bluuebunny/crossref_metadata_2025_split huggingface dataset:
Time-dependent structural transformation analysis to high-level Petri net model with active state transition diagram
Authors: Li Chen , Nagasaki Masao , Saito Ayumu , Miyano Satoru 
Published: April 2010

Abstract

Background
With an accumulation of in silico data obtained by simulating large-scale biological networks, a new interest of research is emerging for elucidating how living organism functions over time in cells.
Investigating the dynamic features of current computational models promises a deeper understanding of complex cellular processes. This leads us to develop a method that utilizes structural properties of the model over all simulation time steps. Further, user-friendly overviews of dynamic behaviors can be considered to provide a great help in understanding the variations of system mechanisms.

Results
We propose a novel method for constructing and analyzing a so-called active state transition diagram (ASTD) by using time-course simulation data of a high-level Petri net. Our method includes two new algorithms. The first algorithm extracts a series of subnets (called temporal subnets) reflecting biological components contributing to the dynamics, while retaining positive mathematical qualities. The second one creates an ASTD composed of unique temporal subnets. ASTD provides users with concise information allowing them to grasp and trace how a key regulatory subnet and/or a network changes with time. The applicability of our method is demonstrated by the analysis of the underlying model for circadian rhythms in Drosophila.

Conclusions
Building ASTD is a useful means to convert a hybrid model dealing with discrete, continuous and more complicated events to finite time-dependent states. Based on ASTD, various analytical approaches can be applied to obtain new insights into not only systematic mechanisms but also dynamics.
Creation of a novel telomere-cutting endonuclease based on the EN domain of telomere-specific non-long terminal repeat retrotransposon, TRAS1
Authors: Yoshitake Kazutoshi , Aoyagi Hideyuki , Fujiwara Haruhiko 
Published: April 2010

Abstract

Background
The ends of chromosomes, termed telomeres consist of repetitive DNA. The telomeric sequences shorten with cell division and, when telomeres are critically abbreviated, cells stop proliferating. However, in cancer cells, by the expression of telomerase which elongates telomeres, the cells can continue proliferating. Many approaches for telomere shortening have been pursued in the past, but to our knowledge, cutting telomeres in vivo has not so far been demonstrated. In addition, there is lack of information on the cellular effects of telomere shortening in human cells.

Results
Here, we created novel chimeric endonucleases to cut telomeres by fusing the endonuclease domain (TRAS1EN) of the silkworm's telomere specific non-long terminal repeat retrotransposon TRAS1 to the human telomere-binding protein, TRF1. An in vitro assay demonstrated that the TRAS1EN-TRF1 chimeric endonucleases (T-EN and EN-T) cut the human (TTAGGG)n repeats specifically. The concentration of TRAS1EN-TRF1 chimeric endonucleases necessary for the cleavage of (TTAGGG)n repeats was about 40-fold lower than that of TRAS1EN alone. When TRAS1EN-TRF1 endonucleases were introduced into human U2OS cancer cells using adenovirus vectors, the enzymes localized at telomeres of nuclei, cleaved and shortened the telomeric DNA by double-strand breaks. When human U2OS and HFL-1 fibroblast cells were infected with EN-T recombinant adenovirus, their cellular proliferation was suppressed for about 2 weeks after infection. In contrast, the TRAS1EN mutant (H258A) chimeric endonuclease fused with TRF1 (ENmut-T) did not show the suppression effect. The EN-T recombinant adenovirus induced telomere shortening in U2OS cells, activated the p53-dependent pathway and caused the senescence associated cellular responses, while the ENmut-T construct did not show such effects.

Conclusions
A novel TRAS1EN-TRF1 chimeric endonuclease (EN-T) cuts the human telomeric repeats (TTAGGG)n specifically in vitro and in vivo. Thus, the chimeric endonuclease which is expressed from an adenoviral vector can suppress cell proliferation of cancer cells.
Prospective monitoring of cefepime in intensive care unit adult patients
Authors: Chapuis Thomas M , Giannoni Eric , Majcherczyk Paul A , Chioléro René , Schaller Marie-Denise , Berger Mette M , Bolay Saskia , Décosterd Laurent A , Bugnon Denis , Moreillon Philippe 
Published: April 2010

AbstractIntroductionCefepime has been associated with a greater risk of mortality than other beta-lactams in patients treated for severe sepsis. Hypotheses for this failure include possible hidden side-effects (for example, neurological) or inappropriate pharmacokinetic/pharmacodynamic (PK/PD) parameters for bacteria with cefepime minimal inhibitory concentrations (MIC) at the highest limits of susceptibility (8 mg/l) or intermediate-resistance (16 mg/l) for pathogens such asEnterobacteriaceae,Pseudomonas aeruginosaandStaphylococcus aureus. We examined these issues in a prospective non-interventional study of 21 consecutive intensive care unit (ICU) adult patients treated with cefepime for nosocomial pneumonia.MethodsPatients (median age 55.1 years, range 21.8 to 81.2) received intravenous cefepime at 2 g every 12 hours for creatinine clearance (CLCr) ≥ 50 ml/min, and 2 g every 24 hours or 36 hours for CLCr< 50 ml/minute. Cefepime plasma concentrations were determined at several time-points before and after drug administration by high-pressure liquid chromatography. PK/PD parameters were computed by standard non-compartmental analysis.ResultsSeventeen first-doses and 11 steady states (that is, four to six days after the first dose) were measured. Plasma levels varied greatly between individuals, from two- to three-fold at peak-concentrations to up to 40-fold at trough-concentrations. Nineteen out of 21 (90%) patients had PK/PD parameters comparable to literature values. Twenty-one of 21 (100%) patients had appropriate duration of cefepime concentrations above the MIC (T>MIC≥ 50%) for the pathogens recovered in this study (MIC ≤ 4 mg/l), but only 45 to 65% of them had appropriate coverage for potential pathogens with cefepime MIC ≥ 8 mg/l. Moreover, 2/21 (10%) patients with renal impairment (CLCr< 30 ml/minute) demonstrated accumulation of cefepime in the plasma (trough concentrations of 20 to 30 mg/l) in spite of dosage adjustment. Both had symptoms compatible with non-convulsive epilepsy (confusion and muscle jerks) that were not attributed to cefepime-toxicity until plasma levels were disclosed to the caretakers and symptoms resolved promptly after drug arrest.ConclusionsThese empirical results confirm the suspected risks of hidden side-effects and inappropriate PK/PD parameters (for pathogens with upper-limit MICs) in a population of ICU adult patients. Moreover, it identifies a safety and efficacy window for cefepime doses of 2 g every 12 hours in patients with a CLCr≥ 50 ml/minute infected by pathogens with cefepime MICs ≤ 4 mg/l. On the other hand, prompt monitoring of cefepime plasma levels should be considered in case of lower CLCror greater MICs.
Genistein Aglycone Does Not Affect Thyroid Function: Results from a Three-Year, Randomized, Double-Blind, Placebo-Controlled Trial
Authors: Bitto Alessandra , Polito Francesca , Atteritano Marco , Altavilla Domenica , Mazzaferro Susanna , Marini Herbert , Adamo Elena Bianca , D'Anna Rosario , Granese Roberta , Corrado Francesco , Russo Silvia , Minutoli Letteria , Squadrito Francesco 
Published: April 2010

Abstract
Context and Objective: Genistein aglycone positively affects postmenopausal symptoms. However, questions about its long-term safety on the thyroid gland still remain.
Design: The parent study was a randomized, double-blind, placebo-controlled trial involving 389 osteopenic, postmenopausal women for 24 months. A subcohort (138 patients) continued therapy for an additional year.
Setting: Patients received ambulatory care.
Patients and Interventions: Participants received 54 mg of genistein aglycone daily (n = 71) or placebo (n = 67), plus calcium and vitamin D3 at therapeutic doses. Circulating thyroid hormones (TSH, free T3, free T4) and autoantibodies (thyroid peroxidase, thyroglobulin, and thyroid microsomal antigen) were assessed in 40 genistein and 37 placebo subjects who completed 3 yr. Thyroid hormone receptor (THRα and THRβ) and retinoid receptor (RARα, RARγ, and RXRα) expression from peripheral blood monocytes was also evaluated at baseline, 12, 24, and 36 months in all 3-yr completers.
Results: Genistein administration over 3 yr did not affect serum thyroid hormones or autoantibodies. In addition, there were no differences in THRα, THRβ, RARα, RARγ, or RXRα mRNA expression between groups.
Conclusion: These data suggest that genistein aglycone intake does not significantly increase the risk of clinical or subclinical hypothyroidism at the dose of 54 mg/d.
A Binomial Approach to Selecting Optimum Working Interest: Corporate Risk and Corporate Confidence III. Ignorance is Not Bliss
Authors: MacKay J. A. , Lerche I. 
Published: April 2010

This third paper in the series is concerned with the situation in which one has virtually no idea whether an exploration opportunity is likely to be a money winner or just awful. Using a variant of the binomial method accounting for the probability that a well will result in successful hydrocarbon finding after a series of dry holes, we show that one can assess the corporate confidence and associated optimum working interest one should take in such an exploration opportunity when one ignores all information about the net present value (NPV). When a corporation wishes to modify the basic pattern to allow for an NPV, and to include a required corporate worth for the opportunity, we show how the corporate confidence and/or the optimum working interest have to be altered to allow for such a factor. When the corporation knows only a low value for the NPV, which is unprofitable, and a high value, which is extremely profitable, we show how one can incorporate this broad range of possibilities within the same binomial framework to assess the likely distribution of optimum working interest (for a fixed corporate confidence) or corporate confidence distribution (for a fixed working interest) for choices of corporate required worth. These calculations allow a corporation to be more sharply focused on the working interest it might wish to take in relation to its corporate confidence that the unknown opportunity NPV might just turn out to be highly profitable, without overly committing too great a fraction of the corporate resources to such speculative ventures.
The Solution of Low Frequency Noise Problems Associated with a Combined Heat and Power Plant
Authors: Marriott Ken , Leventhall Geoff 
Published: April 2010

Complaints of low frequency noise arose following installation of a CHP system in an existing boiler room. Control was by a multi-stage process, the main phases of which were: Reduction of LF noise in the boiler room: Detuning the stack: Reduction of breakout from the stack: Identifying the residual problem. The final phase enabled the correct exhaust silencer to be selected. The end result was that annoying excitation of room modes and irritating throbbing noises were reduced to below complaint level.
Heterogeneities in Adsorption from Aqueous Solution — An Example of the Effect of Surface Coverage
Authors: Lützenkirchen Johannes , Huber Florian 
Published: April 2010

Studies of the interaction of uranyl species with the surface of quartz are reported. Two approaches were applied. These were (i) the classical static batch adsorption approach in which only the forward adsorption uptake reaction is usually studied and (ii) a dynamic column approach in which the retention of a solute during its migration through a porous medium is investigated and where adsorption and desorption are both relevant for the final breakthrough curve. In this paper, we present the results of a column study at pH 4. Under these conditions, the interference of the carbonate ion (via the formation of dissolved or adsorbed uranyl-carbonato species), the effects of quartz surface charge (quartz/silica is virtually uncharged under these conditions) and the potential effects of quartz dissolution on uranyl speciation (via the formation of dissolved or adsorbed uranyl-silicato species) are minimised. The reported batch adsorption results are reasonably predicted by a model which under similar conditions successfully described batch and column data on a quartz sample with grains smaller than the quartz particles used in the present study by a factor of ca. 25. However, this model was incapable of describing the breakthrough behaviour of uranyl species. This failure was attributed to the heterogeneity of the quartz particles used, which may be more important for column breakthrough than for batch adsorption data.
Use of the [Copper(II)/MAA-nylon] Complex for the Adsorption of Residual Acid Dyes
Authors: Makhlouf Chahira , Baouab Mohamed Hassen V , Roudesli Sadok 
Published: April 2010

Nylon fibres were converted into a strong ion-exchange polymer by grafting with methacrylic acid (MAA). The modified nylon fibres were monitored for their ability to remove copper(II) ions and dyes from aqueous solutions. Evidence for the grafting of MAA onto nylon was provided by weight uptake experiments and atomic force microscopy (AFM). The exchange capacity of MAA–nylon was evaluated by potentiometric titration of the grafted acidic groups. Due to complexation, the acidic grafted groups immobilize Cu(II) ions from Clark–Lub's buffered solution at a pH value of 8. The formation of a 1:1 complex was demonstrated by the values of the adsorption limits. The binary [Cu(II)/MAA–nylon] system was then tested for the adsorption of two Acid dyes, i.e. Acid Blue 25 (AB 25) and Calmagite (Calma), as ligands in the metal-coordinating process. The adsorption of Cu(II) onto MAA–nylon and of the dyes onto Cu(II)/MAA–nylon was followed spectrometrically. The observed stoichiometries of the ternary [dye/Cu(II)/MAA–nylon] complex formed were [[Formula: see text]] for AB 25 and [[Formula: see text]] for Calma at 20°C. Theoretical modelling of the adsorption process was performed employing the Langmuir, Freundlich and Jossen equations. Thermodynamic parameters such as the free energy change (ΔG0), the enthalpy change (ΔH0) and the entropy change (ΔS0) for adsorption were also investigated. The adsorption process is exothermic, which leads to a reduction in the extent of dye adsorption with increasing temperature.
A New Pb2+ Ion-selective Hybrid Cation-exchanger — EDTA–Zirconium Iodate: Synthesis, Characterization and Analytical Applications
Authors: Nabi Syed Ashfaq , Ganai Sajad A. , Naushad Mu. 
Published: April 2010

An amorphous sample of the new hybrid cation-exchanger EDTA–zirconium iodate was synthesized by the combination of the inorganic ion-exchanger zirconium iodate with the organic EDTA molecule, thereby providing a new class of organic–inorganic hybrid ion-exchangers with better mechanical and granular properties, good ion-exchange capacity (e.g. 2 mequiv Na+/g dry exchanger), good reproducibility, a higher stability and demonstrating selectivity towards heavy metal ions. The physicochemical properties of this material were examined by instrumental analyses, viz. FT-IR spectroscopy, X-ray diffraction studies and TGA/DTA investigations. Assessments of the elution and distribution behaviour were made and pH titrations undertaken to obtain an understanding of the ion-exchange behaviour of the material. On the basis of the distribution studies, the material was found to be highly selective towards the Pb2+ ion, a highly toxic environmental pollutant. Its selectivity was assessed by examining its use for some important binary separations such as Mg2+–Pb2+, Cd2+–Pb2+, Hg2+–Pb2+, Zn2+–Pb2+, Cu2+–Pb2+ and Al3+–Pb2+ on a packed column of the material. The practical potential of EDTA–zirconium iodate was explored by separating Mg2+ and Al3+ ions quantitatively from a commercially available pharmaceutical formulation, viz. Digene.01.
Study of Nitrogen-Modified Titanium Dioxide as an Adsorbent for Azo Dyes
Authors: Janus Magdalena , Choina Julia , Kusiak Ewelina , Morawski Antoni W. 
Published: April 2010

The removal of two azo dyes from aqueous solution was investigated using a highly active nitrogen-modified titanium dioxide (TiO2/N). This photocatalyst was prepared by pressure modification of a commercial sample of anatase, TiO2 (supplied by Zaklady Chemiczne Police SA, Poland). The adsorption of two azo dyes (Reactive Red 198 — a monoazo dye and Direct Green 99 — a polyazo dye) onto the unmodified and nitrogen-modified TiO2 surface was determined. Adsorption onto unmodified TiO2 led to an isotherm which could be described by the Freundlich model, whereas that onto the nitrogen-modified TiO2 surface was best described by the Langmuir model. The adsorption isotherms of Direct Green 99 onto TiO2/N from aqueous solutions at various pH values were compared with those onto unmodified TiO2 during dye removal under UV irradiation. Such a comparison is important since it provides information as to how solutes interact with adsorbents. Zeta potential measurements of TiO2 provided an explanation for the observed behaviour in terms of the surface charge. The IR spectrum of the photocatalyst obtained exhibited new absorption bands at 1430–1440 cm−1 which were attributed to the bending vibrations of NH+4 and at 1535 cm−1 associated with NH2 groups or NO2 and NO groups.
Yaw Behavior of Horizontal-Axis Small Wind Turbines in an Urban Area
Authors: Nishizawa Yoshifumi , Tokuyama Hideki , Nakajo Yuichi , Ushiyama Izumi 
Published: April 2010

This paper reports the experimental study on passive yaw behavior of a horizontal axis small wind turbines. The yaw angle velocity in a small wind turbine is one of the significant design values and IEC61400-2 Ed.2 prescribes its maximum value should be less than 3 rad/s. However, in practice, in the case of small wind turbines with diameters under 2 m, the yaw angular velocity may exceed the limit of 3 rad/s. The authors conducted a theoretical evaluation as well as a wind tunnel test to examine the possible maximum yaw velocity. The model wind turbine has a diameter of 1 m, blade number of 5, solidity of 0.26 and 2 types of tail fins (large and small). For each tail fin size, the yaw behavior was studied for a range of rotational speeds and wind speeds. The results show that the yaw angular velocity becomes larger with increasing wind velocity and tail fin area. The larger the rotor rotational speed, the smaller the yaw angular velocity. Furthermore, a maximum yaw angular velocity of 3.84 rad/s was observed at a wind speed of 10 m/s, which exceeds the conventional design value of 3 rad/s.
Temperature Trends in the Lower Atmosphere
Authors: Gray Vincent 
Published: April 2010

A new publication by NOAA (US National Oceanic and Atmospheric Administration) claims to have removed the previously evident discrepancies between mean global temperature anomalies measured on the surface and those measured in the lower troposphere. It claims that a combination of attention to inaccuracies and the use of linear regression equations on selected climate sequences have removed these discrepancies. This paper shows that these claims are untrue. The apparent agreement of the two sets of records for the chosen sequences is dependent on the enhanced influence of volcanoes and El Niño events in the lower troposphere, compared with an additional warming factor on the surface. If a temperature sequence comparatively free from these influences, (1979–1997) is chosen, there is no significant warming in the lower atmosphere for six of the seven records, and for the seventh, no significant warming between 1988 and 1997; whereas warming still prevails on the surface over these periods. The supposed enhanced greenhouse effect is thus currently undetectable in the lower atmosphere, where it is supposed to be most prominent, for extended periods, so the warming on the surface over these periods must have some other cause.
Computational Study of Aero- and Acoustic Performance of a Small Axial-Flow Fan
Authors: Cao Renjing , Lee Duck-Joo 
Published: April 2010

This study aims to predict the overall aerodynamic performance, unsteady forces and the tonal noise radiation from a small axial flow fan. The computation is divided into two stages: (a) the computation of the unsteady flow field at design and off-design working conditions, and (b) detailed analysis of the acoustic field. A dual-time scheme for dealing with rotor-stator or wake-struts interactions in turbomachinery environments by introducing a pseudo-time to represent the time variation of source terms and the finite volume control method are applied for the unsteady solutions involving the whole flow passages of the axial flow fan, and the pressure rise against volume flow rate is obtained and shown to be in good agreement with experimental data. The interaction of the rotor wake and the downstream struts has been simulated by investigating the effects of source distribution over the whole blades. And the tonal noise is then predicted based on Lowson's theory. The unsteady force is divided into thrust in the rotational axis direction and drag in the rotational direction for the rotor and struts. It is demonstrated that the unsteady forces acting on the rotor and struts are produced by the interaction between them, and has a close relationship with the rotor wake structure and the strut alignment. In the rotor near wake, both the viscous and potential flow is dominant not only to aerodynamic forces but also to interaction noise. The present study shows that the higher lean angle of struts can gain about 4 dB reduction of overall sound power level compared to the smallest one.
Digital Design and Manufacture Based on Chiloean Boats
Authors: Dujovne David Butelmann , Montoya Claudio Labarca 
Published: April 2010

This paper proposes a design methodology for the manufacture of complex, double-curved surfaces based on the digital reconstruction of traditional structural and constructive elements of Chiloean boats. It also suggests a beneficial association between digital design and CAD CAM for manufacture using locally crafted construction techniques. The incorporation of innovated contemporary digital design and fabrication tools into traditional construction systems, aims to optimize and perpetuate traditional artisanal craft construction of complex shapes developed in the south of Chile. The importance of this research in budget-restricted economies, lies in the possibility of applying local construction and assembly techniques to new sophisticated designs that may satisfy the country's architectural needs. Scale models are used to record the design process and constructive development while information flow charts document the design methodology for the construction of complex geometries.