bluuebunny/crossref_metadata_2025 huggingface dataset:
SHEAF COHOMOLOGY IN o-MINIMAL STRUCTURES
Authors: EDMUNDO MÁRIO J. , JONES GARETH O. , PEATFIELD NICHOLAS J.
Published: May 2007

Here we prove the existence of sheaf cohomology theory in arbitrary o-minimal structures.
REVERSE MATHEMATICS OF MF SPACES
Authors: MUMMERT CARL
Published: May 2007

This paper gives a formalization of general topology in second-order arithmetic using countably based MF spaces. This formalization is used to study the reverse mathematics of general topology.

For each poset P we let MF (P) denote the set of maximal filters on P endowed with the topology generated by {Np | p ∈ P}, where Np = {F ∈ MF (P) | p ∈ F}. We define a countably based MF space to be a space of the form MF (P) for some countable poset P. The class of countably based MF spaces includes all complete separable metric spaces as well as many nonmetrizable spaces.

The following reverse mathematics results are obtained. The proposition that every nonempty Gδ subset of a countably based MF space is homeomorphic to a countably based MF space is equivalent to [Formula: see text] over ACA0. The proposition that every uncountable closed subset of a countably based MF space contains a perfect set is equivalent over [Formula: see text] to the proposition that [Formula: see text] is countable for all A ⊆ ℕ. The proposition that every regular countably based MF space is homeomorphic to a complete separable metric space is equivalent to [Formula: see text] over [Formula: see text].
Production of sex steroid hormones from DHEA in articular chondrocyte of rats
Authors: Takeuchi Satsuki , Mukai Naoki , Tateishi Tetsuya , Miyakawa Shumpei
Published: May 2007

Dehydroepiandrosterone (DHEA), a precursor of sex steroid hormones, is synthesized by cholesterol side-chain cleavage cytochrome P-450 and 17α-hydroxylase cytochrome P-450 mainly from cholesterol and converted to testosterone and estrogen by 3β-hydroxysteroid dehydrogenase (3β-HSD), 17β-HSD, and aromatase cytochrome P-450. Although sex steroid hormones have important effects in the protection of articular cartilage, it is unclear whether articular cartilage has a local steroidogenic enzymatic machinery capable of metabolizing DHEA. This study was aimed to clarify whether steroidogenesis-related enzymes are expressed in articular chondrocytes, whether expression levels are changed by DHEA, and whether articular chondrocytes are capable of synthesizing sex steroid hormones from DHEA. Articular chondrocytes isolated from adult rats were cultured with DHEA for 3 days. All of the mRNA expressions of steroidogenesis-related enzymes were detected in cultured articular chondrocytes of rats, but the mRNA expression levels of testosterone and estradiol in cultured media increased after the addition of DHEA. These findings provided the first evidence that articular chondrocytes expressed steroidogenesis-related enzyme genes and that they are capable of locally synthesizing sex steroid hormones locally from DHEA.
Cell surface expression of LDL receptor in chronic hepatitis C: correlation with viral load
Authors: Petit Jean-Michel , Minello Anne , Duvillard Laurence , Jooste Valérie , Monier Serge , Texier Véronique , Bour Jean-Baptiste , Poussier Alix , Gambert Philippe , Verges Bruno , Hillon Patrick
Published: May 2007

The LDL receptor (LDL-R) has been proposed as the viral receptor for Hepatitis C virus (HCV). This hypothesis has been based exclusively on in vitro studies. In human mononuclear cells, LDL-R gene expression has been demonstrated to be parallel and be coordinately regulated to gene expression in the human liver. The purpose of the current study was to determine the mononuclear cell surface expression of the LDL receptor in patients with HCV chronic infection according to viral load. Sixty-eight consecutive untreated chronic hepatitis C patients were studied to determine the mononuclear cell surface expression of the LDL-R. LDL-Rs were quantified at the surface of mononuclear cells in fresh blood samples taken after fasting using flow cytometry. LDL-R expression was significantly associated with LDL-cholesterol ( r = −0.25; P = 0.03) and HCV-viral load ( r = 0.37, P = 0.002). In multivariate analysis, the LDL-R expression was significantly associated with HCV viral load, whereas genotype, age, body mass index, and fibrosis were not. In conclusion, our data provided by a human study, suggest that the LDL-R may be one of the receptors implicated in HCV replication.
Exercise and diet induced weight loss improves measures of oxidative stress and insulin sensitivity in adults with characteristics of the metabolic syndrome
Authors: Rector R. Scott , Warner Shana O. , Liu Ying , Hinton Pamela S. , Sun Grace Y. , Cox Richard H. , Stump Craig S. , Laughlin M. Harold , Dellsperger Kevin C. , Thomas Tom R.
Published: May 2007

Obesity and insulin resistance (IR) increase the risk for coronary heart disease; however, much of this risk is not attributable to traditional risk factors. We sought to determine whether weight loss associated with supervised aerobic exercise beneficially alters biomarkers of oxidative stress and whether these alterations are associated with improvements in measures of insulin resistance. Twenty-five sedentary and overweight to obese [body mass index (BMI) = 33.0 ± 0.8 kg/m2] individuals, with characteristics of the metabolic syndrome, participated in a 4- to 7-mo weight loss program that consisted of energy restriction (reduced by ∼500 kcal/day) and supervised aerobic exercise (5 days/wk, 45 min/day at 60% V̇o2 max; ∼375 kcal/day). IR and insulin sensitivity were assessed by the calculation of the homeostasis model assessment (HOMA) and quantitative insulin sensitivity check index (QUICKI), respectively. Oxidative stress was assessed by oxidized LDL (oxLDL), myeloperoxidase (MPO), and low- and high- density lipoprotein (LDL and HDL) lipid hydroperoxide concentrations in serum. Indexes for antioxidative status included apolipoprotein A1 (apoA1) concentrations and paraoxonase-1 (PON1) activity and protein concentrations. Exercise- and diet-induced weight loss (∼10%) significantly ( P < 0.05) increased insulin sensitivity and reduced IR, oxLDL, and LDL lipid hydroperoxides but did not alter HDL lipid hydroperoxides or MPO concentrations. Lifestyle modification impacted systemic antioxidative status by increasing apoA1 concentrations and reducing serum PON1 protein and activity. Changes in oxidative stress were not associated with alterations in HOMA or QUICKI. Diet- and exercise-induced weight loss (∼10%) improves measures of insulin sensitivity and beneficially alters biomarkers of oxidative status.
Mechanism of rapid-phase insulin response to elevation of portal glucose concentration
Authors: Fukaya Makiko , Mizuno Akira , Arai Hidekazu , Muto Kazusa , Uebanso Takashi , Matsuo Kaoru , Yamamoto Hironori , Taketani Yutaka , Doi Toshio , Takeda Eiji
Published: May 2007

The hepatoportal region is important for glucose sensing; however, the relationship between the hepatoportal glucose-sensing system and the postprandial rapid phase of the insulin response has been unclear. We examined whether a rapid-phase insulin response to low amounts of intraportal glucose infusion would occur, compared that with the response to intrajugular glucose infusion in conscious rats, and assessed whether this sensing system was associated with autonomic nerve activity. The increases in plasma glucose concentration did not differ between the two infusions at 3 min, but the rapid-phase insulin response was detected only in the intraportal infusion. A sharp and rapid insulin response was observed at 3 min after intraportal infusion of a small amount of glucose but not after intrajugular infusion. Furthermore, this insulin response was also induced by intraportal fructose infusion but not by nonmetabolizable sugars. The rapid-phase insulin response at 3 min during intraportal infusion did not differ between rats that had undergone hepatic vagotomy or chemical sympathectomy with 6-hydroxydopamine compared with control rats, but this response disappeared in rats that had undergone chemical vagotomy with atropine. We conclude that the elevation of glucose concentration in the hepatoportal region induced afferent signals from undetectable sensors and that these signals stimulate pancreas to induce the rapid-phase insulin response via cholinergic nerve action.
Antenna Integration with Composite Sandwich Structures using Gain Enhancement Methods
Authors: Chisang You  , Woonbong Hwang
Published: May 2007

In this study, a new design method for antenna-integrated composite sandwich structures is proposed. First, the effects of sandwich geometry on antennas are investigated in the transmission line analogy. Changes in the gain of an antenna due to a sandwich geometry have been determined. For a facesheet layer, the condition that provides the greatest antenna gain is called the open condition and it is exploited to allow the presence of an antenna in the sandwich structure without loss of antenna performance. Two types of structures are designed, one which uses a stacked-patch microstrip antenna, and the other using an aperture-coupled microstrip antenna for wideband performance. The measured electrical performances of these fabricated structures show that the gains are superior to original antennas, and bandwidths are as wide as specified in the requirements of the present study. Structural performances are the same as those of a conventional sandwich structure, according to the three-point bending test, so that perfect integration is confirmed without reducing either of the mechanical and electrical performances.
On Elastic Properties of Single-walled Carbon Nanotubes as Composite Reinforcing Fillers
Authors: Suzuki Kohji , Nomura Sechi
Published: May 2007

As one of the fundamental prerequisites for composite material applications of single-walled carbon nanotubes, their mechanical properties as reinforcing fillers should be identified in the conventional manner of mechanics of composite materials. In particular, identification of elastic properties under axial tension and compression, i.e., initial Young's modulus and Poisson's ratio in terms of longitudinal straining will have a considerable influence on the estimation accuracy of the mechanical (including elastic) properties of carbon nanotube reinforced composites. In this article, elastic properties of unchiral (arm-chair and zig-zag) single-walled carbon nanotubes of different diameters under infinitesimal, small but finite, and large strain regions are numerically computed based on the definition of tube cross-sectional area which will be adopted in the composite materials communities. A classical molecular dynamics simulation using the well-verified Tersoff-type empirical potential for carbon and hydrocarbon molecules is employed. Contrary to what has been reported so far for the case of infinitesimal straining which has been conducted in this study as well, it has been shown that the elastic properties such as initial Young's modulus and Poisson's ratio of the nanotubes in a small but finite strain range should be more or less treated as chirality-dependent, diameter-dependent, and bi-modal ones. The Mooney—Rivlin constants of unchiral carbon nanotubes are also evaluated. From the present results, it is cautioned that the carbon nanotubes are not always stiff and strong when they are looked upon as reinforcing fibers or fillers of composite materials.
Freedom of expression as liberal fantasy: the debate over The People vs. Larry Flynt
Authors: Petersen Jennifer
Published: May 2007

The People v. Larry Flynt initiated a public discussion in the United States on `freedom of expression'. By analyzing reviews and discussion of the movie in US newspapers and magazines, I look at the way in which `freedom of expression' is constructed as a core American liberty. I argue that this construction is an example of ideological fantasy, which relies on a fetishization of individual expression as proof of freedom. The public discussion I analyze constructs a fantasy of exaggerated `freedom' by focusing on individual and sexual elements of speech and ignoring economic constraints on speech in the movie and in US political and social life.
Financialization, finance rationality and the role of media in Australia
Authors: Greenfield Cathy , Williams Peter
Published: May 2007

This article aims to contribute to understanding the role of media in financialization, understood as the composite of practices involved in making finance central to present-day capitalism and everyday life. To focus on financialization is to consider how it has come to be that the sovereignty of national governments has been eroded by their embedding within a globalized financial environment where financial markets and credit-rating agencies are able to shape the policy preferences and capacities of elected governments, and where the profitable operation of finance markets has become a predominant measure of value. One neglected part of understanding this development is tracing how populations have been equipped with a finance rationality that makes the ethos and affiliations of finance culture into so much `common sense', thereby transforming existing and possible relations of mutuality. This task is undertaken with examples from archival Australian television programming.
Confessions to a new public: Video Nation Shorts
Authors: Matthews Nicole
Published: May 2007

Television made about `ordinary people' and featuring them speaking directly to the camera about their experiences has come to be a staple of popular broadcast television in the UK and elsewhere. This article focuses on one British series, Video Nation, produced between 1995 and 2000, which attempted to assemble a picture of the nation through the voices of such ordinary people. Where many more recent uses of `first person media' have situated themselves explicitly as entertainment television, the Video Nation project was firmly situated within public broadcasting and a tradition of access television. The makers set out to extend the 1930s Mass Observation project. Video Nation, however, attends not so much to the `public' world of graffiti or cinema-queue discussions of politicians as to personal narratives of domestic life. This article will discuss the significance of this shift in emphasis from the 1930s to the 1990s, a shift towards mapping the nation through practices of the self. The article will ask whether confessional style marks a renegotiation of the way we imagine public spaces.
The poetics of indigenous radio in Colombia
Authors: Rodríguez Clemencia , El Gazi Jeanine
Published: May 2007

In 2002, 14 indigenous radio stations began operating in Colombia reaching 78.6 percent of the national indigenous population. Colombian indigenous radio stations are shaped by intense deliberations among each indigenous people about the poetics of information and communication technologies, understood as the exploration of the specific sets of social, cultural and political relations in which each radio station would exist if brought into each indigenous territory. Colombian indigenous peoples' appropriation of information and communication technologies is framed by new legislative frameworks made possible by the Colombian constitutional reform of 1991, by indigenous peoples' critique of Colombian mainstream media and, more significantly, by discussions among indigenous peoples about the adoption of radio — what we call a poetics of radio.
Going public through writing
Authors: Volz Yong Z.
Published: May 2007

This article examines the historical emergence of a women's public sphere in early 20th-century China, a time when modernization was at the top of the national agenda, by looking at how some women — who belonged to the scholar-gentry class and had experience of the West — became journalists. These women carved out a distinctively women's public sphere by establishing a press that was both for women and by women. While Chinese male intellectuals envisioned women's press merely as instrument for enlightening and educating women, women journalists promoted women's journalism as a public forum, particularly for women to participate in discussions of modernization. Struggling against the fact that women in China were traditionally perceived as a subordinate and incapable group, these women journalists had to utilize their elite background to claim credit for their writings and secure their place in the public discursive field.
Fire Protection of Heritage Structures: Use of a Portable Water Mist System under High-altitude Conditions
Authors: Xin Huang  , Xishi Wang  , Xiang Jin  , Guangxuan Liao  , Jun Qin
Published: May 2007

In order to verify the application of water mist on fire protection of the Potala Palace in Tibet and deepen the knowledge of its suppression mechanisms under high-altitude conditions, a series of experiments are performed with a portable water mist fire protection system and with diesel oil, gasoline and, in Lhasa, ghee as fuels. All of the experimental tests are conducted with and without multicomposition (MC) additives. The experimental results show that the MC additive can evidently improve the extinguishing efficiency of water mist for a diesel fire, but the gasoline fire is a little difficult to extinguish. The effects of high-altitude conditions on fire suppression are discussed.
Gypsum Board in Fire — Modeling and Experimental Validation
Authors: Ghazi Wakili K. , Hugi E. , Wullschleger L. , Frank TH
Published: May 2007

The thermal behavior of a commercially widespread gypsum board (810 kg/m 3) under fire condition has been investigated. For this purpose two 12 mm thick gypsum boards are subjected to the standard fire ISO 834 and the temperature distribution within them is measured by means of thermocouples placed at different depths in the samples. The results hereof are used to validate a numerical model based on the density, thermal conductivity, and effective heat capacity of the gypsum board as functions of temperature. The effects of dehydration/calcination and decomposition on these properties are determined by using thermogravimetric analysis, conductivity measurements after different heat treatments, and differential scanning calorimetry under air flow, respectively.
Composite Skin Elastic Constants from Monolithic In-plane Specimens and Bonded Out-of-plane Specimens
Authors: Toftegaard Helmuth , Goutianos Stergios
Published: May 2007

In this study, a full set of elastic constants (in-plane (IP) and out-of-plane (OOP)) is determined/estimated for two sandwich composite skin laminates. For the out-of-plane properties, compression and shear specimens are cut from the skin laminates and bonded together to avoid making thick laminates. This approach gives a relatively low experimental scatter for the elastic constants indicating that the measurements are not affected by the presence of the thin adhesive layers between the laminates. Finite element calculations are performed to further study the effect of the adhesive layers. It is found that the effect of the adhesive layers is minor in the range of strains used to determine the elastic constants.
Ballistic Resistance of 2D and 3D Woven Sandwich Composites
Authors: Grogan Joseph , Tekalur Srinivasan A. , Shukla Arun , Bogdanovich Alex , Coffelt Robert A.
Published: May 2007

In the present study, the ballistic resistance of sandwich composite structures for vehicle armor panel applications is investigated. The core material of each sandwich structure is a layer of tiled alumina ceramic, combined with a layer of two-dimensional (2D)/three-dimensional (3D) S-2 glass-based woven composite laminate, sandwiched between 2D plain weave composite skins. The 2D composite backing consists of a plain woven fiberglass, with fiber orientation predominantly in the direction of plane of the weave. The 3D contains similar in-plane fiber preform structure, with the inclusion of an integral through thickness fiber, creating a 3D structure. The ballistic performance of sandwich composite with several types of 3D woven backings is compared to the baseline 2D plain weave backed sandwiched composites. An IMACON 200 high-speed camera is used to obtain high-speed photographs of the ballistic events of penetration and damage. These images are analyzed to study the real-time damage mechanism of the strike face surface of several targets and subsequently to obtain average resistive force of target points during impact. The velocities of the projectile (M2AP armor piercing bullets) are recorded in all the experiments, and they range from 915 to 975 m/s. Postmortem analyses, which include through thickness sectioning, are performed on each sandwich structure. The results show that armor panels with 3D woven backing have a higher ballistic efficiency than the 2D baseline panels, strike face damage mechanics are predominantly axisymmetric about the impact point and the panels with 3D backing had controlled delamination and fewer complete penetrations.
Neural Network Technique for Fiber Image Recognition
Authors: Bojun Xu  , Bin Dong  , Yan Chen
Published: May 2007

A neural network method of analyzing cross-sectional images of a wool/silk blended yarn is studied. The research has two major components: the process of original yarn cross-sectional images including image enhancement and shape filtering; and the determination of characteristic parameters for distinguishing wool and silk fibers in the enhanced yarn cross-sectional images. A neural network computing approach, single-layer perceptrons, is used for learning the target parameters. The established neural network model features a good capability of tolerance and learning, in contrast to traditional methods of image pattern recognition. The study indicates that preparation of the yarn sample slices is critically important to obtain undistorted fiber images and to ensure the accuracy of fiber recognition by the neural network model. The research concludes that the overall error estimate for recognizing wool or silk fiber is 5%.
A Study of the Structure and Properties of Novel Fabrics for Knee Braces
Authors: Pereira S. , Anand S.C. , Rajendran S. , Wood C.
Published: May 2007

The knee is the most used joint in the human body and is also most prone to injuries. Knee braces are medical devices used in the treatment of some form of injuries providing compression and warmth to the joint thus promoting healing. They can also be used for protection in several contact sports. At the moment there are no regulations governing the textile materials used in braces. The authors believe that knitted spacer fabrics have the desirable mechanical and comfort properties which could make these materials suitable for some medical applications. Commercially available knee braces have been tested and analyzed for their mechanical as well as thermophysiological properties. A range of novel spacer fabrics have been designed, developed, and characterized for comparison with commercial products. It has been found that knitted spacers can be engineered in terms of yarn type and structure used in each of the three layers in order to match and even outperform the properties exhibited by commercially available products, such as neoprene and other knitted fabrics, including composite materials. The test results obtained for a range of existing and novel products studied in this work have been explained in terms of their raw material, structure, and finishing treatments applied to them.
Functionalization of Textile Materials by Plasma Enhanced Modification
Authors: Qufu Wei  , Yingying Wang  , Qin Yang  , Liangyan Yu
Published: May 2007

Textile materials are increasingly used in various industries. In these applications, the surfaces of textile materials play a key role, because a range of performance properties depends on surface characteristics. As with many other types of materials, the surface properties of textiles can be readily altered by the treatment of the materials with gas plasma, without impairment of their bulk mechanical properties. This article presents examples of new approaches to functionalization of textiles using plasma-enhanced modifications. Examples are given of the work on polyethylene terephthalate (PET) nonwoven materials. Micrographs, obtained by scanning probe microscopy (SPM) and environmental scanning electron microscopy (ESEM) are presented to demonstrate changes in the surface topography, surface chemistry, and surface wettability of PET nonwovens. The great potential for significant improvements in the properties of textiles by plasma-enhanced modification is highly promising.
Pivotal contributions of megakaryocytes to the biology of idiopathic myelofibrosis
Authors: Ciurea Stefan O. , Merchant Delwin , Mahmud Nadim , Ishii Takefumi , Zhao Yan , Hu Wenyang , Bruno Edward , Barosi Giovanni , Xu Mingjiang , Hoffman Ronald
Published: May 2007

In order to investigate the biologic processes underlying and resulting from the megakaryocytic hyperplasia that characterizes idiopathic myelofibrosis (IMF), peripheral blood CD34+ cells isolated from patients with IMF, polycythemia vera (PV), and G-CSF–mobilized healthy volunteers were cultured in the presence of stem cell factor and thrombopoietin. IMF CD34+ cells generated 24-fold greater numbers of megakaryocytes (MKs) than normal CD34+ cells. IMF MKs were also shown to have a delayed pattern of apoptosis and to overexpress the antiapoptotic protein bcl-xL. MK hyperplasia in IMF is, therefore, likely a consequence of both the increased ability of IMF progenitor cells to generate MKs and a decreased rate of MK apoptosis. Media conditioned (CM) by CD61+ cells generated in vitro from CD34+ cells were then assayed for the levels of growth factors and proteases. Higher levels of transforming growth factor-β (TGF-β) and active matrix metalloproteinase-9 (MMP9) were observed in media conditioned with IMF CD61+ cells than normal or PV CD61+ cells. Both normal and IMF CD61+ cells produced similar levels of VEGF. MK-derived TGF-B and MMP-9, therefore, likely contribute to the development of many pathological epiphenomena associated with IMF.
Body mass index is associated with reduced exhaled nitric oxide and higher exhaled 8-isoprostanes in asthmatics
Authors: Komakula Sushma , Khatri Sumita , Mermis Joel , Savill Samira , Haque Shireen , Rojas Mauricio , Brown LouAnn , Teague Gerald W , Holguin Fernando
Published: May 2007

Background

Recently, it has been shown that increasing body mass index (BMI) in asthma is associated with reduced exhaled NO. Our objective in this study was to determine if the BMI-related changes in exhaled NO differ across asthmatics and controls, and to determine if these changes are related to increased airway oxidative stress and systemic levels of leptin and adiponectin.

Methods

Observational study of the association of BMI, leptin, and adiponectin with exhaled nitric oxide (NO) and exhaled 8-isoprostanes in 67 non-smoking patients with moderate to severe persistent asthma during baseline conditions and 47 controls. Measurements included plasma levels of leptin, adiponectin, exhaled breath condensates for 8-isoprostanes, exhaled NO, pulmonary function tests, and questionnaires regarding asthma severity and control.

Results

In asthmatics, BMI and the ratio of leptin to adiponectin were respectively associated with reduced levels of exhaled NO (β = -0.04 [95% C.I. -0.07, -0.1], p < 0.003) and (β = -0.0018 [95% C.I. -0.003, -0.00034], p = 0.01) after adjusting for confounders. Also, BMI was associated with increased levels of exhaled 8-isoprostanes (β = 0.30 [95% C.I. 0.003, 0.6], p = 0.03) after adjusting for confounders. In contrast, we did not observe these associations in the control group of healthy non-asthmatics with a similar weight distribution.

Conclusion

In adults with stable moderate to severe persistent asthma, but not in controls, BMI and the plasma ratio of leptin/adiponectin is associated with reduced exhaled NO. Also, BMI is associated with increased exhaled 8-isoprostanes. These results suggest that BMI in asthmatics may increase airway oxidative stress and could explain the BMI-related reductions in exhaled NO.
Greigite: a true intermediate on the polysulfide pathway to pyrite
Authors: Hunger Stefan , Benning Liane G
Published: May 2007

The formation of pyrite (FeS2) from iron monosulfide precursors in anoxic sediments has been suggested to proceed via mackinawite (FeS) and greigite (Fe3S4). Despite decades of research, the mechanisms of pyrite formation are not sufficiently understood because solid and dissolved intermediates are oxygen-sensitive and poorly crystalline and therefore notoriously difficult to characterize and quantify.

In this study, hydrothermal synchrotron-based energy dispersive X-ray diffraction (ED-XRD) methods were used to investigate in situ and in real-time the transformation of mackinawite to greigite and pyrite via the polysulfide pathway. The rate of formation and disappearance of specific Bragg peaks during the reaction and the changes in morphology of the solid phases as observed with high resolution microscopy were used to derive kinetic parameters and to determine the mechanisms of the reaction from mackinawite to greigite and pyrite.

The results clearly show that greigite is formed as an intermediate on the pathway from mackinawite to pyrite. The kinetics of the transformation of mackinawite to greigite and pyrite follow a zero-order rate law indicating a solid-state mechanism. The morphology of greigite and pyrite crystals formed under hydrothermal conditions supports this conclusion and furthermore implies growth of greigite and pyrite by oriented aggregation of nanoparticulate mackinawite and greigite, respectively. The activation enthalpies and entropies of the transformation of mackinawite to greigite, and of greigite to pyrite were determined from the temperature dependence of the rate constants according to the Eyring equation. Although the activation enthalpies are uncharacteristic of a solid-state mechanism, the activation entropies indicate a large increase of order in the transition state, commensurate with a solid-state mechanism.
Magnetic record associated with tree ring density: Possible climate proxy
Authors: Kletetschka Gunther , Pruner Petr , Venhodova Daniela , Kadlec Jaroslav
Published: May 2007

A magnetic signature of tree rings was tested as a potential paleo-climatic indicator. We examined wood from sequoia tree, located in Mountain Home State Forest, California, whose tree ring record spans over the period 600 – 1700 A.D. We measured low and high-field magnetic susceptibility, the natural remanent magnetization (NRM), saturation isothermal remanent magnetization (SIRM), and stability against thermal and alternating field (AF) demagnetization. Magnetic investigation of the 200 mm long sequoia material suggests that magnetic efficiency of natural remanence may be a sensitive paleoclimate indicator because it is substantially higher (in average >1%) during the Medieval Warm Epoch (700–1300 A.D.) than during the Little Ice Age (1300–1850 A.D.) where it is <1%. Diamagnetic behavior has been noted to be prevalent in regions with higher tree ring density. The mineralogical nature of the remanence carrier was not directly detected but maghemite is suggested due to low coercivity and absence of Verwey transition. Tree ring density, along with the wood's magnetic remanence efficiency, records the Little Ice Age (LIA) well documented in Europe. Such a record suggests that the European LIA was a global phenomenon. Magnetic analysis of the thermal stability reveals the blocking temperatures near 200 degree C. This phenomenon suggests that the remanent component in this tree may be thermal in origin and was controlled by local thermal condition.
LIMPIC: a computational method for the separation of protein MALDI-TOF-MS signals from noise
Authors: Mantini Dante , Petrucci Francesca , Pieragostino Damiana , Del Boccio Piero , Di Nicola Marta , Di Ilio Carmine , Federici Giorgio , Sacchetta Paolo , Comani Silvia , Urbani Andrea
Published: May 2007

Background

Mass spectrometry protein profiling is a promising tool for biomarker discovery in clinical proteomics. However, the development of a reliable approach for the separation of protein signals from noise is required. In this paper, LIMPIC, a computational method for the detection of protein peaks from linear-mode MALDI-TOF data is proposed. LIMPIC is based on novel techniques for background noise reduction and baseline removal. Peak detection is performed considering the presence of a non-homogeneous noise level in the mass spectrum. A comparison of the peaks collected from multiple spectra is used to classify them on the basis of a detection rate parameter, and hence to separate the protein signals from other disturbances.

Results

LIMPIC preprocessing proves to be superior than other classical preprocessing techniques, allowing for a reliable decomposition of the background noise and the baseline drift from the MALDI-TOF mass spectra. It provides lower coefficient of variation associated with the peak intensity, improving the reliability of the information that can be extracted from single spectra. Our results show that LIMPIC peak-picking is effective even in low protein concentration regimes. The analytical comparison with commercial and freeware peak-picking algorithms demonstrates its superior performances in terms of sensitivity and specificity, both on in-vitro purified protein samples and human plasma samples.

Conclusion

The quantitative information on the peak intensity extracted with LIMPIC could be used for the recognition of significant protein profiles by means of advanced statistic tools: LIMPIC might be valuable in the perspective of biomarker discovery.
Use of DNA melting simulation software for in silico diagnostic assay design: targeting regions with complex melting curves and confirmation by real-time PCR using intercalating dyes
Authors: Rasmussen John P , Saint Christopher P , Monis Paul T
Published: May 2007

Background

DNA melting curve analysis using double-stranded DNA-specific dyes such as SYTO9 produce complex and reproducible melting profiles, resulting in the detection of multiple melting peaks from a single amplicon and allowing the discrimination of different species. We compare the melting curves of several Naegleria and Cryptosporidium amplicons generated in vitro with in silico DNA melting simulations using the programs POLAND and MELTSIM., then test the utility of these programs for assay design using a genetic marker for toxin production in cyanobacteria.

Results

The SYTO9 melting curve profiles of three species of Naegleria and two species of Cryptosporidium were similar to POLAND and MELTSIM melting simulations, excepting some differences in the relative peak heights and the absolute melting temperatures of these peaks. MELTSIM and POLAND were used to screen sequences from a putative toxin gene in two different species of cyanobacteria and identify regions exhibiting diagnostic melting profiles. For one of these diagnostic regions the POLAND and MELTSIM melting simulations were observed to be different, with POLAND more accurately predicting the melting curve generated in vitro. Upon further investigation of this region with MELTSIM, inconsistencies between the melting simulation for forward and reverse complement sequences were observed. The assay was used to accurately type twenty seven cyanobacterial DNA extracts in vitro.

Conclusion

Whilst neither POLAND nor MELTSIM simulation programs were capable of exactly predicting DNA dissociation in the presence of an intercalating dye, the programs were successfully used as tools to identify regions where melting curve differences could be exploited for diagnostic melting curve assay design. Refinements in the simulation parameters would be required to account for the effect of the intercalating dye and salt concentrations used in real-time PCR. The agreement between the melting curve simulations for different species of Naegleria and Cryptosporidium and the complex melting profiles generated in vitro using SYTO9 verified that the complex melting profile of PCR amplicons was solely the result of DNA dissociation. Other data outputs from these simulations were also used to identify the melting domains that contributed to the observed melting peaks for each of the different PCR amplicons.
Transcript-based redefinition of grouped oligonucleotide probe sets using AceView: High-resolution annotation for microarrays
Authors: Lu Jun , Lee Joseph C , Salit Marc L , Cam Margaret C
Published: May 2007

Background

Extracting biological information from high-density Affymetrix arrays is a multi-step process that begins with the accurate annotation of microarray probes. Shortfalls in the original Affymetrix probe annotation have been described; however, few studies have provided rigorous solutions for routine data analysis.

Results

Using AceView, a comprehensive human transcript database, we have reannotated the probes by matching them to RNA transcripts instead of genes. Based on this transcript-level annotation, a new probe set definition was created in which every probe in a probe set maps to a common set of AceView gene transcripts. In addition, using artificial data sets we identified that a minimal probe set size of 4 is necessary for reliable statistical summarization. We further demonstrate that applying the new probe set definition can detect specific transcript variants contributing to differential expression and it also improves cross-platform concordance.

Conclusion

We conclude that our transcript-level reannotation and redefinition of probe sets complement the original Affymetrix design. Redefinitions introduce probe sets whose sizes may not support reliable statistical summarization; therefore, we advocate using our transcript-level mapping redefinition in a secondary analysis step rather than as a replacement. Knowing which specific transcripts are differentially expressed is important to properly design probe/primer pairs for validation purposes. For convenience, we have created custom chip-description-files (CDFs) and annotation files for our new probe set definitions that are compatible with Bioconductor, Affymetrix Expression Console or third party software.
Colony size measurement of the yeast gene deletion strains for functional genomics
Authors: Memarian Negar , Jessulat Matthew , Alirezaie Javad , Mir-Rashed Nadereh , Xu Jianhua , Zareie Mehri , Smith Myron , Golshani Ashkan
Published: May 2007

Background

Numerous functional genomics approaches have been developed to study the model organism yeast, Saccharomyces cerevisiae, with the aim of systematically understanding the biology of the cell. Some of these techniques are based on yeast growth differences under different conditions, such as those generated by gene mutations, chemicals or both. Manual inspection of the yeast colonies that are grown under different conditions is often used as a method to detect such growth differences.

Results

Here, we developed a computerized image analysis system called Growth Detector (GD), to automatically acquire quantitative and comparative information for yeast colony growth. GD offers great convenience and accuracy over the currently used manual growth measurement method. It distinguishes true yeast colonies in a digital image and provides an accurate coordinate oriented map of the colony areas. Some post-processing calculations are also conducted. Using GD, we successfully detected a genetic linkage between the molecular activity of the plant-derived antifungal compound berberine and gene expression components, among other cellular processes. A novel association for the yeast mek1 gene with DNA damage repair was also identified by GD and confirmed by a plasmid repair assay. The results demonstrate the usefulness of GD for yeast functional genomics research.

Conclusion

GD offers significant improvement over the manual inspection method to detect relative yeast colony size differences. The speed and accuracy associated with GD makes it an ideal choice for large-scale functional genomics investigations.
UbiProt: a database of ubiquitylated proteins
Authors: Chernorudskiy Alexander L , Garcia Alejandro , Eremin Eugene V , Shorina Anastasia S , Kondratieva Ekaterina V , Gainullin Murat R
Published: May 2007

Background

Post-translational protein modification with ubiquitin, or ubiquitylation, is one of the hottest topics in a modern biology due to a dramatic impact on diverse metabolic pathways and involvement in pathogenesis of severe human diseases. A great number of eukaryotic proteins was found to be ubiquitylated. However, data about particular ubiquitylated proteins are rather disembodied.

Description

To fill a general need for collecting and systematizing experimental data concerning ubiquitylation we have developed a new resource, UbiProt Database, a knowledgebase of ubiquitylated proteins. The database contains retrievable information about overall characteristics of a particular protein, ubiquitylation features, related ubiquitylation and de-ubiquitylation machinery and literature references reflecting experimental evidence of ubiquitylation. UbiProt is available at http://ubiprot.org.ru for free.

Conclusion

UbiProt Database is a public resource offering comprehensive information on ubiquitylated proteins. The resource can serve as a general reference source both for researchers in ubiquitin field and those who deal with particular ubiquitylated proteins which are of their interest. Further development of the UbiProt Database is expected to be of common interest for research groups involved in studies of the ubiquitin system.
Discarding duplicate ditags in LongSAGE analysis may introduce significant error
Authors: Emmersen Jeppe , Heidenblut Anna M , Høgh Annabeth Laursen , Hahn Stephan A , Welinder Karen G , Nielsen Kåre L
Published: May 2007

Background

During gene expression analysis by Serial Analysis of Gene Expression (SAGE), duplicate ditags are routinely removed from the data analysis, because they are suspected to stem from artifacts during SAGE library construction. As a consequence, naturally occurring duplicate ditags are also removed from the analysis leading to an error of measurement.

Results

An algorithm was developed to analyze the differential occurrence of SAGE tags in different ditag combinations. Analysis of a pancreatic acinar cell LongSAGE library showed no sign of a general amplification bias that justified the removal of all duplicate ditags. Extending the analysis to 10 additional LongSAGE libraries showed no justification for removal of all duplicate ditags either. On the contrary, while the error introduced in original SAGE by removal of naturally occurring duplicate ditags is insignificant, it leads to an error of up to 3 fold in LongSAGE. However, the algorithm developed for the analysis of duplicate ditags was able to identify individual artifact ditags that originated from rare nucleotide variations of tags and vector contamination.

Conclusion

The removal of all duplicate ditags was unfounded for the datasets analyzed and led to large errors. This may also be the case for other LongSAGE datasets already present in databases. Analysis of the ditag population, however, can identify artifact tags that should be removed from analysis or have their tag count adjusted.
MED: a new non-supervised gene prediction algorithm for bacterial and archaeal genomes
Authors: Zhu Huaiqiu , Hu Gang-Qing , Yang Yi-Fan , Wang Jin , She Zhen-Su
Published: May 2007

Background

Despite a remarkable success in the computational prediction of genes in Bacteria and Archaea, a lack of comprehensive understanding of prokaryotic gene structures prevents from further elucidation of differences among genomes. It continues to be interesting to develop new ab initio algorithms which not only accurately predict genes, but also facilitate comparative studies of prokaryotic genomes.

Results

This paper describes a new prokaryotic genefinding algorithm based on a comprehensive statistical model of protein coding Open Reading Frames (ORFs) and Translation Initiation Sites (TISs). The former is based on a linguistic "Entropy Density Profile" (EDP) model of coding DNA sequence and the latter comprises several relevant features related to the translation initiation. They are combined to form a so-called Multivariate Entropy Distance (MED) algorithm, MED 2.0, that incorporates several strategies in the iterative program. The iterations enable us to develop a non-supervised learning process and to obtain a set of genome-specific parameters for the gene structure, before making the prediction of genes.

Conclusion

Results of extensive tests show that MED 2.0 achieves a competitive high performance in the gene prediction for both 5' and 3' end matches, compared to the current best prokaryotic gene finders. The advantage of the MED 2.0 is particularly evident for GC-rich genomes and archaeal genomes. Furthermore, the genome-specific parameters given by MED 2.0 match with the current understanding of prokaryotic genomes and may serve as tools for comparative genomic studies. In particular, MED 2.0 is shown to reveal divergent translation initiation mechanisms in archaeal genomes while making a more accurate prediction of TISs compared to the existing gene finders and the current GenBank annotation.
In silico segmentations of lentivirus envelope sequences
Authors: Boissin-Quillon Aurélia , Piau Didier , Leroux Caroline
Published: May 2007

Background

The gene encoding the envelope of lentiviruses exhibits a considerable plasticity, particularly the region which encodes the surface (SU) glycoprotein. Interestingly, mutations do not appear uniformly along the sequence of SU, but they are clustered in restricted areas, called variable (V) regions, which are interspersed with relatively more stable regions, called constant (C) regions. We look for specific signatures of C/V regions, using hidden Markov models constructed with SU sequences of the equine, human, small ruminant and simian lentiviruses.

Results

Our models yield clear and accurate delimitations of the C/V regions, when the test set and the training set were made up of sequences of the same lentivirus, but also when they were made up of sequences of different lentiviruses. Interestingly, the models predicted the different regions of lentiviruses such as the bovine and feline lentiviruses, not used in the training set. Models based on composite training sets produce accurate segmentations of sequences of all these lentiviruses.

Conclusion

Our results suggest that each C/V region has a specific statistical oligonucleotide composition, and that the C (respectively V) regions of one of these lentiviruses are statistically more similar to the C (respectively V) regions of the other lentiviruses, than to the V (respectively C) regions of the same lentivirus.