasi-related domains bearing signatures of low complexity that were demonstrated to encompass sites of glycan occupancy. Thus, as in eukaryotes, the broad scope of this system is dictated by the relaxed specificity of the glycan transferase as well as the bulk properties and context of the protein-targeting signal rather than by a strict amino acid consensus sequence. Together, these findings reveal previously unrecognized commonalities linking O-linked protein glycosylation in distantly related life forms.
Impact of sideways and bottom-up control factors on bacterial community succession over a tidal cycle
Authors: Chauhan Ashvini , Cherrier Jennifer , Williams Henry N.
Published: February 2009

In aquatic systems, bacterial community succession is a function of top-down and bottom-up factors, but little information exists on “sideways” controls, such as bacterial predation by
Bdellovibrio
-like organisms (BLOs), which likely impacts nutrient cycling within the microbial loop and eventual export to higher trophic groups. Here we report transient response of estuarine microbiota and BLO spp. to tidal-associated dissolved organic matter supply in a river-dominated estuary, Apalachicola Bay, Florida. Both dissolved organic carbon and dissolved organic nitrogen concentrations oscillated over the course of the tidal cycle with relatively higher concentrations observed at low tide. Concurrent with the shift in dissolved organic matter (DOM) supply at low tide, a synchronous increase in numbers of bacteria and predatorial BLOs were observed. PCR-restriction fragment length polymorphism of small subunit rDNA, cloning, and sequence analyses revealed distinct shifts such that, at low tide, significantly higher phylotype abundances were observed from γ-
Proteobacteria
, δ-
Proteobacteria
,
Bacteroidetes
, and high G+C Gram-positive bacteria. Conversely, diversity of α-
Proteobacteria
, β-
Proteobacteria
, and
Chlamydiales-Verrucomicrobia
group increased at high tides. To identify metabolically active BLO guilds, tidal microcosms were spiked with six
13
C-labeled bacteria as potential prey and studied using an adaptation of stable isotope probing. At low tide, representative of higher DOM and increased prey but lower salinity, BLO community also shifted such that mesohaline clusters I and VI were more active; with an increased salinity at high tide, halotolerant clusters III, V, and X were predominant. Eventually,
13
C label was identified from higher micropredators, indicating that trophic interactions within the estuarine microbial food web are potentially far more complex than previously thought.
Transcription factor function and promoter architecture govern the evolution of bacterial regulons
Authors: Perez J. Christian , Groisman Eduardo A.
Published: February 2009

Evolutionary changes in ancestral regulatory circuits can bring about phenotypic differences between related organisms. Studies of regulatory circuits in eukaryotes suggest that these modifications result primarily from changes in
cis
-regulatory elements (as opposed to alterations in the transcription factors that act upon these sequences). It is presently unclear how the evolution of gene regulatory circuits has proceeded in bacteria, given the rampant effects of horizontal gene transfer, which has significantly altered the composition of bacterial regulons. We now demonstrate that the evolution of the regulons governed by the regulatory protein PhoP in the related human pathogens
Salmonella enterica
and
Yersinia pestis
has entailed functional changes in the PhoP protein as well as in the architecture of PhoP-dependent promoters. These changes have resulted in orthologous PhoP proteins that differ both in their ability to promote transcription and in their role as virulence regulators. We posit that these changes allow bacterial transcription factors to incorporate newly acquired genes into ancestral regulatory circuits and yet retain control of the core members of a regulon.
Genomic identification in the historical case of the Nicholas II royal family
Authors: Rogaev Evgeny I. , Grigorenko Anastasia P. , Moliaka Yuri K. , Faskhutdinova Gulnaz , Goltsov Andrey , Lahti Arlene , Hildebrandt Curtis , Kittler Ellen L. W. , Morozova Irina
Published: February 2009

Accurate unambiguous identification of ancient or historical specimens can potentially be achieved by DNA analysis. The controversy surrounding the fate of the last Russian Emperor, Nicholas II, and his family has persisted, in part, because the bodies of 2 children, Prince Alexei and 1 of his sisters, have not been found. A grave discovered in 1991 contained remains putatively identified as those of the Russian Royal family. However, not all family members were represented. Here, we report the results of genomic analyses of new specimens, the human remains of 2 burned skeletons exhumed from a grave discovered in July 2007, and the results of a comprehensive genomic analysis of remains from the 1991 discovery. Additionally, ≈117 years old archival blood specimens from Nicholas II were obtained and genotyped, which provided critical material for the specific determination of individual identities and kinship identifications. Results of genotypic analyses of damaged historical specimens were evaluated alongside samples from descendants of both paternal and maternal lineages of the European Royal families, and the results conclusively demonstrate that the recently found remains belong to children of Nicholas II: Prince Alexei and his sister. The results of our studies provide unequivocal evidence that the remains of Nicholas II and his entire family, including all 5 children, have been identified. We demonstrate that convergent analysis of complete mitochondrial genome sequences combined with nuclear DNA profiles is an efficient and conclusive method for individual and kinship identification of specimens obtained from old historic relics.
Identification and structural analysis of type I collagen sites in complex with fibronectin fragments
Authors: Erat Michèle C. , Slatter David A. , Lowe Edward D. , Millard Christopher J. , Farndale Richard W. , Campbell Iain D. , Vakonakis Ioannis
Published: February 2009

Collagen and fibronectin are major components of vertebrate extracellular matrices. Their association and distribution control the development and properties of diverse tissues, but thus far no structural information has been available for the complex formed. Here, we report binding of a peptide, derived from the α
1
chain of type I collagen, to the gelatin-binding domain of human fibronectin and present the crystal structure of this peptide in complex with the
8–9
FnI domain pair. Both gelatin-binding domain subfragments,
6
FnI
1–2
FnII
7
FnI and
8–9
FnI, bind the same specific sequence on D-period 4 of collagen I α
1
, adjacent to the MMP-1 cleavage site.
8–9
FnI also binds the equivalent sequence of the α
2
chain. The collagen peptide adopts an antiparallel β-strand conformation, similar to structures of proteins from pathogenic bacteria bound to FnI domains. Analysis of the type I collagen sequence suggests multiple putative fibronectin-binding sites compatible with our structural model. We demonstrate, by kinetic unfolding experiments, that the triple-helical collagen state is destabilized by
8–9
FnI. This finding suggests a role for fibronectin in collagen proteolysis and tissue remodeling.
Geochemical evidence for combustion of hydrocarbons during the K-T impact event
Authors: Belcher Claire M. , Finch Paul , Collinson Margaret E. , Scott Andrew C. , Grassineau Nathalie V.
Published: February 2009

It has been proposed that extensive wildfires occurred after the Cretaceous–Tertiary (K-T) impact event. An abundance of soot and pyrosynthetic polycyclic aromatic hydrocarbons (pPAHs) in marine K-T boundary impact rocks (BIRs) have been considered support for this hypothesis. However, nonmarine K-T BIRs, from across North America, contain only rare occurrences of charcoal yet abundant noncharred plant remains. pPAHs and soot can be formed from a variety of sources, including partial combustion of vegetation and hydrocarbons whereby modern pPAH signatures are traceable to their source. We present results from multiple nonmarine K-T boundary sites from North America and reveal that the K-T BIRs have a pPAH signature consistent with the combustion of hydrocarbons and not living plant biomass, providing further evidence against K-T wildfires and compelling evidence that a significant volume of hydrocarbons was combusted during the K-T impact event.
Schwann cells expressing dismutase active mutant SOD1 unexpectedly slow disease progression in ALS mice
Authors: Lobsiger Christian S. , Boillee Severine , McAlonis-Downes Melissa , Khan Amir M. , Feltri M. Laura , Yamanaka Koji , Cleveland Don W.
Published: February 2009

Neurodegeneration in an inherited form of ALS is non-cell-autonomous, with ALS-causing mutant SOD1 damage developed within multiple cell types. Selective inactivation within motor neurons of an ubiquitously expressed mutant
SOD1
gene has demonstrated that mutant damage within motor neurons is a determinant of disease initiation, whereas mutant synthesis within neighboring astrocytes or microglia accelerates disease progression. We now report the surprising finding that diminished synthesis (by 70%) within Schwann cells of a fully dismutase active ALS-linked mutant (SOD1
G37R
) significantly accelerates disease progression, accompanied by reduction of insulin-like growth factor 1 (IGF-1) in nerves. Coupled with shorter disease duration in mouse models caused by dismutase inactive versus dismutase active SOD1 mutants, our findings implicate an oxidative cascade during disease progression that is triggered within axon ensheathing Schwann cells and that can be ameliorated by elevated dismutase activity. Thus, therapeutic down-regulation of dismutase active mutant SOD1 in familial forms of ALS should be targeted away from Schwann cells.
A unified model of protein dynamics
Authors: Frauenfelder Hans , Chen Guo , Berendzen Joel , Fenimore Paul W. , Jansson Helén , McMahon Benjamin H. , Stroe Izabela R. , Swenson Jan , Young Robert D.
Published: February 2009

Protein functions require conformational motions. We show here that the dominant conformational motions are slaved by the hydration shell and the bulk solvent. The protein contributes the structure necessary for function. We formulate a model that is based on experiments, insights from the physics of glass-forming liquids, and the concepts of a hierarchically organized energy landscape. To explore the effect of external fluctuations on protein dynamics, we measure the fluctuations in the bulk solvent and the hydration shell with broadband dielectric spectroscopy and compare them with internal fluctuations measured with the Mössbauer effect and neutron scattering. The result is clear. Large-scale protein motions are slaved to the fluctuations in the bulk solvent. They are controlled by the solvent viscosity, and are absent in a solid environment. Internal protein motions are slaved to the beta fluctuations of the hydration shell, are controlled by hydration, and are absent in a dehydrated protein. The model quantitatively predicts the rapid increase of the mean-square displacement above ≈200 K, shows that the external beta fluctuations determine the temperature- and time-dependence of the passage of carbon monoxide through myoglobin, and explains the nonexponential time dependence of the protein relaxation after photodissociation.
Identifying compartment-specific non-HLA targets after renal transplantation by integrating transcriptome and “antibodyome” measures
Authors: Li Li , Wadia Persis , Chen Rong , Kambham Neeraja , Naesens Maarten , Sigdel Tara K. , Miklos David B. , Sarwal Minnie M. , Butte Atul J.
Published: February 2009

We have conducted an integrative genomics analysis of serological responses to non-HLA targets after renal transplantation, with the aim of identifying the tissue specificity and types of immunogenic non-HLA antigenic targets after transplantation. Posttransplant antibody responses were measured by paired comparative analysis of pretransplant and posttransplant serum samples from 18 pediatric renal transplant recipients, measured against 5,056 unique protein targets on the ProtoArray platform. The specificity of antibody responses were measured against gene expression levels specific to the kidney, and 2 other randomly selected organs (heart and pancreas), by integrated genomics, employing the mapping of transcription and ProtoArray platform measures, using AILUN. The likelihood of posttransplant non-HLA targets being recognized preferentially in any of 7 microdissected kidney compartments was also examined. In addition to HLA targets, non-HLA immune responses, including anti-MICA antibodies, were detected against kidney compartment-specific antigens, with highest posttransplant recognition for renal pelvis and cortex specific antigens. The compartment specificity of selected antibodies was confirmed by IHC. In conclusion, this study provides an immunogenic and anatomic roadmap of the most likely non-HLA antigens that can generate serological responses after renal transplantation. Correlation of the most significant non-HLA antibody responses with transplant health and dysfunction are currently underway.
Ctip2/Bcl11b controls ameloblast formation during mammalian odontogenesis
Authors: Golonzhka Olga , Metzger Daniel , Bornert Jean-Marc , Bay Brian K. , Gross Michael K. , Kioussi Chrissa , Leid Mark
Published: February 2009

The transcription factor Ctip2/Bcl11b plays essential roles in developmental processes of the immune and central nervous systems and skin. Here we show that Ctip2 also plays a key role in tooth development. Ctip2 is highly expressed in the ectodermal components of the developing tooth, including inner and outer enamel epithelia, stellate reticulum, stratum intermedium, and the ameloblast cell lineage. In
Ctip2
−/−
mice, tooth morphogenesis appeared to proceed normally through the cap stage but developed multiple defects at the bell stage. Mutant incisors and molars were reduced in size and exhibited hypoplasticity of the stellate reticulum. An ameloblast-like cell population developed ectopically on the lingual aspect of mutant lower incisors, and the morphology, polarization, and adhesion properties of ameloblasts on the labial side of these teeth were severely disrupted. Perturbations of gene expression were also observed in the mandible of
Ctip2
−/−
mice: expression of the ameloblast markers
amelogenin
,
ameloblastin
, and
enamelin
was down-regulated, as was expression of
Msx2
and
epiprofin
, transcription factors implicated in the tooth development and ameloblast differentiation. These results suggest that Ctip2 functions as a critical regulator of epithelial cell fate and differentiation during tooth morphogenesis.
Ecological modulation of plant defense via phytochrome control of jasmonate sensitivity
Authors: Moreno Javier E. , Tao Yi , Chory Joanne , Ballaré Carlos L.
Published: February 2009

For plants, the tradeoff between resource investment in defense and increased growth to out-compete neighbors creates an allocation dilemma. How plants resolve this dilemma, at the mechanistic level, is unclear. We found thatArabidopsisplants produced an attenuated defense phenotype under conditions of crowding and when exposed to far-red (FR) radiation, a light signal that plants use to detect the proximity of neighbors via the photoreceptor phytochrome. This phenotype was detectable through standard bioassays that measured the growth ofSpodoptera frugiperdacaterpillars. Two possible explanations for the effect of FR are: (i) a simple by-product of the diversion of resources to competition, and (ii) a specific effect of phytochrome on defense signaling. The first possibility was ruled out by the fact that the auxin-deficientsav3mutant, which fails to induce growth responses to FR, still responded to FR with an attenuated defense phenotype. In support of the second hypothesis, we found that phytochrome inactivation by FR caused a strong reduction of plant sensitivity to jasmonates, which are key regulators of plant immunity. The effects of FR on jasmonate sensitivity were restricted to certain elements of the pathway. Supporting the idea that the FR effects on jasmonate signaling are functionally significant, we found that FR failed to increase tissue quality injar1, a mutant impaired in jasmonate response. We conclude that the plant modulates its investment in defense as a function of the perceived risk of competition, and that this modulation is effected by phytochrome via selective desensitization to jasmonates.
Epithelial ovarian cancer: Does the time interval between primary surgery and postoperative chemotherapy have any prognostic importance?
Authors: LARSEN ERLING , BLAAKÆR JAN
Published: February 2009

Worldwide, much effort is used every day to perform optimal surgery in the treatment of epithelial ovarian cancer. Treatment of ovarian cancer is a combination of surgery with optimal debulking followed by chemotherapy. However, the optimal timing of postoperative chemotherapy for ovarian cancer remains poorly defined. The literature is made up of seven studies performed in different ways and which have included varying prognostic factors. The general supposition is that the time interval (TI) does not have a prognostic influence but experimental studies have shown that it does affect the prognosis of the cancer. This commentary focuses on the importance of the TI between surgery and postoperative chemotherapy in this horrible disease.
Negative energy waves and MHD stability of rotating plasmas
Authors: Ilgisonis V.I. , Khalzov I.V. , Smolyakov A.I.
Published: February 2009

Eigenmode analysis of ideal magnetohydrodynamic (MHD) systems with flows is performed. It is shown that the energy of stable oscillatory modes (waves) can be both positive and negative. Negative energy waves always correspond to non-symmetric modes which are nonuniform along the direction of the flow. Coupling of negative and positive energy waves is shown to be a universal mechanism of non-symmetric MHD instabilities in flowing media. To study the stability of non-symmetric modes, a new variational approach is developed based on Lyapunov theory. This approach provides a sufficient and (under some assumptions) necessary stability condition. Specific examples are given to illustrate the developed approach.
Tauberian conditions for geometric maximal operators
Authors: Hagelstein Paul , Stokolos Alexander
Published: February 2009

Let

B

\mathcal {B}

be a collection of measurable sets in

R

n

\mathbb {R}^{n}

. The associated geometric maximal operator

M

B

M_{\mathcal {B}}

is defined on

L

1

(

R

n

)

L^{1}(\mathbb {R}^n)

by
<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" alttext="upper M Subscript script upper B Baseline f left-parenthesis x right-parenthesis equals sup Underscript x element-of upper R element-of script upper B Endscripts StartFraction 1 Over StartAbsoluteValue upper R EndAbsoluteValue EndFraction integral Underscript upper R Endscripts StartAbsoluteValue f EndAbsoluteValue">

M

B

f
(
x
)
=

sup

x
∈
R
∈

B

1

|

R

|

∫

R

|

f

|

M_{\mathcal {B}}f(x) = \sup _{x \in R \in \mathcal {B}}\frac {1}{|R|}\int _{R}|f|

. If

α
>
0

\alpha > 0

,

M

B

M_\mathcal {B}

is said to satisfy a Tauberian condition with respect to

α
\alpha

if there exists a finite constant

C
C

such that for all measurable sets

E
⊂

R

n

E \subset \mathbb {R}^n

the inequality
<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" alttext="StartAbsoluteValue StartSet x colon upper M Subscript script upper B Baseline chi Subscript upper E Baseline left-parenthesis x right-parenthesis greater-than alpha EndSet EndAbsoluteValue less-than-or-equal-to upper C StartAbsoluteValue upper E EndAbsoluteValue">

|

{
x
:

M

B

χ

E

(
x
)
>
α
}

|

≤
C

|

E

|

|\{x : M_{\mathcal {B}} \chi _{E}(x) > \alpha \}| \leq C|E|

holds. It is shown that if

B

\mathcal {B}

is a homothecy invariant collection of convex sets in

R

n

\mathbb {R}^{n}

and the associated maximal operator

M

B

M_{\mathcal {B}}

satisfies a Tauberian condition with respect to some

0
>
α
>
1

0 > \alpha > 1

, then

M

B

M_\mathcal {B}

must satisfy a Tauberian condition with respect to

γ
\gamma

for all

γ
>
0

\gamma > 0

and moreover

M

B

M_{\mathcal {B}}

is bounded on

L

p

(

R

n

)

L^{p}(\mathbb {R}^{n})

for sufficiently large

p
p

. As a corollary of these results it is shown that any density basis that is a homothecy invariant collection of convex sets in

R

n

\mathbb {R}^{n}

must differentiate

L

p

(

R

n

)

L^{p}(\mathbb {R}^{n})

for sufficiently large 𝑝.
Stationary discs glued to a Levi non-degenerate hypersurface
Authors: Blanc-Centi Léa
Published: February 2009

We obtain an explicit parametrization of stationary discs glued to some Levi non-degenerate hypersurfaces. These discs form a family which is invariant under the action of biholomorphisms. We use this parametrization to construct a local circular representation of these hypersurfaces. As a corollary, we get the uniqueness of biholomorphisms with given 1-jet at some convenient point.
The 𝐾-theory of toric varieties
Authors: Cortiñas G. , Haesemeyer C. , Walker Mark , Weibel C.
Published: February 2009

Recent advances in computational techniques for

K
K

-theory allow us to describe the

K
K

-theory of toric varieties in terms of the

K
K

-theory of fields and simple cohomological data.
On the analyticity of the semigroup generated by the Stokes operator with Neumann-type boundary conditions on Lipschitz subdomains of Riemannian manifolds
Authors: Mitrea Marius , Monniaux Sylvie
Published: February 2009

We study the analyticity of the semigroup generated by the Stokes operator equipped with Neumann-type boundary conditions onLpL^pspaces in Lipschitz domains. Our strategy is to regularize this operator by considering the Hodge Laplacian, which has the additional property that it commutes with the Leray projection.
Multibump solutions and critical groups
Authors: Arioli Gianni , Szulkin Andrzej , Zou Wenming
Published: February 2009

We consider the Newtonian system

−

q
¨

+
B
(
t
)
q
=

W
q

(
q
,
t
)

-\ddot q+B(t)q = W_q(q,t)

with

B
B

,

W
W

periodic in

t
t

,

B
B

positive definite, and show that for each isolated homoclinic solution

q
0

q_0

having a nontrivial critical group (in the sense of Morse theory), multibump solutions (with

2
≤
k
≤
∞

2\le k\le \infty

bumps) can be constructed by gluing translates of

q
0

q_0

. Further we show that the collection of multibumps is semiconjugate to the Bernoulli shift. Next we consider the Schrödinger equation

−
Δ
u
+
V
(
x
)
u
=
g
(
x
,
u
)

-\Delta u+V(x)u = g(x,u)

in

R

N

\mathbb {R}^N

, where

V
V

,

g
g

are periodic in

x
1

,
…
,

x
N

x_1,\ldots ,x_N

,

σ
(
−
Δ
+
V
)
⊂
(
0
,
∞
)

\sigma (-\Delta +V)\subset (0,\infty )

, and we show that similar results hold in this case as well. In particular, if

g
(
x
,
u
)
=

|

u

|

2
∗

−
2

u

g(x,u)=|u|^{2^*-2}u

,

N
≥
4

N\ge 4

and

V
V

changes sign, then there exists a solution minimizing the associated functional on the Nehari manifold. This solution gives rise to multibumps if it is isolated.
Boundedness of projection operators and Cesàro means in weighted 𝐿^{𝑝} space on the unit sphere
Authors: Dai Feng , Xu Yuan
Published: February 2009

For the weight function

∏

i
=
1

d
+
1

|

x
i

|

2

κ
i

\prod _{i=1}^{d+1}|x_i|^{2\kappa _i}

on the unit sphere, sharp local estimates of the orthogonal projection operators are obtained and used to prove the convergence of the Cesàro

(
C
,
δ
)

(C,\delta )

means in the weighted

L
p

L^p

space for

δ
\delta

above the critical index. Similar results are also proved for corresponding weight functions on the unit ball and on the simplex.
PSIBLAST_PairwiseStatSig: reordering PSI-BLAST hits using pairwise statistical significance
Authors: Agrawal Ankit , Huang Xiaoqiu
Published: February 2009

Summary: We present an add-on to BLAST and PSI-BLAST programs to reorder their hits using pairwise statistical significance. Using position-specific substitution matrices to estimate pairwise statistical significance has been recently shown to give promising results in terms of retrieval accuracy, which motivates its use to refine PSI-BLAST results, since PSI-BLAST also constructs a position-specific substitution matrix for the query sequence during the search. The obvious advantage of the approach is more accurate estimates of statistical significance because of pairwise statistical significance, along with the advantage of BLAST/PSI-BLAST in terms of speed.

Availability: The implementation as a C library is freely available at www.cs.iastate.edu/∼ankitag/PSIBLAST_PairwiseStatSig.html

Contact:  ankitag@cs.iastate.edu

Supplementary information:  Supplementary data are available at Bionformatics online.
A robust peak detection method for RNA structure inference by high-throughput contact mapping
Authors: Kim Jinkyu , Yu Seunghak , Shim Byonghyo , Kim Hanjoo , Min Hyeyoung , Chung Eui-Young , Das Rhiju , Yoon Sungroh
Published: February 2009

Motivation: For high-throughput prediction of the helical arrangements of large RNA molecules, an innovative method termed multiplexed hydroxyl radical (·OH) cleavage analysis (MOHCA) has been proposed. A key step in this promising technique is to detect peaks accurately from noisy radioactivity profiles. Since manual peak finding is laborious and prone to error, an automated peak detection method to improve the accuracy and throughput of MOHCA is required. Existing methods were not applicable to MOHCA due to their high false positive rates.

Results: We developed a two-step computational method that can detect peaks from MOHCA profiles in a robust manner. The first step exploits an ensemble of linear and non-linear signal processing techniques to find true peak candidates. In the second step, a binary classifier trained with the characteristics of true and false peaks is used to eliminate false peaks out of the peak candidates. We tested the proposed approach with 2002 MOHCA cleavage profiles and obtained the median recall, precision and F-measure values of 0.917, 0.750 and 0.830, respectively. Compared with the alternatives considered, the proposed method was able to handle false peaks substantially better, thus resulting in 51.0–71.8% higher median values of precision and F-measure.

Availability: The software and supplementary data are available at http://dna.korea.ac.kr/pub/mohca

Contact:  sryoon@korea.ac.kr
mkESA: enhanced suffix array construction tool
Authors: Homann Robert , Fleer David , Giegerich Robert , Rehmsmeier Marc
Published: February 2009

Summary: We introduce the tool mkESA, an open source program for constructing enhanced suffix arrays (ESAs), striving for low memory consumption, yet high practical speed. mkESA is a user-friendly program written in portable C99, based on a parallelized version of the Deep-Shallow suffix array construction algorithm, which is known for its high speed and small memory usage. The tool handles large FASTA files with multiple sequences, and computes suffix arrays and various additional tables, such as the LCP table (longest common prefix) or the inverse suffix array, from given sequence data.

Availability: The source code of mkESA is freely available under the terms of the GNU General Public License (GPL) version 2 at http://bibiserv.techfak.uni-bielefeld.de/mkesa/.

Contact:  rhomann@techfak.uni-bielefeld.de
WSsas: a web service for the annotation of functional residues through structural homologues
Authors: Talavera David , Laskowski Roman A. , Thornton Janet M.
Published: February 2009

Motivation: Annotation tools help scientists to traverse the gap between characterized and uncharacterized proteins. Tools for the prediction of protein function include those which predict the function of entire proteins or complexes, those annotating functional domains and those which predict specific residues within the domain. We have developed WSsas, a web service focused on the annotation of essential functional residues. WSsas uses similarity searches and pairwise alignments to transfer functional information about binding, catalytic and protein–protein interaction residues from solved structures to query sequences. In addition, WSsas can supply information about the relevant functional atoms. The web service definition (WSDL) file and a Perl client are freely available at http://www.ebi.ac.uk/thornton-srv/databases/WSsas/.

Contact:  talavera@ebi.ac.uk
The vertical separation of fish in the aft end of a demersal trawl
Authors: Krag Ludvig Ahm , Holst René , Madsen Niels
Published: February 2009

Krag, L. A., Holst, R., and Madsen, N. 2009. The vertical separation of fish in the aft end of a demersal trawl. – ICES Journal of Marine Science, 66: 772–777. Two multi-compartment separator frames were used to study the vertical separation of some commercially important fish species in the aft end of a trawl, with the aim of separating cod (Gadus morhua) from other species. A non-linear multinomial model with random effects was used to analyse the data and to compare the performance of the two frames. The vertical distribution of cod in the aft end of the trawl was close to uniform, whereas haddock (Melanogrammus aeglefinus), whiting (Merlangius merlangus), plaice (Pleuronectes platessa), and lemon sole (Microstomus kitt) showed more uneven distributions. The use of guiding bars in the separator frame significantly (p < 0.05) increased the catch of cod, plaice, and lemon sole in the upper compartment. The vertical separation of cod was density-dependent; high densities of fish resulted in a more uniform distribution of cod. The species separations found differ from those reported from the studies of species separation in the region of the trawl mouth.