bluuebunny/crossref_metadata_2025_split huggingface dataset:
The roles of binding site arrangement and combinatorial targeting in microRNA repression of gene expression
Authors: Hon Lawrence S , Zhang Zemin 
Published: August 2007

Abstract
Background
MicroRNAs (miRNAs) are small noncoding RNAs that bind mRNA target transcripts and repress gene expression. They have been implicated in multiple diseases, such as cancer, but the mechanisms of this involvement are not well understood. Given the complexity and degree of interactions between miRNAs and target genes, understanding how miRNAs achieve their specificity is important to understanding miRNA function and identifying their role in disease.

Results
Here we report factors that influence miRNA regulation by considering the effects of both single and multiple miRNAs targeting human genes. In the case of single miRNA targeting, we developed a metric that integrates miRNA and mRNA expression data to calculate how changes in miRNA expression affect target mRNA expression. Using the metric, our global analysis shows that the repression of a given miRNA on a target mRNA is modulated by 3' untranslated region length, the number of target sites, and the distance between a pair of binding sites. Additionally, we show that some miRNAs preferentially repress transcripts with longer CTG repeats, suggesting a possible role for miRNAs in repeat expansion disorders such as myotonic dystrophy. We also examine the large class of genes targeted by multiple miRNAs and show that specific types of genes are progressively more enriched as the number of targeting miRNAs increases. Expression microarray data further show that these highly targeted genes are downregulated relative to genes targeted by few miRNAs, which suggests that highly targeted genes are tightly regulated and that their dysregulation may lead to disease. In support of this idea, cancer genes are strongly enriched among highly targeted genes.

Conclusion
Our data show that the rules governing miRNA targeting are complex, but that understanding the mechanisms that drive such control can uncover miRNAs' role in disease. Our study suggests that the number and arrangement of miRNA recognition sites can influence the degree and specificity of miRNA-mediated gene repression.
A simple projection moiré system to measure displacements of aircraft structures
Authors: Galietti U , Genovese K , Lamberti L , Posa D 
Published: August 2007

This work presents a simple projection moiré system (PMS) to measure displacements of large-scale aeronautical components. The system includes standard optics, uses a standard fringe-processing method, and relies on a simple analytical model to recover topographic information. An extensive calibration campaign, based on design of experiments, is conducted in order to find the best analytical model for retrieving the out-of-plane displacement field from the moiré pattern and to find the optimal combination of parameters involved in the measurement system. In order to check the suitability of the present PMS device for practical industrial applications, distortions induced by aerodynamic loads on a landing-light glazing of an Airbus A340 are measured. Experimental results are in good agreement with other measurements carried out independently.
Finite element method analysis of a spur gear with a corrected profile
Authors: Pasta A , Mariotti G Virzí 
Published: August 2007

The difference between the stress value calculated by a two-dimensional finite element model of spur gears and those obtained by the rules in ISO 6336 was evaluated. Hertz theory, which provides information on the extension of the contact area and the maximum value of the contact pressure, was used to choose the dimensions of the elements. The mesh was created using the stress analytical solution relative to a model consisting of two cylinders in contact. Analogous optimization was executed for the mesh of the teeth feet; a mesh of 15 elements was considered optimum, because it minimized the difference to 0.5 per cent in the bending stress calculation. Stress values, obtained using the finite element method (FEM), are generally lower than those obtained with the ISO rules. Hence, this approach yields a conservative determination of the effective material strength. In all the examined cases, the difference was less than 2.5 per cent. The set FEM technique gives a result accuracy of better than 1 per cent; the difference between the stress obtained by FEM and those obtained by ISO 6336 is less than 2.5 per cent, so that the FEM confirmed, consistent with the ISO rules, that correction of the profile results in significant benefits with respect to determination of the mechanical resistance of spur gears.
Optimization of stratification combustion in a spark ignition engine by double-pulse port fuel injection
Authors: Wang T , Peng Z , Liu S-L , Xiao H-D , Zhao H 
Published: August 2007

The potential of lean burn in a spark-ignition (SI) engine with optimized fuel injection was experimentally investigated and numerically simulated. The experiments were carried out on a production SI engine which has a port fuel injection (PFI) system. The previous port electronic fuel injection system was modified and the technique of double-pulse fuel injection (DFI) was employed. By regulating injection timings and proportions of DFI, the air-fuel mixture stratification was significantly improved and the expected lean burn was implemented. The experimental results showed that the reduction of fuel consumption with DFI could be above 10 per cent over quite a wide load range, compared to single fuel injection. With optimized fuel injection timings and double-pulse proportions, the ideal engine performance and emissions can be achieved with a two to three times higher air-fuel ratio (AFR) than single fuel injection. With numerical simulation, the effects of mixture stratification formed by different fuel injection amounts and timings were analysed using a phenomenological model. The mixture in the cylinder was divided into different regions that distribute spherically around the spark plug and consist of a central region of stoichiometric air-fuel mixture and a gradually leaner outside region. Simulation results demonstrated that the improvements in fuel economy and emissions with DFI were mainly attributed to increased stratification zones and a reduced AFR gradient in the stratification zones.
Residual gas fraction measurement and computation
Authors: Giansetti P , Colin G , Higelin P , Chamaillard Y 
Published: August 2007

To meet future pollutant emissions standards, it is crucial to be able to estimate not only the cycle-by-cycle mass but also the cycle-by-cycle composition of the combustion chamber charge. This charge consists of fresh air, fuel, and residual gas from the previous cycle. Unfortunately, the residual gas fraction cannot be directly measured. Two experimental methods have been designed to determine the residual gas fraction. The reference method is based on an in-cylinder sampling method. The second one is based on a hydrocarbon (HC) analysis of the exhaust gases. Two models have been compared to the experimental results. A one-dimensional computational fluid dynamics (CFD) code (WAVE) and a zero-dimensional model (AMESIM), which takes into account gas compressibility. The aim of the study was to compare the results of CFD codes (one- and zero-dimensional) to experimental results. If the code is validated by the experiments, it should be possible to determine residual gas fractions without needing a large experimental set-up.
A study of the dimethyl ether spray characteristics and ignition delay
Authors: Kim Y , Lim J , Min K 
Published: August 2007

The characteristics of the spray behaviour and ignition delay of dimethyl ether (DME) were investigated in both experiment and simulation. DME spray images were taken in a constant-volume vessel by using Mie scattering and shadowgraph methods to measure the spray tip penetration and the spray angle of the liquid and vapour phase. The images were acquired at low- and high-temperature conditions and it was found that the spray development was dependent on the ambient density. The ignition delay of DME spray was also measured under high pressure and temperature conditions and compared with that of diesel spray in the same conditions. To predict the ignition and combustion characteristics of DME, a reduced chemical kinetic mechanism consisting of 28 species and 45 reactions was derived from a detailed mechanism. Calculated results in homogeneous conditions agreed well with the measured data from shock tube experiments. Then three-dimensional simulation of spray development and ignition delay of DME spray was performed using a flamelet model associated with a computational fluid dynamics (CFD) code and the reduced chemical kinetic mechanism. The results showed good agreement with the above experimental results.
Stress and fatigue analysis of a bow-door arm
Authors: Karlsson U , Ulfvarson A , Johnson E , Kjell G 
Published: August 2007

Bow-door systems are designed according to the class rules, of which the IACS UR S8 rules serve as a base. Even though bow-door arms, with the purpose of carrying the bow-doors in an open position, are subjected to some dynamic loads, they are dimensioned according to static loads. On one ferry, a large crack arose in one of the bow-door arms. If the arm had cracked off completely, the bow-door would probably have been lost at sea, as the arm was part of the locking arrangement. This analysis has been carried out in order to analyse whether arms, dimensioned according to a static load, should be allowed to be a part of the locking arrangements of bow-doors. The analysis was carried out with field measurements, in the form of strain and acceleration measurements on an arm during the different load cases it is subjected to. The measured results were applied on a finite element model of the arm in order to find the stress and stress ranges everywhere in the arm during the different load cases. With this information, areas subjected to large stress ranges were identified for which fatigue calculations were carried out. None of the load cases proved to give rise to any serious fatigue, except for the bow propellers, which, in certain situations, excite the arms into resonance cycling. The resonance gives rise to a great number of stress cycles with amplitudes large enough to cause fatigue failure.
Potential seasonal predictability of the observed Euro‐Atlantic atmospheric variability using SST forced ECHAM4‐T42 simulations
Authors: Friederichs P. , Frankignoul C. 
Published: August 2007

AbstractTo estimate the potential seasonal predictability of the Euro‐Atlantic atmospheric variability, canonical correlation analysis is used, and a comparison is made between the NCEP reanalysis with ensemble simulations of ECHAM4‐T42 forced with observed sea surface temperature (SST) and sea‐ice boundaries for 1951–94 and changing CO2 concentration. The method identifies those atmospheric modes of variability that have similar temporal evolution in the observations and the ensemble mean of the simulations. Signals due to long‐term changes in the forcing were first reduced by removing a third‐order polynomial from all data.Significant covariability in the 500 hPa geopotential height over the Euro‐Atlantic region is found from autumn to spring. The best agreement between the patterns is seen in late winter, where a mixed Pacific–North America (PNA) and tropical/northern‐hemisphere teleconnection pattern is the dominant signal. Although it tends to modulate the North Atlantic Oscillation (NAO), the direct influence over Europe is limited. In all cases, the covariability seems to be due to remote forcing by tropical Pacific SST. However, the model response to the El Niño Southern Oscillation (ENSO) always shows a PNA pattern, while the related observed signal undergoes large seasonal changes.The sea level pressure (SLP) over the Euro‐Atlantic region seems to be much less sensitive to remote ENSO forcing, although traces of its influence can be detected in late winter. On the other hand, a highly significant covariability is found between modelled and observed SLP anomalies in autumn, reflecting the influence of the North Atlantic SST on the NAO. However, the model does not reproduce the observed SLP structure. It is also shown that the reproducibility of the NAO in the undetrended ECHAM4 ensemble simulations in winter that was found by Latif et al. in the same simulations is related to long‐term trends in tropical Pacific and Indian Ocean SST variability. However, its origin cannot be determined as the CO2 concentration was specified from the observations in the simulations. Copyright © 2003 Royal Meteorological Society
On a threefold classification of extratropical cyclogenesis
Authors: Plant R. S. , Craig G. C. , Gray S. L. 
Published: August 2007

AbstractA recently proposed extension to the twofold extratropical cyclogenesis classification scheme of Petterssen and Smebye is discussed. A third class of extratropical cyclone (type C) is described, in which initial development is controlled by a pre‐existing upper‐level potential vorticity (PV) anomaly. In its early stages, such a system is indistinguishable from the classical type B cyclone of the Petterssen and Smebye scheme. However, subsequent development cannot be understood in terms of a co‐operative interaction of the upper‐level feature with a low‐level baroclinic zone. Rather, the cyclogenetic dynamics of type C systems are dominated by the action of strong midlevel latent heating. Such heating can generate important anomalies of PV that act to suppress the formation of a low‐level thermal anomaly and that interact destructively with the pre‐existing upper‐level feature.Candidate type C events are identified using recently developed, height‐attributable, quasi‐geostrophic, vertical‐motion diagnostics. The application of one such diagnostic to a climatology of instantaneous cyclonic features suggests that type C events may occur with reasonable frequency. The generic behaviour of system types in the proposed threefold classification scheme is compared with the actual dynamics of some cyclones from the Fronts and Atlantic Storm‐Track EXperiment (FASTEX). The analysis is based on piecewise PV inversions and numerical simulations. This approach is able to provide a good description of a case of standard type B development, consistent with the qualitative description of Petterssen and Smebye and with the quasi‐geostrophic diagnostics. Within the same framework, two systems are discussed whose behaviours do not fit the simple A/B classification, but are consistent with the proposed type C mechanism. Copyright © 2003 Royal Meteorological Society
Nonlinear growth of singular‐vector‐based perturbations
Authors: Reynolds C. A. , Rosmond T. E. 
Published: August 2007

AbstractThe nonlinearity of singular‐vector‐based (SV‐based) perturbation growth is examined within the context of a global atmospheric forecast model. The characteristics of these nonlinearities and their impact on the utility of SV‐based diagnostics are assessed both qualitatively and quantitatively. Nonlinearities are quantified by examining the symmetry of evolving positive and negative ‘twin’ perturbations. Perturbations initially scaled to be consistent with estimates of analysis uncertainty become significantly nonlinear by 12 h. However, the relative magnitude of the nonlinearities is a strong function of scale and metric. Small scales become nonlinear very quickly while synoptic scales can remain significantly linear out to three days. Phase differences between the positive and negative perturbation patterns relative to each other can result in significant nonlinearities even when the basic anomaly patterns are quite similar. Thus, SVs may be qualitatively useful even when nonlinearities are large.Post‐time forecast corrections using SV‐based pseudo‐inverse perturbations show that, despite significant nonlinear perturbation growth, the nonlinear forecast corrections are similar to the expected linear corrections, even at 72 h. When the nonlinear correction does differ significantly from the expected linear correction, the nonlinear correction is usually better, indicating that in some cases the pseudo‐inverse correction effectively suppresses error growth outside the subspace defined by the leading (dry) SVs. Because a significant portion of the nonlinear growth occurs outside of the dry SV subspace, an a priori relative nonlinearity index based on the full perturbations is not a good predictor of when pseudo‐inverse‐based corrections will be ineffective. However, one can construct a reasonable predictor of pseudo‐inverse ineffectiveness by considering the nonlinearities in the synoptic scales or in the SV subspace only. Copyright © 2003 Royal Meteorological Society
Diverse mechanisms and machineries for import of mitochondrial proteins
Authors: Milenkovic Dusanka , Müller Judith , Stojanovski Diana , Pfanner Nikolaus , Chacinska Agnieszka 
Published: August 2007

Abstract
Mitochondria are ubiquitous organelles that play an essential role in energy conversion and biosynthetic pathways in eukaryotic cells. Most mitochondrial proteins must be imported from the cytosol and sorted into one of the four mitochondrial subcompartments, the outer membrane, the intermembrane space, the inner membrane and the matrix. Studies in recent years revealed a remarkable diversity of mechanisms and machineries that are required for the import of proteins into mitochondria. At least four different pathways for the sorting and assembly of nuclear-encoded mitochondrial proteins have been identified.
Cellular expression of plasma prekallikrein in human tissues
Authors: Fink Edwin , Bhoola Kanti D. , Snyman Celia , Neth Peter , Figueroa Carlos D. 
Published: August 2007

Abstract
Plasma prekallikrein (PPK) is synthesised in hepatocytes and secreted into the blood, where it participates in the surface-dependent activation of blood coagulation, fibrinolysis, kinin generation and inflammation. Recently we demonstrated by quantitative RT-PCR that the human PPK gene is transcribed not only in the liver, but also in various non-hepatic human tissues at significant levels. However, up to now no reliable information is available concerning protein synthesis in the corresponding human tissues. Here we demonstrate by immunohistochemical studies that PPK or plasma kallikrein (PK) is localised in cells of different embryologically derived human tissues. In the human nephron, single cells of the distal tubules stained intensely, while the cytoplasm of cells forming proximal tubules and collecting ducts stained uniformly. PPK/PK was localised in hepatic epithelial cells of the liver, in cells of the pancreatic islet of Langerhans, in the interstitial Leydig cells of the testes, in the follicular and thecal granulosa cells of the ovary, and in the parotid gland, oesophagus, skin, respiratory tract, prostate and breast. We conclude that the cellular localisation of PPK/PK in multiple different progenitor-derived cells indicates specific cellular functions of this enzyme, in addition to its known function in the blood.
Sumoylation of the zinc finger protein ZXDC enhances the function of its transcriptional activation domain
Authors: Jambunathan Srikarthika , Fontes Joseph D. 
Published: August 2007

Abstract
The transcription of major histocompatibility complex class II (MHC II) genes is dependent on the co-activator protein class II trans-activator (CIITA). We have recently identified a protein known as zinc finger X-linked duplicated family member C (ZXDC) that, along with its binding partner ZXDA, forms a complex that interacts with CIITA and regulates MHC II transcription. Western blot analysis with anti-ZXDC antibodies identified two species of the ZXDC protein, one migrating near its predicted molecular mass and one with slower electrophoretic mobility. We report here that the slower migrating form is the result of sumoylation at a single lysine residue within the transcriptional activation domain of ZXDC. Three SUMO proteins (SUMO-1, -2 and -3) can modify the ZXDC protein. Multiple SUMO E3 ligase enzymes and HDAC4 can facilitate ZXDC sumoylation, and one ligase, PIASy, interacts with a specific region of the ZXDC protein. We found that sumoylation does not appear to disrupt or modulate the interaction of ZXDC with its binding partners. Rather, sumoylation of ZXDC is required for full activity of the transcriptional activation domain. Our findings suggest that sumoylation is an important regulator of ZXDC.
Molecular machinery of mitochondrial dynamics in yeast
Authors: Merz Sandra , Hammermeister Miriam , Altmann Katrin , Dürr Mark , Westermann Benedikt 
Published: August 2007

Abstract
Mitochondria are amazingly dynamic organelles. They continuously move along cytoskeletal tracks and frequently fuse and divide. These processes are important for maintenance of mitochondrial functions, for inheritance of the organelles upon cell division, for cellular differentiation and for apoptosis. As the machinery of mitochondrial behavior has been highly conserved during evolution, it can be studied in simple model organisms, such as yeast. During the past decade, several key components of mitochondrial dynamics have been identified and functionally characterized in Saccharomyces cerevisiae. These include the mitochondrial fusion and fission machineries and proteins required for maintenance of tubular shape and mitochondrial motility. Taken together, these findings reveal a comprehensive picture that shows the cellular processes and molecular components required for mitochondrial inheritance and morphogenesis in a simple eukaryotic cell.
Mechanisms of protein import into thylakoids of chloroplasts
Authors: Schünemann Danja 
Published: August 2007

Abstract
The thylakoid membrane of chloroplasts contains the major photosynthetic complexes, which consist of several either nuclear or chloroplast encoded subunits. The biogenesis of these thylakoid membrane complexes requires coordinated transport and subsequent assembly of the subunits into functional complexes. Nuclear-encoded thylakoid proteins are first imported into the chloroplast and then directed to the thylakoid using different sorting mechanisms. The cpSec pathway and the cpTat pathway are mainly involved in the transport of lumenal proteins, whereas the spontaneous pathway and the cpSRP pathway are used for the insertion of integral membrane proteins into the thylakoid membrane. While cpSec-, cpTat- and cpSRP-mediated targeting can be classified as ‘assisted’ mechanisms involving numerous components, ‘unassisted’ spontaneous insertion does not require additional targeting factors. However, even the assisted pathways differ fundamentally with respect to stromal targeting factors, the composition of the translocase and energy requirements.