bluuebunny/crossref_metadata_2025 huggingface dataset:
Electric field strength analysis of 216 and 270 kHz broadcast signals recorded during 9 years
Authors: Biagi P. F. , Castellana L. , Maggipinto T. , Ermini A. , Perna G. , Capozzi V.
Published: August 2006

The electric field strength analysis of Czech Republic (CZE) (270 kHz) and Monte Carlo (MCO) (216 kHz) broadcast signals, collected with a 10 min sampling frequency by a receiver located in central Italy from 1996 to 2004, is presented. The distance from transmitter to receiver ranges from 515 km (MCO) to 818 km (CZE). The daytime data and the nighttime data were extracted and then in the daytime data the data collected in winter (21 December to 21 March) were separated from the data collected in summer (21 June to 21 September). Under the hypothesis that the simple addition of the ground wave and sky wave contributions holds, at first, the analysis was focused on the comparison between the experimental and theoretical values of these waves. The theoretical values were calculated by the ground wave (GRWAVE) algorithm and the wave hop theory, respectively. Ratios between the experimental and theoretical values ranging from a few tenths of decibels to some decibels were obtained. Then the analysis of the sunspots' influence on the sky wave propagation mode was performed, and the electric field strength of the two radio signals reveals a reduction of some decibels in sunspot maximum years with respect to the values during the sunspot minimum years. In addition, an influence of the sunspots also was recognized for the ground wave propagation mode.
A method for vibrational assessment of cortical bone
Authors: Song Yan , Gunaratne Gemunu H.
Published: August 2006

Large bones from many anatomical locations of the human skeleton consist of an outer shaft (cortex) surrounding a highly porous internal region (trabecular bone) whose structure is reminiscent of a disordered cubic network. Age related degradation of cortical and trabecular bone takes different forms. Trabecular bone weakens primarily by loss of connectivity of the porous network, and recent studies have shown that vibrational response can be used to obtain reliable estimates for loss of its strength. In contrast, cortical bone degrades via the accumulation of long fractures and changes in the level of mineralization of the bone tissue. In this paper, we model cortical bone by an initially solid specimen with uniform density to which long fractures are introduced; we find that, as in the case of trabecular bone, vibrational assessment provides more reliable estimates of residual strength in cortical bone than is possible using measurements of density or porosity.
Chaotic dynamics in a class of three dimensional Glass networks
Authors: Li Qingdu , Yang Xiao-Song
Published: August 2006

In this paper, we study chaotic dynamics of a class of three-dimensional Glass networks with different decay constants, illustrate how the horseshoe is generated, and present a rigorous computer-assisted verification of chaoticity by virtue of interval analysis and topological horseshoe theory.
Degeneracy of time series models: The best model is not always the correct model
Authors: Judd Kevin , Nakamura Tomomichi
Published: August 2006

There are a number of good techniques for finding, in some sense, the best model of a deterministic system given a time series of observations. We examine a problem called model degeneracy, which has the consequence that even when a perfect model of a system exists, one does not find it using the best techniques currently available. The problem is illustrated using global polynomial models and the theory of Gröbner bases.
Direct observation of a “devil’s staircase” in wave-particle interaction
Authors: Doveil Fabrice , Macor Alessandro , Elskens Yves
Published: August 2006

We report the experimental observation of a “devil’s staircase” in a time-dependent system considered as a paradigm for the transition to large-scale chaos in the universality class of Hamiltonian systems. A test electron beam is used to observe its non-self-consistent interaction with externally excited wave(s) in a traveling wave tube (TWT). A trochoidal energy analyzer records the beam energy distribution at the output of the interaction line. An arbitrary waveform generator is used to launch a prescribed spectrum of waves along the slow wave structure (a 4m long helix) of the TWT. The resonant velocity domain associated to a single wave is observed, as well as the transition to large-scale chaos when the resonant domains of two waves and their secondary resonances overlap. This transition exhibits a “devil’s staircase” behavior for increasing excitation amplitude, due to the nonlinear forcing by the second wave on the pendulum-like motion of a charged particle in one electrostatic wave.
Standing solutions of one-dimensional Boiti-Leon-Pempinelli-Spire system localized in space and periodical in time
Authors: Bai Cheng-Lin , Zhao Hong
Published: August 2006

By means of a special variable separation approach, a common formula with two arbitrary functions has been obtained for suitable physical quantity of (1+1)-dimensional model such as Boiti-Leon-Pempinelli-Spire system. Based on the derived formula, some significant types of solitons such as compacton, peakon, and loop solutions localized in space and periodical in time are simultaneously constructed from the (1+1)-dimensional soliton system by entrancing appropriate piecewise smooth functions and multivalued functions.
Tracking unstable steady states and periodic orbits of oscillatory and chaotic electrochemical systems using delayed feedback control
Authors: Kiss István Z. , Kazsu Zoltán , Gáspár Vilmos
Published: August 2006

Experimental results are presented on successful application of delayed-feedback control algorithms for tracking unstable steady states and periodic orbits of electrochemical dissolution systems. Time-delay autosynchronization and delay optimization with a descent gradient method were applied for stationary states and periodic orbits, respectively. These tracking algorithms are utilized in constructing experimental bifurcation diagrams of the studied electrochemical systems in which Hopf, saddle-node, saddle-loop, and period-doubling bifurcations take place.
Mechanical milling-induced room-temperature ferromagnetic phase in MnO2–ZnO system
Authors: Tanaka Katsuhisa , Fukui Kazuya , Murai Shunsuke , Fujita Koji
Published: August 2006

Mechanical milling of a mixture of powders composed of 2mol% MnO2 and 98mol% ZnO leads to a ferromagnetic phase with Curie temperature above 300K. The magnetic field dependence of magnetization manifests a residual magnetization of 2.84×10−4emu∕g and a coercive force of 76Oe at 300K; the residual magnetization of the as-milled sample is larger than those of heat-treated samples. It is speculated that the ferromagnetic behavior is imposed to Zn-doped manganese oxide phases formed on the surface of MnO2 particles via the mechanical milling.
Density inhomogeneity in ferroelectric thin films
Authors: Cao Jiang-Li , Solbach Axel , Klemradt Uwe , Weirich Thomas , Mayer Joachim , Böttger Ulrich , Schorn Peter J. , Waser Rainer
Published: August 2006

Structural investigations of Pb(Zr,Ti)O3 (PZT) ferroelectric thin films derived by chemical solution deposition on Pt∕TiOx electrode stacks were performed using grazing incidence x-ray specular reflectivity of synchrotron radiation and transmission electron microscopy. A density inhomogeneity, i.e., a sublayer structure, in the PZT thin films was observed; the upper PZT sublayer had a lower density and the lower sublayer had a higher density. The influence of the density inhomogeneity, as a possible extrinsic contribution to size effects in ferroelectric thin films, was discussed.
Application of carbon nanotubes to human breath dynamics characterization
Authors: Hou Zhongyu , Cai Bingchu , Xu Dong
Published: August 2006

The carbon nanotube composite material and its fabrication techniques are introduced to construct a chip-based electrode system for human breath dynamics characterization. The application of 10V dc bias can generate electric field high enough to effectively collect the charged particles in the human breath. Without using breath collecting tubes, the field tests in the open air exhibit that the system is technologically promising for long-time and noncontact human breath dynamics monitoring, due to its high stability, sensitivity, and safety operation performance with power consumption in the order of 10−5W.
Direct shoot regeneration from epicotyl explants of grasspea (Lathyrus sativus)
Authors: Barik Durga Prasad , Mohapatra Umaballava , Chand Pradeep Kumar
Published: August 2006

A reproducible procedure is described for adventitious shoot organogenesis in epicotyl segments resulting in prolific plant regeneration of a grain legume grasspea (Lathyrus sativus L.). Among seedling explant types examined, epicotyl segments were most responsive. The highest percentage of direct shoot regeneration was elicited on Murashige–Skoog (MS) medium augmented with 4.0 mg L–1 6-benzyladenine (BA) + 2.0 mg L–1 α-naphthaleneacetic acid (NAA). Compared with four other genotypes examined, IC-120487 showed the highest shoot regeneration frequency (approximately 80%) with maximum shoot numbers (averaging eight shoots per explant) and longest average shoot length (approximately 4 cm). Rhizogenesis was induced in ~78% of the regenerated shoots in half-strength MS medium containing 0.5 mg L–1 indole-3-acetic acid (IAA). Plantlets were acclimated in vermi-compost and 75% of those transferred to soil survived and set viable seeds.
Identification of candidate phosphorus stress induced genes in Phaseolus vulgaris through clustering analysis across several plant species
Authors: Graham Michelle A. , Ramírez Mario , Valdés-López Oswaldo , Lara Miguel , Tesfaye Mesfin , Vance Carroll P. , Hernandez Georgina
Published: August 2006

Common bean (Phaseolus vulgaris L.) is the world’s most important grain legume for direct human consumption. However, the soils in which common bean predominate are frequently limited by the availability of phosphorus (P). Improving bean yield and quality requires an understanding of the genes controlling P acquisition and use, ultimately utilising these genes for crop improvement. Here we report an in silico approach for the identification of genes involved in adaptation of P. vulgaris and other legumes to P-deficiency. Some 22 groups of genes from four legume species and Arabidopsis thaliana, encoding diverse functions, were identified as statistically over-represented in EST contigs from P-stressed tissues. By combining bioinformatics analysis with available micro / macroarray technologies and clustering results across five species, we identified 52 P. vulgaris candidate genes belonging to 19 categories as induced by P-stress response. Transport-related, stress (defence and regulation) signal transduction genes are abundantly represented. Manipulating these genes through traditional breeding methodologies and / or biotechnology approaches may allow us to improve crop P-nutrition.
Stimulation of phosphatidylinositol kinase type I-mediated phosphatidylinositol (4,5)-bisphosphate synthesis by AP-2μ–cargo complexes
Authors: Krauss Michael , Kukhtina Viktoria , Pechstein Arndt , Haucke Volker
Published: August 2006

Phosphatidylinositol (4,5)-bisphosphate [PI(4,5)P
2
] is an important factor for a variety of cellular functions ranging from cell signaling to actin cytoskeletal dynamics and endocytic membrane traffic. Here, we have identified the clathrin adaptor complex AP-2 as a regulator of phosphatidylinositol 4-phosphate 5-kinase (PIPK)-mediated PI(4,5)P
2
synthesis. AP-2 directly interacts with the kinase core domain of type I PIPK isozymes via its μ2-subunit
in vitro
and in native protein extracts. Endocytic cargo protein binding to μ2 leads to a potent stimulation of PIPK activity. These data thus identify a positive feedback loop consisting of endocytic cargo proteins, AP-2μ, and PIPK type I which may provide a specific pool of PI(4,5)P
2
dedicated to clathrin/AP-2-dependent receptor internalization.
Nanostructure of fibrillin-1 reveals compact conformation of EGF arrays and mechanism for extensibility
Authors: Baldock Clair , Siegler Veronique , Bax Daniel V. , Cain Stuart A. , Mellody Kieran T. , Marson Andrew , Haston J. Louise , Berry Richard , Wang Ming-Chuan , Grossmann J. Günter , Roessle Manfred , Kielty Cay M. , Wess Tim J.
Published: August 2006

Fibrillin-1 is a 330-kDa multidomain extracellular matrix protein that polymerizes to form 57-nm periodic microfibrils, which are essential for all tissue elasticity. Fibrillin-1 is a member of the calcium-binding EGF repeat family and has served as a prototype for structural analyses. Nevertheless, both the detailed structure of fibrillin-1 and its organization within microfibrils are poorly understood because of the complexity of the molecule and the resistance of EGF arrays to crystallization. Here, we have used small-angle x-ray scattering and light scattering to analyze the solution structure of human fibrillin-1 and to produce
ab initio
structures of overlapping fragments covering 90% of the molecule. Rather than exhibiting a uniform rod shape as current models predict, the scattering data revealed a nonlinear conformation of calcium-binding EGF arrays in solution. This finding has major implications for the structures of the many other EGF-containing extracellular matrix and membrane proteins. The scattering data also highlighted a very compact, globular region of the fibrillin-1 molecule, which contains the integrin and heparan sulfate-binding sites. This finding was confirmed by calculating a 3D reconstruction of this region using electron microscopy and single-particle image analysis. Together, these data have enabled the generation of an improved model for microfibril organization and a previously undescribed mechanism for microfibril extensibility.
Crystal structure and mechanistic determinants of SARS coronavirus nonstructural protein 15 define an endoribonuclease family
Authors: Ricagno Stefano , Egloff Marie-Pierre , Ulferts Rachel , Coutard Bruno , Nurizzo Didier , Campanacci Valérie , Cambillau Christian , Ziebuhr John , Canard Bruno
Published: August 2006

The ≈30-kb coronavirus (+)RNA genome is replicated and transcribed by a membrane-bound replicase complex made up of 16 viral nonstructural proteins (nsp) with multiple enzymatic activities. The complex includes an RNA endonuclease, NendoU, that is conserved among nidoviruses but no other RNA virus, making it a genetic marker of this virus order. NendoU (nsp15) is a Mn
2+
-dependent, uridylate-specific enzyme, which leaves 2′–3′-cyclic phosphates 5′ to the cleaved bond. Neither biochemical nor sequence homology criteria allow a classification of nsp15 into existing endonuclease families. Here, we report the crystal structure of the severe acute respiratory syndrome coronavirus nsp15 at 2.6-Å resolution. Nsp15 exhibits a unique fold and assembles into a toric hexamer with six potentially active, peripheric catalytic sites. The structure and the spatial arrangement of the catalytic residues into an RNase A-like active site define a separate endonuclease family, endoU, and represent another spectacular example of convergent evolution toward an enzymatic function that is critically involved in the coronavirus replication cycle.
Nitric oxide activation of guanylyl cyclase in cells revisited
Authors: Roy Brijesh , Garthwaite John
Published: August 2006

Nitric oxide (NO) elicits physiological effects in cells largely by activating guanylyl cyclase (GC)-coupled receptors, leading to cGMP accumulation. Like other receptor-coupled effector mechanisms, NO stimulation of GC activity was previously considered to be a graded, concentration-dependent response, with deactivation following swiftly once the agonist disappeared. Recently, a new and unconventional mechanism has been proposed from experiments on purified protein [Cary, S. P. L., Winger, J. A. & Marletta, M. A. (2005)Proc. Natl. Acad. Sci. USA102, 13064–13069]. It was concluded that GCin vivowill display a dual regulation by NO: a long-lasting tonic activity (10–20% of maximum) due to persistent occupation by NO of the heme binding site and phasic activity due to engagement of another unidentified, lower affinity site. The hypothesis was first tested by monitoring GC activity in rat platelets maintainedin vitroand exposed to calibrated NO transients. The kinetics was as expected for a single binding site for NO (EC50= 10 nM), with activation and deactivation of enzyme activity conforming to the predictions of a simple receptor model. No tonic GC activity attributable to long-term NO binding was detected after exposure to the full range of active NO concentrations (peaking at 2–500 nM). Comparable results were obtained by using neural cells isolated from the cerebellum. After exposure to high NO concentrations, persistent GC activity could be recorded, but this activity was caused artifactually by secondary NO sources being formed in the medium. The new scheme for regulation of GC activity by NO is of doubtful relevance to cells.
Manipulation of
Arabidopsis
fatty acid amide hydrolase expression modifies plant growth and sensitivity to
N
-acylethanolamines
Authors: Wang Yuh-Shuh , Shrestha Rhidaya , Kilaru Aruna , Wiant William , Venables Barney J. , Chapman Kent D. , Blancaflor Elison B.
Published: August 2006

In vertebrates, the endocannabinoid signaling pathway is an important lipid regulatory pathway that modulates a variety of physiological and behavioral processes.
N
-Acylethanolamines (NAEs) comprise a group of fatty acid derivatives that function within this pathway, and their signaling activity is terminated by an enzyme called fatty acid amide hydrolase (FAAH), which hydrolyzes NAEs to ethanolamine and their corresponding free fatty acids. Bioinformatic approaches led to the identification of plant homologues of FAAH that are capable of hydrolyzing NAEs
in vitro
. To better understand the role of NAEs in plants, we identified T-DNA knockouts to
Arabidopsis
FAAH (
AtFAAH
; At5g64440) and generated plants overexpressing
AtFAAH
. Here we show that seeds of
AtFAAH
knockouts had elevated levels of endogenous NAEs, and seedling growth was hypersensitive to exogenously applied NAE. On the other hand, seeds and seedlings of
AtFAAH
overexpressors had lower endogenous NAE content, and seedlings were less sensitive to exogenous NAE. Moreover,
AtFAAH
overexpressors displayed enhanced seedling growth and increased cell size.
AtFAAH
expression and FAAH catalytic activity increased during seed germination and seedling growth, consistent with the timing of NAE depletion during seedling establishment. Collectively, our results show that AtFAAH is one, but not the only, modulator of endogenous NAE levels in plants, and that NAE depletion likely participates in the regulation of plant growth.
Clonogenic multipotent stem cells in human adipose tissue differentiate into functional smooth muscle cells
Authors: Rodríguez Larissa V. , Alfonso Zeni , Zhang Rong , Leung Joanne , Wu Benjamin , Ignarro Louis J.
Published: August 2006

Smooth muscle is a major component of human tissues and is essential for the normal function of a multitude of organs including the intestine, urinary tract and the vascular system. The use of stem cells for cell-based tissue engineering and regeneration strategies represents a promising alternative for smooth muscle repair. For such strategies to succeed, a reliable source of smooth muscle precursor cells must be identified. Adipose tissue provides an abundant source of multipotent cells. In this study, the capacity of processed lipoaspirate (PLA) and adipose-derived stem cells to differentiate into phenotypic and functional smooth muscle cells was evaluated. To induce differentiation, PLA cells were cultured in smooth muscle differentiation medium. Smooth muscle differentiation of PLA cells induced genetic expression of all smooth muscle markers and further confirmed by increased protein expression of smooth muscle cell-specific α actin (ASMA), calponin, caldesmon, SM22, myosin heavy chain (MHC), and smoothelin. Clonal studies of adipose derived multipotent cells demonstrated differentiation of these cells into smooth muscle cells in addition to trilineage differentiation capacity. Importantly, smooth muscle-differentiated cells, but not their precursors, exhibit the functional ability to contract and relax in direct response to pharmacologic agents. In conclusion, adipose-derived cells have the potential to differentiate into functional smooth muscle cells and, thus, adipose tissue can be a useful source of cells for treatment of injured tissues where smooth muscle plays an important role.
Unique players in the BMP pathway: Small C-terminal domain phosphatases dephosphorylate Smad1 to attenuate BMP signaling
Authors: Knockaert Marie , Sapkota Gopal , Alarcón Claudio , Massagué Joan , Brivanlou Ali H.
Published: August 2006

Smad transcription factors are key signal transducers for the TGF-β/bone morphogenetic protein (BMP) family of cytokines and morphogens. C-terminal serine phosphorylation by TGF-β and BMP membrane receptors drives Smads into the nucleus as transcriptional regulators. Dephosphorylation and recycling of activated Smads is an integral part of this process, which is critical for agonist sensing by the cell. However, the nuclear phosphatases involved have remained unknown. Here we provide functional, biochemical, and embryological evidence identifying the SCP (small C-terminal domain phosphatase) family of nuclear phosphatases as mediators of Smad1 dephosphorylation in the BMP signaling pathway in vertebrates.
Xenopus
SCP2/Os4 inhibits BMP activity in the presumptive ectoderm and leads to neuralization. In
Xenopus
embryos, SCP2/Os4 and human SCP1, 2, and 3 cause selective dephosphorylation of Smad1 compared with Smad2, inhibiting BMP- and Smad1-dependent transcription and leading to the induction of the secondary dorsal axis. In human cells, RNAi-mediated depletion of SCP1 and SCP2 increases the extent and duration of Smad1 phosphorylation in response to BMP, the transcriptional action of Smad1, and the strength of endogenous BMP gene responses. The present identification of the SCP family as Smad C-terminal phosphatases sheds light on the events that attenuate Smad signaling and reveals unexpected links to the essential phosphatases that control RNA polymerase II in eukaryotes.
A genomewide screen for components of the RNAi pathway in
Drosophila
cultured cells
Authors: Dorner Silke , Lum Lawrence , Kim Michelle , Paro Renato , Beachy Philip A. , Green Rachel
Published: August 2006

Posttranscriptional silencing by RNAi is initiated by dsRNAs that are processed into siRNAs that ultimately target homologous mRNAs for degradation. We used luciferase reporter constructs and a cultured cell-based assay to perform a genomewide screen for components of the RNAi pathway in
Drosophila melanogaster
. The screen identified seven genes that affect the RNAi response, five with previously described function (
AGO2
,
Tis11
,
Hsc70-3
,
Hsc70-4
, and
hdc
) and two annotated genes (
CG17265
and
CG10883
).
A critical role for TPP1 and TIN2 interaction in high-order telomeric complex assembly
Authors: O'Connor Matthew S. , Safari Amin , Xin Huawei , Liu Dan , Songyang Zhou
Published: August 2006

Mammalian telomeric proteins function through dynamic interactions with each other and telomere DNA. We previously reported the formation of a high-molecular-mass telomeric complex (the mammalian telosome) that contains the six core proteins TRF1, TRF2, RAP1, TIN2, POT1, and TPP1 (formerly named PTOP/PIP1/TINT1) and mediates telomere end-capping and length control. In this report, we sought to elucidate the mechanism of six-protein complex (or shelterin) formation and the function of this complex. Through reconstitution experiments, we demonstrate here that TIN2 and TPP1 are key components in mediating the six-protein complex assembly. We demonstrate that not only TIN2 but also TPP1 are required to bridge the TRF1 and TRF2 subcomplexes. Specifically, TPP1 helps to stabilize the TRF1–TIN2–TRF2 interaction and promote six-protein complex formation. Consistent with this model, overexpression of TPP1 enhanced TIN2–TRF2 association. Conversely, knocking down TPP1 reduced the ability of endogenous TRF1 to associate with the TRF2 complex. Our results suggest that coordinated interactions among TPP1, TIN2, TRF1, and TRF2 may ensure robust assembly of the telosome, telomere targeting of its subunits, and, ultimately, regulated telomere maintenance.
Importance of dosage standardization for interpreting transcriptomal signature profiles: Evidence from studies of xenoestrogens
Authors: Shioda Toshi , Chesnes Jessica , Coser Kathryn R. , Zou Lihua , Hur Jingyung , Dean Kathleen L. , Sonnenschein Carlos , Soto Ana M. , Isselbacher Kurt J.
Published: August 2006

To obtain insights into similarities and differences in the biological actions of related drugs or toxic agents, their transcriptomal signature profiles (TSPs) have been examined in a large number of studies. However, many such reports did not provide proper justification for the dosage criteria of each agent. Using a well characterized cell culture model of estrogen-dependent proliferation of MCF7 human breast cancer cells, we demonstrate how different approaches to dosage standardization exert critical influences on TSPs, leading to different and even conflicting conclusions. Using quantitative cellular response (QCR)-based dosage criteria, TSPs were determined by Affymetrix microarray when cells were proliferating at comparable rates in the presence of various estrogens. We observed that TSPs of the xenoestrogens (e.g., genistein or bisphenol A) were clearly different from the TSP of 17β-estradiol; namely, the former strongly enhanced expression of genes involved in mitochondrial oxidative phosphorylation, whereas the latter showed minimal effects. In contrast, TSPs for genistein and 17β-estradiol were indistinguishable by using the marker gene expression-based dosage criteria, conditions in which there was comparable expression of the mRNA transcripts for the estrogen-inducible
WISP2
gene. Our findings indicate that determination and interpretation of TSPs in pharmacogenomic and toxicogenomic studies that examine the transcriptomal actions of related agents by microarray require a clear rationale for the dosage standardization method to be used. We suggest that future studies involving TSP analyses use quantitative and objective dosage standardization methods, such as those with quantitative cellular response or marker gene expression-based dosage criteria.
Evaluation of psychosomatic stress in children by measuring salivary chromogranin A
Authors: Lee Tsubasa , Shimizu Toshiaki , Iijima Megumi , Obinata Kaoru , Yamashiro Yuichiro , Nagasawa Shingo
Published: August 2006

Aim: To investigate the usefulness of salivary chromogranin A (CgA) and cortisol as stress markers, and the effects of distraction on the suppression of stress in children. Methods: We examined salivary CgA and cortisol responses before and after venipuncture in hospitalized children with and without distraction using a kaleidoscope. Results: Salivary CgA levels immediately after venipuncture were significantly higher than those immediately before it, and at 60 min after venipuncture they were significantly lower than those immediately after it. However, salivary cortisol showed no significant differences at any of the three time points. In contrast, distracted by the kaleidoscope, there were no significant differences in salivary CgA and cortisol levels at all three time points.

Conclusion: In children, salivary CgA level is a useful marker of stress. As an index of the effect of distraction, the measurement of salivary CgA is useful.
Protection from lethal septic peritonitis by neutralizing the biological function of interleukin 27
Authors: Wirtz Stefan , Tubbe Ingrid , Galle Peter R. , Schild Hans J. , Birkenbach Mark , Blumberg Richard S. , Neurath Markus F.
Published: August 2006

The immune response to bacterial infections must be tightly controlled to guarantee pathogen elimination while preventing tissue damage by uncontrolled inflammation. Here, we demonstrate a key role of interleukin (IL)-27 in regulating this critical balance. IL-27 was rapidly induced during murine experimental peritonitis induced by cecal ligation and puncture (CLP). Furthermore, mice deficient for the EBI3 subunit of IL-27 were resistant to CLP-induced septic peritonitis as compared with wild-type controls, and this effect could be suppressed by injection of recombinant single-chain IL-27. EBI3−/− mice displayed significantly enhanced neutrophil migration and oxidative burst capacity during CLP, resulting in enhanced bacterial clearance and local control of infection. Subsequent studies demonstrated that IL-27 directly suppresses endotoxin-induced production of reactive oxygen intermediates by isolated primary granulocytes and macrophages. Finally, in vivo blockade of IL-27 function using a newly designed soluble IL-27 receptor fusion protein led to significantly increased survival after CLP as compared with control-treated mice. Collectively, these data identify IL-27 as a key negative regulator of innate immune cell function in septic peritonitis. Furthermore, in vivo blockade of IL-27 is a novel potential therapeutic target for treatment of sepsis.
Flow of dense granular material: towards simple constitutive laws
Authors: Pouliquen O , Cassar C , Jop P , Forterre Y , Nicolas M
Published: August 2006

Recent experiments and numerical simulations of dry granular flows suggest that a simple
rheological description in terms of a friction coefficient varying both with shear
rate and pressure through a dimensionless inertial number may be sufficient to
capture the major properties of granular flows. In this paper we first present the
empirical constitutive laws and their interpretation using dimensional analysis,
before analysing the prediction for different flow configurations. The successes and
limits of the approach are discussed based on comparison with recent studies.
Intrinsic Harnack estimates for nonnegative local solutions of degenerate parabolic equations
Authors: DiBenedetto Emmanuele , Gianazza Ugo , Vespri Vincenzo
Published: August 2006

We establish the intrinsic Harnack inequality for nonnegative solutions of the parabolic

p
p

-Laplacian equation by a proof that uses neither the comparison principle nor explicit self-similar solutions. The significance is that the proof applies to quasilinear

p
p

-Laplacian-type equations, thereby solving a long-standing problem in the theory of degenerate parabolic equations.
Evaluation and comparison of gene clustering methods in microarray analysis
Authors: Thalamuthu Anbupalam , Mukhopadhyay Indranil , Zheng Xiaojing , Tseng George C.
Published: August 2006

Motivation: Microarray technology has been widely applied in biological and clinical studies for simultaneous monitoring of gene expression in thousands of genes. Gene clustering analysis is found useful for discovering groups of correlated genes potentially co-regulated or associated to the disease or conditions under investigation. Many clustering methods including hierarchical clustering, K-means, PAM, SOM, mixture model-based clustering and tight clustering have been widely used in the literature. Yet no comprehensive comparative study has been performed to evaluate the effectiveness of these methods.

Results: In this paper, six gene clustering methods are evaluated by simulated data from a hierarchical log-normal model with various degrees of perturbation as well as four real datasets. A weighted Rand index is proposed for measuring similarity of two clustering results with possible scattered genes (i.e. a set of noise genes not being clustered). Performance of the methods in the real data is assessed by a predictive accuracy analysis through verified gene annotations. Our results show that tight clustering and model-based clustering consistently outperform other clustering methods both in simulated and real data while hierarchical clustering and SOM perform among the worst. Our analysis provides deep insight to the complicated gene clustering problem of expression profile and serves as a practical guideline for routine microarray cluster analysis.

Contact: ctseng@pitt.edu

Supplementary information: Supplementary data are available at Bioinformatics online.
PYCHEM: a multivariate analysis package for python
Authors: Jarvis Roger M. , Broadhurst David , Johnson Helen , O'Boyle Noel M. , Goodacre Royston
Published: August 2006

Summary: We have implemented a multivariate statistical analysis toolbox, with an optional standalone graphical user interface (GUI), using the Python scripting language. This is a free and open source project that addresses the need for a multivariate analysis toolbox in Python. Although the functionality provided does not cover the full range of multivariate tools that are available, it has a broad complement of methods that are widely used in the biological sciences. In contrast to tools like MATLAB, PyChem 2.0.0 is easily accessible and free, allows for rapid extension using a range of Python modules and is part of the growing amount of complementary and interoperable scientific software in Python based upon SciPy. One of the attractions of PyChem is that it is an open source project and so there is an opportunity, through collaboration, to increase the scope of the software and to continually evolve a user-friendly platform that has applicability across a wide range of analytical and post-genomic disciplines.

Availability:

Contact: Roger.Jarvis@manchester.ac.uk or admin@pychem.org.uk

Supplementary information: Further information is available from the project home page at whilst details of data generation are available at
BREASTS ARE BACK! COLETTE'S CRITIQUE OF FLAPPER FASHION
Authors: Freadman Anne
Published: August 2006

This paper focuses on Colette's writing for the periodical press, particularly her writing on fashion, and sets out to discuss it in terms of its capacity to effect the high purposes of satire. Its method of reading is contextualizing, rather than immanent — it brings it into relation with a number of issues on which it bears: the history of fashion, the history of the body, generational change, the visual determinants of the fashions of the early twentieth century. Although humour is prominent, Colette is not content merely to make jokes. Ancient satire, which derives from the rhetoric of praise and blame, is the source of literary and art criticism, and Colette borrows both its modes and its vocation to elevate fashion writing to the level of cultural critique. Moralistic, it teaches something about social mores by making fun of them. Hence, Colette makes us laugh at the fact that fashion affects not only clothes, but bodies; style fashions the body and hence the self.
Loss of Trigeminal Sensitivity Reduces Olfactory Function
Authors: Husner Alexander , Frasnelli Johannes , Welge‐Lüssen Antje , Reiss Gilfe , Zahnert Thomas , Hummel Thomas
Published: August 2006

The trigeminal and olfactory nerves share overlapping innervation areas in the nasal cavity and seem to work in an interactive way. Loss of olfactory function leads to a decreased trigeminal sensitivity, as shown in anosmic subjects. To report the impact of disturbed trigeminal sensitivity on the olfactory function, we present a patient with unilateral loss of trigeminal function resulting from a meningeoma. Thresholds to a selective olfactory stimulus were elevated by a factor of 64 on the affected side. Recordings of event‐related potentials in response to olfactory stimuli showed a significantly reduced response on the affected side. This report indicates that loss of trigeminal function may affect the sense of smell.
Intraparotid Sentinel Lymph Node Biopsy for Head and Neck Melanoma
Authors: Loree Thom R. , Tomljanovich Paul I. , Cheney Richard T. , Hicks Wesley L. , Rigual Nestor R.
Published: August 2006

Objective: The objective of this retrospective clinical review was to assess the safety and accuracy of intraparotid sentinel node biopsy in patients with melanoma.

Setting. This study was conducted at a tertiary referral center.

Patients: Twenty‐eight patients with cutaneous melanoma of the head and neck undergoing sentinel lymph node (SLN) biopsy in which the radionuclide localized to the parotid gland on preoperative lymphoscintigraphy were studied.

Methods: All patients underwent wide local excision of the tumor and intraparotid sentinel node biopsy using intraoperative gamma probe localization.

Results: There were 25 men and 3 women ranging in age from 34 to 81 years. The primary site was on the auricle in 14 patients: temple, 4; forehead, 5; cheek, 3; and on the neck in 2 patients, respectively. The mean Breslow thickness was 2.3 mm (range, 0.9–7.0 mm). In 27 of 28 patients, an intraparotid SLN was identified. In one patient, final pathology did not reveal lymphoid tissue despite a high count in the parotid tissue excised. Median number of SLN per patient was two. Six patients had microscopic metastases in the SLN. In two of these patients, additional microscopic lymph node metastases were found in the neck after subsequent formal lymphadenectomy. The pathologic staging for the group (n = 14) was: stage 1B, 4; 2A, 4; stage 2B, 3; and stage 3B, 3 patients, respectively. All patients are alive and without evidence of disease (mean follow up, 31 months). There were no surgical complications, specifically no patient experienced temporary or permanent facial paralysis.

Conclusion: Intraparotid SLN biopsy for staging cutaneous head and neck melanoma is a reliable, accurate, and safe procedure.
Presence of Human Papillomavirus DNA in Tonsillectomy Specimens
Authors: Sisk Jamie , Schweinfurth John M. , Wang Xiaohong T. , Chong Kong
Published: August 2006

Objectives: The objectives of this prospective case–control study were to study the prevalence of human papillomavirus (HPV) in tonsillectomy specimens from pediatric patients without recurrent respiratory papillomatosis (RRP), and to study methods of HPV detection.

Methods: Fifty pediatric patients without known RRP undergoing tonsillectomy for hypertrophy or recurrent tonsillitis were enrolled in the study. After tonsillectomy, a 20‐mg section was subjected to DNA extraction, and DNA content and purity were confirmed with spectrophotometry. Polymerase chain reaction (PCR) was performed using consensus primer pools PGMY 09/11 targeted at the L1 region. Amplification products were detected and analyzed with standard agarose gel electrophoresis. Positive samples were then subjected to reverse line blot assay to determine virus genotype. Laryngeal papilloma specimens of 15 patients obtained during routine debulking procedures were also analyzed and served as positive controls.

Results: Of 50 tonsil samples tested, two were positive for HPV DNA after PCR and gel electrophoresis. One of these samples was confirmed with typing and tested positive for HPV 11. All 15 papilloma specimens were positive for DNA of HPV types 6 and/or 11.

Conclusions: In the current study, the prevalence of HPV DNA in tonsillar tissue of patients without RRP is 2%, whereas the incidence of this disease is 2 to 4 cases per 100,000 (0.004%). These findings are significantly different (P = .005 within a 95% confidence interval) suggesting that host factors in addition to infection play a role in pathogenesis of RRP. The molecular methods described in this study are well suited for detection of HPV in tonsillar tissue.
Management of Frontal Sinus Fractures: A Review of 96 Cases
Authors: Gossman David G. , Archer Sanford M. , Arosarena Oneida
Published: August 2006

Objectives: The optimal treatment algorithm for frontal sinus fracture management remains ill‐defined. The purpose of the study was to classify fracture types, review management methods, document associated injuries, and identify complications associated with various treatment options.

Study Design: The authors conducted a retrospective chart review evaluating a 13‐year experience with frontal sinus fracture management.

Methods: Complete medical records of 96 frontal sinus fracture patients treated by the University of Kentucky Otolaryngology Service from 1990 to 2003 were reviewed.

Results: The average patient age was 39 years. Fifty percent of the fractures involved the anterior table of the frontal sinus alone, and 50% involved both anterior and posterior tables. Forty‐seven percent of the injuries were managed with observation, whereas 50% of patients underwent surgical repair. In the surgical group, 60% underwent open reduction and internal fixation (ORIF), 23% had a cranialization procedure, and 17% underwent sinus obliteration. The average length of follow up was 9 months. Complications occurred in 17% of the patients (5% in the nonsurgical group and 12% in the surgical group).

Conclusion: Our results support conservative management of nondisplaced or minimally displaced fractures based on the low complication rate seen in this series. Significant bone displacement can frequently be managed with simple ORIF. Complex fractures affecting the orbit or intracranial contents require cranialization or possibly obliteration. A subset of patients with suspected frontal sinus outflow obstruction can be considered for observation or simple ORIF with close follow up and endoscopic repair if outflow complications manifest.
Comparison of Oral Versus Rectal Administration of Acetaminophen With Codeine in Postoperative Pediatric Adenotonsillectomy Patients
Authors: Owczarzak Vicki , Haddad Joseph
Published: August 2006

Objective: To examine whether acetaminophen with codeine administered per rectum is an effective alternative for pain control compared with oral administration after an adenotonsillectomy.

Study Design: A prospective, randomized control study.

Methods: Seventy‐five children aged 1 to 5 were recruited for this study. Each child was assigned randomly to receive either rectal or oral postoperative pain medication. A journal with eight questions was kept for 10 days after the operation, and an overall survey of five questions was filled out at the first postoperative visit.

Results: Postoperative pain was adequately controlled in those patients receiving suppositories when compared with those patients receiving oral pain medication. Adverse effects and total number of doses given per day were similar. Parents found the suppositories easy to administer, and more parents would switch or consider switching from oral pain medication to suppositories if given the choice.

Conclusions: The suppositories achieved equivalent pain control as oral medication with few side effects and good tolerance. Furthermore, many parents preferred the suppositories to oral medication in maintaining postoperative pain control because of ease of administration. If given the choice for future surgeries, many parents would switch or consider switching from oral pain medication to suppositories.
Electrical Resistivity Measurements in the Mammalian Cochlea After Neural Degeneration
Authors: Micco Alan G. , Richter Claus‐Peter
Published: August 2006

Objectives/Hypothesis: In the present series of experiments, the effect of neural degeneration on the cochlear structure electrical resistivities was evaluated to test if it alters the current flow in the cochlea and if increased current levels are needed to stimulate the impaired cochlea. In cochlear implants, frequency information is encoded in part by stimulating discrete populations of spiral ganglion cells along the cochlea. However, electrical properties of the cochlear structures result in shunting of the current away from the auditory neurons. This consumes energy, makes cochlear implants less efficient, and drastically reduces battery life. Models of the electrically stimulated cochlea serve to make predictions on current paths using modified and improved cochlear implant electrodes. However, one of the model's shortcomings is that most of the values for tissue impedances are not direct measurements. They are derived from bulk impedance measurements, which are fitted to lumped‐element models.

Study Design: The four‐electrode reflection–coefficient technique was used to measure resistivities in the gerbil cochlea. In vivo and in vitro (the hemicochlea) models were used. Measurements were made in normal and in deafened animals. Cochlear damage was induced by neomycin injection into the animals' middle ears. Neural degeneration was allowed to occur over 2 months before performing the measurements in the deafened animals.

Results: The resistivity values in deafened animals were smaller than in the normal‐hearing animals, thus altering the current flow within the cochlea.

Conclusions: Resistivity changes and subsequent changes in current path should be considered in future designs of cochlear implants.
Rotational feeding in caecilians: putting a spin on the evolution of cranial design
Authors: Measey G. John , Herrel Anthony
Published: August 2006

Caecilians are a poorly known group of amphibians with a highly derived skull and cranial musculature that has evolved in response to their specialized head-first burrowing lifestyle. They possess a unique jaw-closing system, which is shown to be capable of generating considerable bite forces for its head width (1.09±0.34 and 0.62±0.31 N for
Schistometopum thomense
and
Boulengerula taitanus
, respectively). However, comprehensive dietary studies indicate that there is no need for large bite forces, since most caecilians appear to be generalist predators of subterranean macrofauna. Here, we demonstrate, based on
in vivo
external and X-ray video recordings of animals feeding, that long-axis body rotations are used independent of prey size by these two species of caeciliid caecilians when feeding underground. Further, we show that individuals are capable of generating a substantial spinning force, which is greater than their bite force (1.35±0.26 and 1.02±0.18 N, respectively). These observations shed light on the functional and the evolutionary significance of several unique features of the cranial design in derived caecilians; spinning may allow the individuals to judge prey size and subsequently reduce oversized prey within gape limits.