bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genotype networks in metabolic reaction spaces
Authors: Samal Areejit , Matias Rodrigues João F , Jost Jürgen , Martin Olivier C , Wagner Andreas 
Published: March 2010

Abstract

Background
A metabolic genotype comprises all chemical reactions an organism can catalyze via enzymes encoded in its genome. A genotype is viable in a given environment if it is capable of producing all biomass components the organism needs to survive and reproduce. Previous work has focused on the properties of individual genotypes while little is known about how genome-scale metabolic networks with a given function can vary in their reaction content.

Results
We here characterize spaces of such genotypes. Specifically, we study metabolic genotypes whose phenotype is viability in minimal chemical environments that differ in their sole carbon sources. We show that regardless of the number of reactions in a metabolic genotype, the genotypes of a given phenotype typically form vast, connected, and unstructured sets -- genotype networks -- that nearly span the whole of genotype space. The robustness of metabolic phenotypes to random reaction removal in such spaces has a narrow distribution with a high mean. Different carbon sources differ in the number of metabolic genotypes in their genotype network; this number decreases as a genotype is required to be viable on increasing numbers of carbon sources, but much less than if metabolic reactions were used independently across different chemical environments.

Conclusions
Our work shows that phenotype-preserving genotype networks have generic organizational properties and that these properties are insensitive to the number of reactions in metabolic genotypes.
B-lymphocyte stimulator/a proliferation-inducing ligand heterotrimers are elevated in the sera of patients with autoimmune disease and are neutralized by atacicept and B-cell maturation antigen-immunoglobulin
Authors: Dillon Stacey R , Harder Brandon , Lewis Kenneth B , Moore Margaret D , Liu Hong , Bukowski Thomas R , Hamacher Nels B , Lantry Megan M , Maurer Mark , Krejsa Cecile M , Ellsworth Jeff L , Pederson Susan , Elkon Keith B , Wener Mark H , Dall'Era Maria , Gross Jane A 
Published: March 2010

Abstract
Introduction
B-lymphocyte stimulator (BLyS) and a proliferation-inducing ligand (APRIL) are members of the tumor necrosis factor (TNF) family that regulate B-cell maturation, survival, and function. They are overexpressed in a variety of autoimmune diseases and reportedly exist in vivo not only as homotrimers, but also as BLyS/APRIL heterotrimers.

Methods
A proprietary N-terminal trimerization domain was used to produce recombinant BLyS/APRIL heterotrimers. Heterotrimer biologic activity was compared with that of BLyS and APRIL in a 4-hour signaling assay by using transmembrane activator and CAML interactor (TACI)-transfected Jurkat cells and in a 4-day primary human B-cell proliferation assay. A bead-based immunoassay was developed to quantify native heterotrimers in human sera from healthy donors (n = 89) and patients with systemic lupus erythematosus (SLE; n = 89) or rheumatoid arthritis (RA; n = 30). Heterotrimer levels were compared with BLyS and APRIL homotrimer levels in a subset of these samples.

Results
The recombinant heterotrimers consisted mostly of one BLyS and two APRIL molecules. Heterotrimer signaling did not show any significant difference compared with APRIL in the TACI-Jurkat assay. Heterotrimers were less-potent inducers of B-cell proliferation than were homotrimeric BLyS or APRIL (EC50, nMol/L: BLyS, 0.02; APRIL, 0.17; heterotrimers, 4.06). The soluble receptor fusion proteins atacicept and B-cell maturation antigen (BCMA)-immunoglobulin (Ig) neutralized the activity of BLyS, APRIL, and heterotrimers in both cellular assays, whereas B-cell activating factor belonging to the TNF family receptor (BAFF-R)-Ig neutralized only the activity of BLyS. In human sera, significantly more patients with SLE had detectable BLyS (67% versus 18%; P < 0.0001), APRIL (38% versus 3%; P < 0.0002), and heterotrimer (27% versus 8%; P = 0.0013) levels compared with healthy donors. Significantly more patients with RA had detectable APRIL, but not BLyS or heterotrimer, levels compared with healthy donors (83% versus 3%; P < 0.0001). Heterotrimer levels weakly correlated with BLyS, but not APRIL, levels.

Conclusions
Recombinant BLyS/APRIL heterotrimers have biologic activity and are inhibited by atacicept and BCMA-Ig, but not by BAFF-R-Ig. A novel immunoassay demonstrated that native BLyS/APRIL heterotrimers, as well as BLyS and APRIL homotrimers, are elevated in patients with autoimmune diseases.
Compound-archery-bow nocking-point locus in the vertical plane
Authors: Park J L 
Published: March 2010

In general, the path taken by the nocking point of an archery bow in the vertical plane is not a straight line perpendicular to the rest position of the string; it may vary significantly from that. Any deviation from a straight line at a draw length around the full-draw position will potentially lead to significant inaccuracy if the draw length varies by small amounts from arrow to arrow. This can occur for a compound bow if the cams do not come to their full-draw position simultaneously. The path taken by the nocking point over the length of the bow's draw, and especially near the bow's brace height, can be expected to influence significantly the way that the arrow flexes and rotates about its centre of mass as it leaves the bow and enters the airstream. Hence it is of importance in relation to the arrow's position on the string relative to the bow's launcher (or arrow rest) at the brace height. This paper provides a model for the nocking-point locus in the vertical plane. While examples are provided for several configurations of compound bow, it is generally applicable to longbows and recurve bows as well. It is noted that asymmetric degrees of freedom in the cam configuration of a compound bow are required if the nocking-point locus is to be both straight and perpendicular to the rest position of the string, and that this cannot be achieved for some compound-bow configurations or for a longbow or recurve bow unless the arrow pass is in the geometric centre of the string.
Methane Mitigation Conference Report
Authors: Schultz Karl H 
Published: March 2010

The Second International Methane Mitigation Conference, held June 18–23, 2000, in Novosibirsk, Russia, drew 200 participants from nearly 30 countries to address opportunities and issues related to methane mitigation. Methane is a potent greenhouse gas, and, depending on the source, implementing reduction strategies can improve operational efficiency, provide a viable energy source, or improve agricultural productivity. During the conference, participants developed a stronger understanding of the specific measures that can lead to the most pragmatic and cost-effective emission reductions, and set forth recommendations to improve conditions for the development of projects. The Conference, jointly organized by the Russian Academy of Sciences and the U.S. Environmental Protection Agency, with co-sponsorship by a number of private and governmental bodies, included presentations on a variety of topics related to greater project realization, such as project finance, markets for emission credits, institutional barriers, technical options, and project opportunities. During the conference's source-specific technical sessions, participants shared information and experiences on mitigating methane emissions from coal mining, natural gas systems, solid waste landfills, and agricultural and natural sources. This exchange of information was further developed during field trips, where conference participants had the opportunity to visit methane sources in southwestern Siberia, and to meet with local experts to discuss technical merits of different methane mitigation measures. Throughout the conference, participants were asked to seek answers to these four basic questions: 1) Analyses indicate that methane mitigation is often very cost-effective. What steps are necessary for greater project realization? 2) International institutions are looking for greenhouse gas reduction projects that are reliable and measurable. How well do methane mitigation projects meet these criteria, and what work needs to be undertaken to make this clear? 3) How are technical advances impacting project attractiveness? What is in store for the future? 4) What roles can industry, governments, multi-lateral institutions, and researchers play to promote methane mitigation? What collaborative efforts should be undertaken? At the end of each source-specific technical session, participants gathered to formulate findings, conclusions, and recommendations to present during the concluding plenary session. These recommendations are presented in the next section.
A 2004 View of the Kyoto Protocol
Authors: Singer Fred 
Published: March 2010

It may not be a household word, but by now the Kyoto Protocol has become a well-known political slogan. It is either “fundamentally flawed” (George W. Bush) or it is essential for saving the climate and humanity (Al Gore). There seems to be no in between. The Kyoto Protocol is a treaty to limit (i.e., ration) the use of energy to satisfy the concerns of environmental groups and other believers in global warming catastrophes. This group includes not only certified kooks but also such notables as former Treasury Secretary Paul O'Neill and Sir David King, chief scientific adviser to Her Majesty's government who equates the threat of warming with that of international terrorism. But Kyoto is quite ineffective, that is, it cannot really affect climate or even change the composition of the atmosphere. It is costly. And it is probably also defunct. Where did this treaty come from? Why is it being adopted by some countries but not by others? And what is its likely future?
Dynamics of Practical Premixed Flames, Part I: Model Structure and Identification
Authors: Huber A. , Polifke W. 
Published: March 2010

For the analysis of thermoacoustic instabilities it is most important to determine the dynamic flame response to acoustic disturbances. Premixed flames are often modelled as single-input single-output system, where the “output” (the overall rate of heat release) responds to a single “input” variable (often the velocity at the exit of the burner nozzle). However, for practical premixed flames, where perturbations of pressure or velocity at the fuel injector will modulate the fuel equivalence ratio, the heat release rate will respond to fluctuations of equivalence ratio as well as nozzle mass flow rate. In this case, a multiple-input, single-output (MISO) model structure for the flame is appropriate. Such a model structure is developed in the present paper. Staged fuel injection as well as fuel line impedances can be taken into account, the integration with low-order or finite-element based models for stability analysis is straightforward. In order to determine unit impulse and frequency response functions for such a model structure, an identification scheme based on unsteady CFD calculation with broadband excitation followed by correlation analysis is proposed and validated successfully. Identification of MISO model coefficients is a challenging task, especially in the presence of noise. Therefore criteria are introduced which allow to ascertain a posteriori how well the identified model represents the true system dynamics. Using these criteria, it is investigated how excitation signal type, time series length and signal-to-noise ratio influence the results of the identification process. Consequences for passive design strategies based on multi-stage fuel injection and experimental work on practical premixed flame dynamics are discussed.
Water-Uptake Capacity of Bentonites
Authors: Kaufhold S. , Dohrmann R. , Klinkenberg M. 
Published: March 2010

AbstractThe present study compares the water-vapor adsorption capacity of bentonites (natural cation population) with the Enslin-Neff method. Water-vapor adsorption at 50% r.h. (relative humidity) or 70% r.h. is known to depend heavily on the amount of permanent charge and on the type of exchangeable cation. At ~80% r.h. Na+- and Ca2+/Mg2+-dominated bentonites take up equal amounts of water. Comparing the water-uptake capacity at 80% r.h. with the cation exchange capacity (CEC) revealed a close correlation between these two variables. Appreciable scatter apparent from this plot, however, suggests that additional factors influence the water-uptake capacity.Water adsorption at external surfaces was considered to be one of these factors and was, in fact, implicated by N2-adsorption data. The ratio of external/internal water ranged from 0 to 1, which suggests that water-adsorption values cannot be applied in the calculation of the internal surface area without correction for external water.The Enslin-Neff water-uptake capacity, on the other hand, is unaffected by microstructural features (e.g. specific surface area and porosity). The amount of exchangeable Na+ is themost important factor. However, the relationship between the Na+ content and the Enslin value is not linear but may be explained by percolation theory.
Stacking Disorder in a Sedimentary Kaolinite
Authors: Kogure Toshihiro , Elzea-Kogel Jessica , Johnston Cliff T. , Bish David L. 
Published: March 2010

AbstractAlthough structural disorder in kaolinite has been investigated extensively, it is still not understood properly. To investigate the problem, a kaolinite specimen of sedimentary origin from Capim, Brazil, was examined, mainly by transmission electron microscopy (TEM). Selected-area electron diffraction (SAED) along the Xi ([100], [110], and []) directions shows various features, from completely discrete patterns to heavily streaked ones along the c* direction, suggesting that the degree of stacking disorder is variable among individual grains. High-resolution TEM images indicate that stacking faults are mainly caused by disorder of alternating t1 (~ −a/3) and t2 (−a/3 +b/3) layer displacements. Furthermore, stacking faults have been observed (1) as isolated stacking faults (e.g. insertion of an isolated t2 `fault' in an ordered sequence with t1 layer displacement) and (2) as interstratification of two kinds of multilayer blocks having regular t1 and t2 layer displacements. A mixture of grains with various degrees and modes of disorder with alternating t1 and t2 layer displacements may explain the experimental profile of the 02, 11 X-ray diffraction band.Faults related to displacement of the octahedral vacancy and/or to layer rotation were also observed in HRTEM images. The SAED patterns along the Yi ([010], [310], and []) directions occasionally have extra spots and/or streaks, suggesting the presence of stacking sequences with (±60°, 180°) mutual layer rotation and/or with (0, ±b/3) layer displacements. The local dickite or nacrite-like fragments formed by these faults are in qualitative agreement with recent low-temperature FTIR results from this sample, where distinct ν(OH) absorption bands reflect multiple interlayer O-H⋯O environments that are possibly ascribed to dickite and nacrite.
Ab InitioMolecular Dynamics Study of Fe-Containing Smectites
Authors: Liu Xiandong , Meijer Evert Jan , Lu Xiancai , Wang Rucheng 
Published: March 2010

AbstractIn order to identify the influences imposed by Fe substitution, density functional theory-based Car-Parrinello molecular dynamics simulations were employed to study both oxidized and reduced Febearing smectites. The following basic properties were investigated: local structures in the clay layer, hydroxyl orientations, and the vibration dynamics of H and Si. Structural analyses indicated that the average Fe-O bond lengths are ~2.08 Å and 2.02 Å in the reduced and oxidized models, respectively, and the Fe substitutions did not affect the coordination structures of the Al-O and Si-O polyhedra. For hydroxyl orientations, Fe(III) substitution had no obvious influence but Fe(II) forces the coordinated hydroxyls to present a wide-angle distribution. Furthermore, the present work has shown that both substitutions can red-shift the hydroxyl in-plane bending mode. The analyses also revealed that Fe(III) substitution has no effect on the Si-O stretching, while Fe reduction causes a blue-shift of the out-of-plane stretching mode. The results provide quantitative constraints and clues for future research.
Performance of Natural Zeolite and Sepiolite in the Removal of Free Cyanide and Copper-Complexed Cyanide ([Cu(CN)3]2−)
Authors: Tarlan-Yel Esra , Önen Vildan 
Published: March 2010

AbstractThe chemical and biological methods employed to date in the removal of free cyanide (CN−) and metal-cyanide complexes from aqueous fluids have proved expensive and problematic. A simpler and more economical approach was attempted in the present study using zeolite and sepiolite. The effectiveness of zeolite from Manisa-Gördes (Turkey) and of sepiolite Eskişehir-Sivrihisar (Turkey) at removing free and Cu-complexed cyanide, [Cu(CN)3]2− was investigated. For removal of CN−, the system performance was examined in terms of concentration, particle size, and retention time. Material with smaller particle sizes (<0.106 mm) performed better, particularly in the case of sepiolite. The maximum CN− removal capacities of zeolite and sepiolite were calculated as 571 and 695 meq/100 g for free CN adsorption, and 455 and 435 meq/100 g for Cu-complexed CN adsorption, respectively. The time to reach equilibrium was calculated as 1050 min. Acid activation, a simple cation adsorption removal method, did not improve the process, instead leading to reduced CN adsorption. Hydroxylated surfaces of metal oxides at the edges of zeolite develop charges and exchange with anions in water. Mg2+ ions located at the edges of the octahedral sheet can create complexes with CN− anions. Moreover, hydrogen bonding with anions (CN− in this case) and H+ of zeolitic water bonded to coordinated water molecules can also create complexes. These two complexes are considered to be effective mechanisms for sepiolite. The effects of both acid activation and CN adsorption were clearly observed in the Fourier-transform infrared spectra. Removal of CN was characterized by the Langmuir isotherm, indicating monolayer coverage with chemical bonding to the surface, which deteriorated during acid activation. The study indicated that zeolite and sepiolite can be used efficiently and easily for removal of free and Cu-complexed CN.
A methodological reappraisal of total and high molecular weight adiponectin determination in human peripheral circulation: comparison of four immunometric assays
Authors: Caselli Chiara , Melaiu Ombretta , Maltinti Maristella , Del Ry Silvia , Cabiati Manuela , Prescimone Tommaso , Neglia Danilo , Giannessi Daniela 
Published: March 2010

Abstract

Background: Adiponectin, present in different multimeric forms in circulation, is increasingly used in clinical settings as a cardiometabolic marker. The development of several commercially available enzyme-linked immunosorbent assays (ELISA) has allowed for the widespread measurement of adiponectin in research as well as in clinical practice. The comparative performance of these assays is thus an issue of major relevance.

Methods: The analytical performance of four different ELISAs (LINCO, B-Bridge, SPIbio and ALPCO) was evaluated. Samples from 102 cardiac patients and 40 healthy subjects were tested using LINCO and ALPCO. The latter is able to measure the concentrations of multimers. For the multimer assay, an error propagation study was performed. A subset of subjects was tested by all four ELISAs for comparison purposes.

Results: Bland-Altman plots revealed differences between the results of the four ELISAs, mainly for ALPCO. However, a strong correlation between the different ELISAs (ALPCO, r=0.83; B-Bridge, r=0.98; SPIbio, r=0.91 vs. LINCO) was observed. Total adiponectin measured by LINCO showed a better association with cardiac disease [receiver-operating characteristic (ROC) curves] than total and high molecular weight adiponectin measured by ALPCO.

Conclusions: The results of this study contribute to a better understanding of the methodological features of the several ELISAs, and help in the evaluation and comparison of the relative results.
Clin Chem Lab Med 2010;48:561–8.
New quantitative electrochemiluminescence method (ECLIA) for interleukin-6 (IL-6) measurement
Authors: Prieto Belén , Miguel Diego , Costa Marta , Coto Daniel , Álvarez Francisco V. 
Published: March 2010

Abstract

Background: A new interleukin-6 (IL-6) electrochemiluminescent immunoassay (ECLIA, Roche Diagnostics) was evaluated and compared to a previous semiquantitative immunoassay (Milenia Biotec). Reference ranges for cord blood plasma were also calculated.

Methods: The new IL-6 ECLIA test was performed using a Cobas E601 analyzer (Roche Diagnostics). The comparison method (Milenia Biotec) was a semiquantitative lateral flow immunoassay, coupled to a digital image capture system (PicoScan). Healthy at term newborns were recruited to establish reference ranges for IL-6 in cord blood plasma.

Results: Total imprecision ranged from 3.7% to 8.0% depending on the IL-6 concentrations. The calculated limit of detection for IL-6 measured by ECLIA was 2.63 pg/mL, almost twice as high as that claimed by the manufacturer (1.5 pg/mL). The linearity of the method was verified to 5000 pg/mL. The IL-6 reference limit, obtained from 148 cord blood samples, was 30 pg/mL (90% confidence interval: 19–48 pg/mL).

Conclusions: The new quantitative ECLIA method showed good reproducibility, linearity and functional sensitivity. Additional clinically based studies are needed to elucidate the usefulness of the IL-6 reference limit, calculated here for the first time by ECLIA in cord blood plasma, to aid in the diagnosis of vertical transmission of sepsis.
Clin Chem Lab Med 2010;48:835–8.
Microsatellite polymorphisms in intron 2 of the toll-like receptor 2 gene and their association with susceptibility to pulmonary tuberculosis in Han Chinese
Authors: Xue Yun , Jin Lei , Li A-Zhong , Wang Hua-Jun , Li Meng , Zhang Yu-Xiang , Wang Yu , Li Ji-Cheng 
Published: March 2010

Abstract

Background: Toll-like receptor 2 (TLR2) is essential for the immune response to tuberculosis (TB). The goal of the present study was to investigate whether the guanine-thymine (GT) repeat microsatellite polymorphism in intron 2 of the TLR2 gene might be correlated with susceptibility to TB in Han Chinese.

Methods: The number of (GT)n repeats was determined by gene scanning from 244 patients with TB and 233 control subjects. The expression of TLR2 on CD14+ peripheral blood mononuclear cells was determined using flow cytometry.

Results: No association in allelic polymorphism between control subjects and patients with TB was found. However, the S/M genotype of the microsatellite polymorphism was more frequent in TB patients than in healthy controls (p=0.01). The S/L genotype was more popular in controls than in patients with TB (p=0.007). TLR2 expression was higher in subjects with the S/L genotype than in those with the S/M genotype (p<0.05).

Conclusions: Our data suggest that the S/M genotype of the microsatellite (GT)n polymorphisms in intron 2 of the TLR2 gene may increase susceptibility to TB in Chinese, and the S/L genotype may act as a negative risk factor.
Clin Chem Lab Med 2010;48:785–9.