bluuebunny/crossref_metadata_2025_split huggingface dataset:
A kinetic model of TBP auto-regulation exhibits bistability
Authors: Gokhale Sucheta A , Roshan Reema , Khetan Vivek , Pillai Beena , Gadgil Chetan J 
Published: August 2010

Abstract

Background
TATA Binding Protein (TBP) is required for transcription initiation by all three eukaryotic RNA polymerases. It participates in transcriptional initiation at the majority of eukaryotic gene promoters, either by direct association to the TATA box upstream of the transcription start site or by indirectly localizing to the promoter through other proteins. TBP exists in solution in a dimeric form but binds to DNA as a monomer. Here, we present the first mathematical model for auto-catalytic TBP expression and use it to study the role of dimerization in maintaining the steady state TBP level.

Results
We show that the autogenous regulation of TBP results in a system that is capable of exhibiting three steady states: an unstable low TBP state, one stable state corresponding to a physiological TBP concentration, and another stable steady state corresponding to unviable cells where no TBP is expressed. Our model predicts that a basal level of TBP is required to establish the transcription of the TBP gene, and hence for cell viability. It also predicts that, for the condition corresponding to a typical mammalian cell, the high-TBP state and cell viability is sensitive to variation in DNA binding strength. We use the model to explore the effect of the dimer in buffering the response to changes in TBP levels, and show that for some physiological conditions the dimer is not important in buffering against perturbations.

Conclusions
Results on the necessity of a minimum basal TBP level support the in vivo observations that TBP is maternally inherited, providing the small amount of TBP required to establish its ubiquitous expression. The model shows that the system is sensitive to variations in parameters indicating that it is vulnerable to mutations in TBP. A reduction in TBP-DNA binding constant can lead the system to a regime where the unviable state is the only steady state. Contrary to the current hypotheses, we show that under some physiological conditions the dimer is not very important in restoring the system to steady state. This model demonstrates the use of mathematical modelling to investigate system behaviour and generate hypotheses governing the dynamics of such nonlinear biological systems.

Reviewers
This article was reviewed by Tomasz Lipniacki, James Faeder and Anna Marciniak-Czochra.
Research Resource: Tissue-Specific Transcriptomics and Cistromics of Nuclear Receptor Signaling: A Web Research Resource
Authors: Ochsner Scott A. , Watkins Christopher M. , LaGrone Benjamin S. , Steffen David L. , McKenna Neil J. 
Published: August 2010

Abstract
Nuclear receptors (NRs) are ligand-regulated transcription factors that recruit coregulators and other transcription factors to gene promoters to effect regulation of tissue-specific transcriptomes. The prodigious rate at which the NR signaling field has generated high content gene expression and, more recently, genome-wide location analysis datasets has not been matched by a committed effort to archiving this information for routine access by bench and clinical scientists. As a first step towards this goal, we searched the MEDLINE database for studies, which referenced either expression microarray and/or genome-wide location analysis datasets in which a NR or NR ligand was an experimental variable. A total of 1122 studies encompassing 325 unique organs, tissues, primary cells, and cell lines, 35 NRs, and 91 NR ligands were retrieved and annotated. The data were incorporated into a new section of the Nuclear Receptor Signaling Atlas Molecule Pages, Transcriptomics and Cistromics, for which we designed an intuitive, freely accessible user interface to browse the studies. Each study links to an abstract, the MEDLINE record, and, where available, Gene Expression Omnibus and ArrayExpress records. The resource will be updated on a regular basis to provide a current and comprehensive entrez into the sum of transcriptomic and cistromic research in this field.
Liquid–Liquid Relaxation in the Supercooled Liquid State of Ethylbenzene: Thermal Studies Using a Prototype DTA Sensor for the Study of Vapor-deposited Samples
Authors: Ishii Kikujiro , Yokoyama Yuki , Moriyama Ryo , Nakayama Hideyuki 
Published: August 2010

Abstract
A prototype sensor for differential thermal analysis (DTA) was developed for in situ studies of the thermal behavior of molecular films vapor-deposited onto a cold substrate in a vacuum. The system was applied to the study of ethylbenzene (EB). By raising the temperature at a constant rate, we observed in the supercooled liquid (SCL) state a small exothermic peak simultaneously with the characteristic light scattering reported previously. These observations and additional optical experiments on the irreversibility of the phenomena indicated that a structural relaxation occurred from a less stable SCL to a more stable SCL.
Synthesis and CO2 Absorption Properties of Single-phase Li2CuO2 as a CO2 Absorbent
Authors: Matsukura Yusuke , Okumura Takeshi , Kobayashi Ryota , Oh-ishi Katsuyoshi 
Published: August 2010

Abstract
Synthesis and CO2 absorption properties of single-phase Li2CuO2 oxide were studied by X-ray powder diffraction and thermogravimetry. Samples of Li2CuO2 were prepared in solid state using Li2CO3 and CuO as starting reagents. A mixture of Li2CO3 and CuO was heated at temperatures of 600–1000 °C and then quenched to room temperature. From XRD, it was found that single-phase Li2CuO2 can be obtained by heat treatment at 680–685 °C with the quenching operation. The single phase was never obtained without quenching; that is, quenching rate (°C s−1) seems to be an important factor which determinates whether sample is obtained as a single phase or not. From thermogravimetry, it was found that Li2CuO2 begins to absorb CO2 at around 230 °C, then drastically absorbs CO2 at over 600 °C, reaching 40.2 mass % maximum CO2 absorption, and finally emits CO2 over 900 °C. The maximum CO2 absorption (40.2 mass %) is larger than that (36.7 mass %) of Li4SiO4 CO2 absorbent.
Resolution of 1,2,3,3a,4,8b-Hexahydrocyclopenta[b]indole via Diastereomeric Salt Formation with N-Tosyl-(R)-phenylglycine
Authors: Higashijima Shinji , Inoue Yukiko , Maehashi Takaya , Miura Hidetoshi , Kubota Yasuhiro , Funabiki Kazumasa , Matsui Masaki 
Published: August 2010

Abstract
Enantiopure 1,2,3,3a,4,8b-hexahydrocyclopenta[b]indole, the starting material of indoline dyes, could be obtained from the diastereomeric salt with N-tosyl-(R)-phenylglycine in ethanol.
Control of Ag+ Permeation by Na+ Concentration on the Basis of Volume Change in Poly(acrylic acid) Gel
Authors: Takada Kazutake , Shibata Atsushi , Yuchi Akio 
Published: August 2010

Abstract
A molecular gate for Ag+ ion, consisting of poly(acrylic acid) (PAA) gel-coated Au mesh, was developed based on a volume change of the gel in response to the Na+ concentration. The permeation of Ag+ through the gate was reduced when the Na+ concentration was lower than 1 × 10−3 M where the gel swells, whereas it increased when the concentration was higher than 1 × 10−2 M where the gel contracts.
Textural and Structural Modification of Homo-Ionic Montmorillonite
Authors: Hassan Mervat S. 
Published: August 2010

The textural and structural modifications of calcium bentonite (CaB) induced by ion exchange, heat treatment and acid leaching were studied by infrared spectroscopy (IR), scanning electron microscopy (SEM) and nitrogen adsorption/desorption methods. The cation-exchange capacities (CEC) and the spontaneous and mechanical dispersion of the heat-treated samples were also measured. CaB taken from the northern coast of Egypt consisting of calcium montmorillonite (85%) and kaolinite, in addition to traces of quartz, was used in this study. CaB and its sodium and lithium forms, NaB and LiB, were calcined at 600 °C for times ranging from 2 h to 20 h, while selected calcined samples were leached with H2SO4 for 1 h. Upon heating, the decrease in the layer charge caused by the fixation of Ca2+, Na+ and Li+ ions in the structure, as revealed by the CEC values, led to an upward shift of the Si–O stretching band in the IR spectrum to the frequency at which the Si–O groups of pyrophyllite absorb. The CEC values showed that the layer charge of the homo-ionic montmorillonite decreased with increasing thermal treatment time and that the amounts of fixed cations were in the order: Li+ > Na+ > Ca2+. The dispersability of the thermally-treated CaB was higher than that of NaB and LiB, both before and after mechanical dispersion. The high dispersability of CaB arises from the inability of the large Ca2+ cation to penetrate further into the lattice. The textural parameters of heated samples showed that the zig-zag alignment of the silicate chains varied as a function of the heat-treatment time, irrespective of the nature of the exchangeable cations. A significant increase in the amount of pores with diameters in the range 13–38 Å was detected in the case of LiB. Heating LiB further for up to 20 h led to a slight increase in the specific surface area and pore volume, but with a considerable reduction in microporosity. On the other hand, thermal treatment after leaching led to a considerable increase in the specific surface areas, pore volumes and microporosities for those samples subjected to heating for a short time, but decreased progressively with increasing heating time, with no difference being observed to the exchangeable cations. This increase in surface area was mainly due to the presence of micropores whose formation was attributed to the leaching of octahedral cations. On the other hand, following calcination for a long time, the magnitude of the textural parameters diminished due to the gradual collapse of the microporous structure.
Status and Constraints of Wind Energy Resources Utilization in Kenya
Authors: Makanga Jacob T. , Ngondi Eric N. 
Published: August 2010

Energy has been identified as the prime mover that propels the wheel of economic development. Access to modern energy affects quality of life and supports the main aspects of sustainable development namely social, equality, economic growth and environmental protection (1). Sub-Saharan Africa and many other countries with low per capita commercial energy consumption continue to exhibit correspondingly low per capita gross domestic products. In a continent where both per capita income and energy consumption are low, the use of renewable energy resources including biomass, solar, wind, geothermal and hydro power energy resources will be among the main solutions to clean and sustainable energy that will fuel economic growth and spearhead the fight against poverty (2–12). In an attempt to reveal the status and constraints of wind energy resources utilization in Kenya, studies were conducted in several parts of the country. The results indicate that utilization of wind energy is possible after overcoming some constraints.
Thoughts about the Acoustic Properties of a Closed Space: An Application to Middle Age Churches in Western Europe
Authors: Vernhes Claude , Drabowitch Serge 
Published: August 2010

The two reasons for this theoretical analysis of the acoustics of medieval churches are: first, to explain how the pointed arch vaulting in the nave is directed to improve acoustic efficiency; and secondly, to show how the architecture of the churches is uniquely configured to produce an extraordinary resonance for the plain-chant. In an enclosed space, the emission of any sound inevitably produces reverberations; but if we construct a vault of appropriate dimensions, then most of this reverberation can be directed in a coherent way without untoward resonance, whatever the timbre of the original sound. The reverberant sound increases loudness and gives the sound a sonority which is particularly advantageous for religious chants. In this study, we shall explain the methodology used and the theory behind the structural characteristics of the pointed arch vaulting [1]. After reviewing the acoustic characteristics of a closed space, we will examine the structures of these churches in relation to specifying the sound bandwidth and reflection quality needed to produce such sonority supported by measurement is of reverberation times. These measurements were made by the University of Genoa in several abbatial churches in Provence.
Second-Order Analysis and Design of Wall-Framed Structures Allowing for Imperfections
Authors: Liu Y.P. , Chan S.L. , Zhou Z.H. , So D. , Yu R. 
Published: August 2010

In design of steel structures including bare steel frames, composite steel-concrete structures and those with walls and slabs, the conventional method considers each member separately and the effective length is then assumed for member resistance check. This involves inconsistency between the analysis method and the design method. The primitive and rather inadequate second-order P-Δ-only analysis considering only the sway effect has been used extensively in industry and in many computer programs. However, as the P-δ effect for member bowing is ignored, the effective length is still required to be assumed for every member. Researchers in PolyU have completed the second-order P-Δ-δ analysis and design method for bare steel frames and recent research has been directed to the design of walled frames such that the effective length is not required for flexural buckling check. In this paper, the structural shear wall is modeled by finite shell element whereas the imperfect stability function is employed to model beam-column members. The slab is proposed to be modeled by efficient floor elements. The model is compared well with the results by others. The P-δ effect for member bowing is considered so that the section capacity check alone is sufficient to check the structural adequacy without the assumption of effective length, classification of sway and non-sway frame mode and the tedious individual member resistance check.
Measurements and wall Modeled LES Simulation of Trailing Edge Noise Caused by a Turbulent Boundary Layer
Authors: Greschner Björn , Grilliat J. , Jacob M.C. , Thiele F. 
Published: August 2010

A successful comparison between CFD-CAA and measurements of trailing edge noise is shown for a highly loaded and cambered NACA 5510 airfoil at a chord based Reynolds number of aprox. 1 million placed in a quiet low Mach number flow. The simulation is based on a new variant of the DES - the Improved Delayed Detached Eddy Simulation (IDDES). The flow is fully attached to the airfoil and therefore only the small turbulent boundary structures that interact with the trailing edge generate significant broadband noise in the far field. The IDDES approach is designed to extend the LES region of the original DES approach (hybrid RANS/LES) from Spalart et. al. (1997) to the turbulent boundary layer, as proposed first by Travin et. al. in 2006. The non-zonal blending occures therefore inside the boundary layer - the RANS model acts as a wall model for the LES. The actual work shows the capabilities of this novel approach for the simulation of broadband noise for attached flows. The simulation is compared to measurements from the EC Lyon including PIV and LDA data around the airfoil and unsteady on-wall pressure measurements near the trailing edge. Far field computations are carried out by applying the Ffowcs–Williams and Hawkings analogy to the unsteady wall pressure field and compared to acoustic measurements as well as to a far field prediction based on a trailing edge noise model that is applied to the experimental aerodynamic pressure field.
Explosions in Complex Geometries — A Comparison of Several Approaches
Authors: Larcher Martin , Casadei Folco 
Published: August 2010

For the design and calculation of structures loaded by air blast waves, especially from inside the structure, assumptions on the applied load are needed. This paper presents several simulation methods for the air blast loading of structures and their ability to be used for complex geometries. Experimental-analytical pressure-time functions of spherical load conditions applied to the structure by disregarding the air are not applicable in such cases because they do not account for reflections, shadowing and channelling effects. Fluid calculations, which model also the solid explosive, are very expensive due to the extremely small elements for the explosive and the air nearby. This paper therefore presents a review of a well-known simulation method, which uses a balloon with compressed air instead of the explosive. A procedure is developed which makes it possible to determine the overpressure of such a balloon for a given size of the explosive more accurately than before. The pressure-time function and the impulse-distance function of calculations using this method show good correspondence with experimental-analytical data. The functioning of the method is verified against experimental results.
Analysis of Fracture in Aluminum Joints Bonded with a Bi-Component Epoxy Adhesive
Authors: Alfano M. , Furgiuele F. , Pagnotta L. , Paulino G. H. 
Published: August 2010

Abstract
Adhesive bonding is a viable alternative to traditional joining systems (e.g., riveting or welding) for a wide class of components belonging to electronic, automotive, and aerospace industries. However, adhesive joints often contain flaws; therefore, the development of such technology requires reliable knowledge of the corresponding fracture properties. In the present paper, the candidate mode I fracture toughness of aluminum/epoxy joints is determined using a double cantilever beam fracture specimen. A proper data reduction scheme for fracture energy calculation has been selected based on the results of a sensitivity analysis. Furthermore, a scanning electron microscope is used in order to explore the locus of failure. Finally, the experimental findings are assessed by means of numerical simulations of crack growth carried out using a cohesive zone model.
Pituitary adenomas in childhood, adolescence and young adulthood: presentation, management, endocrine and metabolic outcomes
Authors: Steele Caroline A , MacFarlane Ian A , Blair Joanne , Cuthbertson Daniel J , Didi Mohammed , Mallucci Conor , Javadpour Mohsen , Daousi Christina 
Published: August 2010

ObjectiveTo elucidate the long-term outcomes of pituitary adenomas diagnosed in childhood and adolescence, knowledge of which remains sparse.Design and methodsA retrospective review of patients aged ≤21 years at diagnosis of pituitary adenoma, attending a neuroendocrine service in Liverpool, UK, between 1984–2009.ResultsThere were 41 patients (33 female), mean age at diagnosis 17.3 years (range 11–21) and mean follow-up 9.6 years; 29 patients had prolactinomas (15 macroprolactinomas), 6 non-functioning pituitary adenomas (NFPAs), 5 Cushing's disease (CD) and 1 acromegaly. All prolactinoma patients received dopamine agonists (DAs) and three also underwent pituitary surgery. Furthermore, ten patients underwent surgery: five with CD, one with acromegaly and four with NFPA. Four received radiotherapy after surgery. Another ten patients received hormone replacement: nine hydrocortisone, five thyroxine, seven sex steroids and five GH; another seven had severe asymptomatic GH deficiency. Three female patients were treated for infertility (two successfully). Thirteen patients gained significant weight (body mass index (BMI) increase >2 kg/m2) since diagnosis and 16 in total are now obese (BMI>30 kg/m2). Five were treated with orlistat and one attended a weight management service. Two received antihypertensive medications, two had type 2 diabetes and four were treated for dyslipidaemia.ConclusionsThis is one of the largest reviews of patients aged 21 or younger at diagnosis of pituitary adenoma followed up by a single service. Two-thirds had prolactinomas, all were treated with DAs and three underwent surgery. Increased cardiovascular risk factors (obesity and dyslipidaemia) and infertility are important sequelae and active identification and treatment are necessary.
A Concept of the Object State Identification
Authors: Grabski Franciszek , Jaźwiński Jerzy 
Published: August 2010

A Concept of the Object State Identification
Relations between features and requirements are the basis for an object state identification. States of the object are defined by a finite partition of the Cartesian product of the future space C and the requirements space W. In many cases there are possible measurement random errors in assessing futures of the object. Hence, two type errors may be made. A I - Type error and a II -Type error are defined in this paper. Several examples of the introduced notions application are presented in this paper.
Reliability Assessment of Existing Concrete Bridges
Authors: Marková Jana 
Published: August 2010

Reliability Assessment of Existing Concrete Bridges
The remaining working life of an existing reinforced concrete bridge is analysed considering the serviceability limit states of crack width. Two new models of crack width provided Eurocode EN 1992 and in the Model Code 2010 are applied. The probabilistic methods of structural reliability are used for assessing the crack width limits and remaining working life of existing concrete bridges. It appears that the initial reliability with respect to the serviceability requirements resulting from the original design of the bridge seems to satisfy the required target reliability level recommended in Eurocodes. However, the reliability index significantly decreases with the reduction of the reinforcement area due to corrosion.
Fuzzy Interpretation of a Transport System Operation Quality Assessment
Authors: Muślewski Łukasz 
Published: August 2010

Fuzzy Interpretation of a Transport System Operation Quality Assessment
The paper deals with issues connected with an assessment of transport systems operation quality. The considerations concern real, systems with an intended set of operations, belonging to socio - technical systems of the type whose operation quality assessment is performed depending on value changes of features describing actions of operators, technical objects operated by them and he impact of he environment. Their assessment and providing them with the required functional and operational quality, both in terms of their operation safety efficiency, reliability and ecology, provides basis for accomplishment of the transport service according to the set requirements. This work presents possibilities of application of elements of fuzzy logic in selected stages of the assessment, on the basis of the developed method and the assessment model. Operation quality has been defined as being expressed by means of numerical values identified features, whereas it should be emphasized, that in some cases their direct identification is a significant problem. In connection with this, there was built a fuzzy assessment model for which the scope of changes of the system analyzed features is covered with fuzzy numbers, whereas, their sharp values account for the model initial data. Then, there was presented a fuzzy representation of values of features determined for the system assessment, their graphic interpretation was presented, along with an example of application of fuzzy logic elements for a municipal transport system assessment.
Computer-Aided Risk Analysis of Power Units
Authors: Rusin Andrzej , Wojaczek Adam 
Published: August 2010

Computer-Aided Risk Analysis of Power Units
Analysis of technical risk connected with operation of power units constitutes very important element of general assessment of operation quality. It takes into consideration and connects together economic aspects and unit operation safety. The SKOR computer software described below is provided for technical risk quantitative assessment created by power units elements. Results of calculations of damage probability of turbine caused by various damages scenarios are presented in the paper. The programme allows the risk assessment in off-line mode of specific power unit. It may constitute an essential help for inspection, control, planning, operation and repairs services.