bluuebunny/crossref_metadata_2025 huggingface dataset:
Influence of surgical preparation on the in-vivo response of osteochondral defects
Authors: Vizesi F , Oliver R , Smitham P , Gothelf T , Yu Y , Walsh W R
Published: August 2007

Cartilage has an extremely poor capacity to heal, which has lead to intensive research into biomaterials and tissue engineering for the purpose of regenerating cartilage in vivo. Many of these techniques have shown great promise in vitro; however, the results do not always carry across to the in-vivo scenario. Healthy cartilage autografts often do not integrate with the adjacent cartilage, suggesting that cartilage is rarely capable of healing even under ideal conditions. It is hypothesized in this study that the surgical creation of defects in cartilage causes significant damage to the adjacent tissues, leading to further degradation of the cartilage and poor outcome for the repair in general. This study compares the healing response of osteochondral defects created with either a punch or a drill in the weight-bearing region of the sheep knee at 4 and 26 weeks following surgery. The use of a drill to create the defect creates a more aggressive inflammatory response at 4 weeks compared with a punch. However, by 26 weeks, defects created with a punch scored higher on the O'Driscoll cartilage grading scale. Tissue damage at the time of surgery plays an important part in the sequence of events for healing of cartilage defects. This knowledge will help to characterize and refine the ovine model for cartilage regeneration and may have an influence on surgical technique and instrumentation for clinical cartilage repair.
Gene therapy for articular cartilage repair
Authors: Trippel S , Cucchiarini M , Madry H , Shi S , Wang C
Published: August 2007

Articular cartilage serves as the gliding surface of joints. It is susceptible to damage from trauma and from degenerative diseases. Restoration of damaged articular cartilage may be achievable through the use of cell-regulatory molecules that augment the reparative activities of the cells, inhibit the cells' degradative activities, or both. A variety of such molecules have been identified. These include insulin-like growth factor I, fibroblast growth factor 2, bone morphogenetic proteins 2, 4, and 7, and interleukin-1 receptor antagonist. It is now possible to transfer the genes encoding such molecules into articular cartilage and synovial lining cells. Although preliminary, data from in-vitro and in-vivo studies suggest that gene therapy can deliver such potentially therapeutic agents to protect existing cartilage and to build new cartilage.
Stem cells for tissue engineering of articular cartilage
Authors: Gao J , Yao J Q , Caplan A I
Published: August 2007

Articular cartilage injuries are one of the most common disorders in the musculo-skeletal system. Injured cartilage tissue cannot spontaneously heal and, if not treated, can lead to osteoarthritis of the affected joints. Although a variety of procedures are being employed to repair cartilage damage, methods that result in consistent durable repair tissue are not yet available. Tissue engineering is a recently developed science that merges the fields of cell biology, engineering, material science, and surgery to regenerate new functional tissue. Three critical components in tissue engineering of cartilage are as follows: first, sufficient cell numbers within the defect, such as chondrocytes or multipotent stem cells capable of differentiating into chondrocytes; second, access to growth and differentiation factors that modulate these cells to differentiate through the chondrogenic lineage; third, a cell carrier or matrix that fills the defect, delivers the appropriate cells, and supports cell proliferation and differentiation. Stem cells that exist in the embyro or in adult somatic tissues are able to renew themselves through cell division without changing their phenotype and are able to differentiate into multiple lineages including the chondrogenic lineage under certain physiological or experimental conditions. Here the application of stem cells as a cell source for cartilage tissue engineering is reviewed.
Characteristics of low temperature and low oxygen diesel combustion with ultra-high exhaust gas recirculation
Authors: Ogawa H , Li T , Miyamoto N
Published: August 2007

Ultra-low NOx and smokeless operation at higher loads up to half of the rated torque is attempted with large rates of cold exhaust gas recirculation (EGR). NOx decreases below 6 ppm (0.05 g/kW h) and soot significantly increases when first decreasing the oxygen concentration to 16 per cent with cold EGR. However, after peaking at 12–14 per cent oxygen, soot then decreases sharply to essentially zero at 9–10 per cent oxygen while maintaining ultra-low NOx, regardless of fuel injection quantity and injection pressure. However, at higher loads, with the oxygen concentration below 9–10 per cent, the air-fuel ratio has to be over-rich to exceed half of the rated torque, and thermal efficiency, CO, and THC deteriorate significantly. As the EGR rate increases, exhaust gas emissions and thermal efficiency vary with the intake oxygen content rather than with the excess air ratio. Longer ignition delays due to either advancing or retarding the injection timing reduced the smoke emissions, but advancing the injection timing has the advantages of maintaining the thermal efficiency and preventing misfiring. A reduction in the compression ratio is effective to reduce the in-cylinder temperature and increase the ignition delay as well as to expand the smokeless combustion range in terms of EGR and i.m.e.p. (indicated mean effective pressure).
Sustainable technologies for inland leisure craft
Authors: Landamore M J , Birmingham R W , Downie M J , Wright P N H
Published: August 2007

This paper presents the results of a study of sustainable technologies that could be used in the design of an inland leisure craft carried out with particular reference to the Norfolk and Suffolk Broads. The first phase of the study involved identifying the appropriate technologies and ranking them using stakeholder consultation and expert opinion. Subsequently life cycle analysis and life cycle costing were carried out for a hypothetical fleet of leisure craft utilizing the identified high-ranking technologies. On the basis of the outcome of the analyses, cost effective eco-friendly technologies have been identified for leisure craft design within specified scenarios.
Near‐real‐time approach to assimilation of satellite‐retrieved 3D ozone fields in a global model using a simplified Kalman filter
Authors: El Serafy G. Y. , Kelder H. M.
Published: August 2007

In this paper, a near‐real‐time approach to data assimilation for the estimation of the three‐dimensional global ozone distribution based on the transport model TM3 is presented. TM3 uses the meteorological data from European Centre for Medium‐Range Weather Forecasts to transport the ozone field. The ozone profiles used in the assimilation are retrieved from measurements of the Global Ozone Monitoring Experiment instrument (GOME) on the European Space Agency's European Remote Sensing‐2 satellite. A simplified Kalman filter technique is chosen as a data assimilation technique since it not only estimates the ozone distribution globally but also quantifies the uncertainty in its estimate. The NRT data assimilation technique is demonstrated for the period of March–June 2000. The results presented in this paper show that the estimated profiles deviate from the measurements by, on a global average, 15% of the ozone values in pressure layer 163–119 hPa and ranging from 6% to 2% of the ozone values between 119 hPa and 40 hPa. The deviation of the estimate from the measurements decreases with altitude and reaches 0.05% of the ozone value in the layer 2–0 hPa. Comparison with ozone‐sonde observations shows that the model driven by observed meteorological fields is capable of describing the main spatial and temporal variations. Comparison with data from the Halogen Occultation Experiment instrument on the Upper Atmosphere Research Satellite shows that assimilating the retrieved profiles from GOME improves the vertical description of ozone profiles mainly in the stratosphere and the upper troposphere. Moreover, the integrated ozone‐profile estimate is compared with the total‐column ozone measurements made by the Total Ozone Mapping Spectrometer. This shows that assimilating the ozone profiles results in a better description of the total column than the ten‐day forecast. Copyright © 2003 Royal Meteorological Society
Experiments on 4D‐Var assimilation of rainfall data using an incremental formulation
Authors: Marécal Virginie , Mahfouf Jean‐François
Published: August 2007

Assimilations of isolated surface rainfall observations are performed using two methodologies compatible with the incremental formulation of the European Centre for Medium‐Range Weather Forecasts operational 4D‐Var system. In a first method (defined as ‘1D−Var+4D−Var’) 1D‐Var retrievals of total column water vapour in rainy areas are assimilated in 4D‐Var, while a second approach assimilates rainfall rates in 4D‐Var directly. In addition, the behaviour of two contrasted convection schemes (mass‐flux and adjustment) is examined. The minimization performs generally better for the adjustment scheme and for the ‘1D−Var+4D−Var’ method (i.e. larger decrease of the cost function). The usefulness of the direct 4D‐Var is limited by various inconsistencies present in the current incremental formulation and by the extreme sensitivity of the convection schemes to small changes in humidity. The two methods produce similar and small modifications to the dynamical fields, that are partly explained by the fact that the observation is assimilated early in the time window of 4D‐Var (3 hours). This study demonstrates the need for convection schemes with smooth Jacobians in the variational context. It also confirms the robustness of the ‘1D−Var+4D−Var’ approach than can be used for operational rainfall‐rate assimilation as long as identified problems with the incremental 4D‐Var are not solved. Copyright © 2003 Royal Meteorological Society
Early detection of abnormal weather conditions using a probabilistic extreme forecast index
Authors: Lalaurette F.
Published: August 2007

A new method to extract information related to unusual forecast distributions from probabilistic (e.g. ensemble) prediction systems is presented. It consists of an extreme forecast index (EFI) that ranks the departure between the forecast and the model climate between −1 (forecast given 100% probability that record‐breaking low values will be reached) and +1 (record‐breaking high values). First the new index is derived, it is related to other measures of statistical significance, and a few properties are given. It is then demonstrated how the accumulation of ensemble forecasts every day allows the quick build‐up of a model pseudo‐climate that is representative enough to detect large departures from normal conditions while being representative of the latest developments in terms of resolution or physical parametrizations. The EFI is then subjected to several severe weather events that have happened in Europe over the last few years, and it is shown to be potentially useful in alerting forecasters to the risk of severe weather up to three or four days in advance. Finally, objective verification over five months in 2001–02 is presented. Although the results confirm that the model pseudo‐climate is good enough to set up thresholds for severe weather evenly throughout Europe, the false‐alarm rates are much larger than usually expected by forecasters or users. It is argued, however, that operating characteristics in the early medium range for severe weather have largely been ignored in the past. Although the signal is weak in the 3 to five‐day range, it is undoubtedly associated with a forecast skill that might be used for setting up pre‐alerts to be used either internally by meteorological services, or externally by advanced users aware of its error characteristics. Copyright © 2003 Royal Meteorological Society
Bimodality in tropical water vapour
Authors: Zhang Chidong , Mapes Brian E. , Soden Brian J.
Published: August 2007

Probability distribution functions of tropospheric water vapour in the tropics are shown to be commonly bimodal. This bimodality implies sharp gradients between dry and moist regimes in space and time. A method of testing for and quantifying bimodality is introduced. Using this method, the bimodality of water vapour is surveyed in satellite and in situ observations, as well as in global model re‐analysis data and simulations. The bimodality suggests that the radiative drying time after an injection of moisture by convection is short (1–2 days) compared to a homogenizing time, whether physical (mixing) or mathematical (averaging). It is shown that the local bimodality found in cloud‐model simulations and in situ point measurements disappears with modest time averaging (18 h and 200 km), but then reappears on the global‐scale, where dry and moist regions are separated so widely that synoptic‐ and large‐scale mixing times exceed the drying time‐scale. Large discrepancies exist in the ability to reproduce the global‐scale bimodality by global model re‐analysis and simulations. Copyright © 2003 Royal Meteorological Society
The potential of high‐density observations for numerical weather prediction: A study with simulated observations
Authors: Liu Z.‐Q. , Rabier F.
Published: August 2007

The skill of numerical weather prediction depends to a large extent upon the quantity of globally available observations. Only a fraction of the available observations (especially high‐density observations) is used in current operational assimilation systems. In this paper, the potential of high‐density observations is studied in a practical four‐dimensional variational assimilation context. Two individual meteorological situations are used to examine the impact of different observation densities on the analysis and the forecast. A series of observing‐system simulation experiments are performed. Both direct observations (temperature and surface pressure) and indirect observations (radiance) are simulated, with uncorrelated or correlated errors. In general, it is verified that a small reduction (increase) of the initial error in a sensitive area can produce a considerable improvement (degradation) of the targeted forecast. In particular, the results show that increasing the observation density for the uncorrelated‐error case can generally improve the analysis and the forecast. However, for correlated observation errors and the use of a diagonal observation‐error covariance matrix in the assimilation, an increase in the observation number such that the error correlation between two adjacent observations becomes greater than a threshold value (around 0.2) degrades the analysis and the forecast. Posterior diagnostics of the sub‐optimality of the assimilation scheme for correlated observation errors are analysed. Finally, it is shown that a risk of using high‐density observations and poor vertical resolution is that deficiencies in the background‐error statistics can lead to unrealistic analysis increments at some levels where no observations are present, and so produce a degradation of the analysis at these levels. Copyright © 2003 Royal Meteorological Society
Validity of anelastic and other equation sets as inferred from normal‐mode analysis
Authors: Davies Terry , Staniforth Andrew , Wood Nigel , Thuburn John
Published: August 2007

Various simplifications of the fully compressible inviscid (Euler) equations have been made over the years to filter out rapidly‐propagating acoustic oscillations, resulting in various anelastic, hydrostatic and pseudo‐incompressible equation sets. The principal tool used to develop approximate equation sets, and to assess their validity as a function of flow regime, has been scale analysis which has proven quite subtle to apply. Here it is shown that normal‐mode analysis provides a useful complementary tool for assessing the validity of the abovementioned approximate equation sets for both small‐ and large‐scale flows, and leads to the following conclusions. Whilst of key importance for small‐scale theoretical studies and process modelling, the anelastic equations are not recommended for either operational numerical weather prediction or climate simulation at any scale. The pseudo‐incompressible set appears to be viable for numerical weather prediction, but only at short horizontal scales. For global non‐hydrostatic modelling, only the fully compressible equations are suitable. Advances in numerical techniques in the past decade allow these to be integrated in a computationally efficient manner. © Crown copyright, 2003. Royal Meteorological Society
Simulations of the effects of interannual and decadal variability on the clear‐sky outgoing long‐wave radiation spectrum
Authors: Brindley Helen E. , Allan Richard P.
Published: August 2007

Using atmospheric profiles derived from the Hadley Centre atmosphere climate model version 3 (HadAM3) as input to a radiative transfer code, the sensitivity of the resolved spectrum of clear‐sky outgoing long‐wave radiation to both interannual and longer‐term atmospheric variability has been analysed. A comparison of the simulated spectra with available observations from two satellite‐based instruments indicates a reasonable match, although consistent differences are present. These may be explained by a combination of uncertainties in the atmospheric state, and in the relative calibration of the two instruments. Focusing on the simulations: if HadAM3 is forced by the observed sea surface temperature (SST) record alone, and long‐term alterations in the well‐mixed greenhouse gases are imposed in the radiance simulations, the changes seen within the major absorption bands are robust. Under a second scenario, where the effects of solar variability, volcanic aerosol, ozone changes and increases in the well‐mixed greenhouse gases are also included in the forcing of HadAM3, the long‐term profile changes tend to show an enhanced upper‐tropospheric warming and low/mid‐stratospheric cooling, with increased near‐surface humidities compared to the SST‐only case. However, the tropospheric response of the system, manifested in the spectral change pattern over the atmospheric window and water vapour bands, falls within the range of year‐to‐year variability. Copyright © Royal Meteorological Society, 2003. R. P. Allan's contribution is Crown copyright.
Clear‐sky infrared aerosol radiative forcing at the surface and the top of the atmosphere
Authors: Markowicz Krzysztof M. , Flatau Piotr J. , Vogelmann Andrew M. , Quinn Patricia K. , Welton Ellsworth J.
Published: August 2007

We study the aerosol radiative forcing at infrared (IR) wavelengths using data from the Aerosol Characterization Experiment, ACE‐Asia, cruise of the National Oceanic and Atmospheric Administration research vessel Ronald H. Brown. The analyses apply to the daytime periods of clear‐sky conditions for the area within the immediate vicinity of the ship. An optical model is derived from chemical measurements, lidar profiles, and visible‐extinction measurements, which are used to estimate the IR aerosol optical thickness and the single‐scattering albedo. The IR model results are compared to detailed Fourier transform interferometer‐based IR aerosol forcing estimates, pyrgeometer‐based IR downward fluxes, and to observations of the direct aerosol solar forcing. This combined approach attests to the self‐consistency of the optical model, and allows us to derive quantities such as the IR forcing at the top of the atmosphere (TOA) and the IR optical thickness. The mean IR aerosol optical thickness at 10 µm is 0.08 and the single‐scattering albedo is 0.55. The modelled IR aerosol surface forcing reaches 10 W m−2 during the cruise, which is a significant contribution compared to the total direct aerosol forcing. The surface IR aerosol radiative forcing is between 10 and 25% of the short‐wave aerosol forcing. The IR aerosol forcing at the TOA can be up to 19% of the solar aerosol forcing. We show good agreement between TOA aerosol IR forcing derived from the model and from the CERES (Clouds and the Earth's Radiant Energy System) satellite data. Over the Sea of Japan, the average IR aerosol radiative forcing is 4.6 W m−2 at the surface, and 1.5 W m−2 at the TOA. The IR forcing efficiency at the TOA is a strong function of aerosol temperature (which is coupled to vertical structure) and changes between 10 and 18 W m−2 (per IR optical depth unit), while the surface IR forcing efficiency varies between 37 and 55 W m−2 (per IR optical depth unit). Copyright © 2003 Royal Meteorological Society
Dynamic predictability of intraseasonal variability associated with the Asian summer monsoon
Authors: Waliser D. E. , Stern W. , Schubert S. , Lau K. M.
Published: August 2007

The objective of this study is to estimate the limit of dynamical predictability for the tropical intraseasonal oscillation (ISO) associated with the Asian summer monsoon. Ensembles of ‘twin’ predictability experiments were carried out with the National Aeronautics and Space Administration Goddard Laboratory for the Atmospheres atmospheric general circulation model using specified annual cycle sea surface temperatures. Initial conditions were taken from a 10‐year control simulation during periods of strong ISO activity identified via extended empirical orthogonal function analysis of 30–90 day band‐passed tropical rainfall. From this analysis, 21 cases were chosen for each of four distinct phases of the ISO cycle, making 84 cases in total. Two different sets of small random perturbations were added to these 84 initial states. Simulations were then performed for 90 days from each of these 168 perturbed initial conditions. A measure of potential predictability was constructed based on a ratio of the signal associated with the ISO, in terms of rainfall or 200 hPa velocity potential (VP200), and the mean‐square difference between sets of twin forecasts. This ratio indicates that the limit of predictability for this model's ISO extends out to about 25 days for VP200 and to about 15 days for rainfall. The predictability measure shows modest dependence on the strength of the ISO events, with stronger events having a greater limit of predictability by a few days. It also exhibits a dependence on the phase of the ISO, with greater predictability for the convective phase at short (≲5 days) lead times and for the suppressed phase at longer (≳15 days) lead times. The implications of these results as well as their associated model and analysis caveats are discussed. Copyright © 2003 Royal Meteorological Society
On the time variability of the net ocean‐to‐atmosphere heat flux in midlatitudes, with application to the North Atlantic basin
Authors: Czaja Arnaud
Published: August 2007

A new diagnostic to investigate the role of ocean dynamics in midlatitude air–sea interactions is presented and tested against observations. It is based on the analysis of the time variability of the net ocean‐to‐atmosphere heat flux (FS).

A hierarchy of air–sea interaction models indicate that, in the absence of ocean dynamics, the power spectrum of FS should be blue at time‐scales longer than a threshold set by the late‐winter ocean mixed‐layer thickness and the sensitivity of FS to sea surface temperature anomalies. Comparison of the predicted FS spectrum with observations over the North Atlantic shows a good agreement over the subpolar gyre where the deep ocean mixed layer combined with strong stochastic forcing allows large fluctuations in FS at decadal and longer time‐scales. Discrepancies, however, arise over the Gulf Stream extension region. Here it is suggested that the observed variability of FS at time‐scales longer than a decade is controlled by geostrophic ocean dynamics rather than local atmospheric forcing.

The diagnostic appears to be a useful and simple tool to investigate the role of ocean dynamics in the upper‐ocean heat budget. It is particularly well suited to the analysis of long simulations of coupled ocean–atmosphere models.

One implication of the study for ocean‐only numerical simulations is that one cannot specify externally the low‐frequency variability of FS. The latter should only arise as a consequence of ocean dynamics. Copyright © 2003 Royal Meteorological Society
Simulation of wind profiles from a space‐borne Doppler wind lidar
Authors: Marseille G. J. , Stoffelen A.
Published: August 2007

The importance of wind observations for meteorological analysis has been recognized for many years. The current global observing system lacks a uniform distribution of tropospheric wind measurements, especially in the tropics and southern hemisphere, and over the northern‐hemisphere oceans. A Doppler wind lidar (DWL) mounted on a space‐borne platform has the potential to provide a global three‐dimensional coverage of wind data. The European Space Agency has decided to fly in 2007 a DWL on a polar‐orbiting satellite platform as part of the Atmospheric Dynamics Mission, now called Aeolus. The proposed DWL is a non‐scanning single‐perspective instrument, operating in the ultraviolet part of the electromagnetic spectrum, providing profiles of line‐of‐sight (LOS) wind components from detected light backscattered from the illuminated atmospheric volume. The concept has been simulated and was used in observation‐system simulation experiments to assess its potential impact on numerical weather prediction and climate processes. This paper describes the simulation of Aeolus LOS wind‐component profiles and their expected quality in cloud‐free and cloudy conditions. Copyright © 2003 Royal Meteorological Society
Water vapour line and continuum absorption in the thermal infrared—reconciling models and observations
Authors: Taylor Jonathan P. , Newman Stuart M. , Hewison Tim J. , McGrath Andrew
Published: August 2007

High‐spectral‐resolution thermal infrared radiance observations made with the Airborne Research Interferometer Evaluation System instrument on the Met Office C130 aircraft in tropical and sub‐arctic atmospheres are used to evaluate the water vapour continuum and line absorption. Coincident microwave radiometer measurements at 183 GHz are used to help constrain the water vapour profile. Through careful selection of wavelengths where the water vapour continuum has varying impacts on the observed radiances, analysis shows that the continuum is too strong; this is using the General Line‐by‐line Atmospheric Transmittance and Radiance Model with the CKD2.4 water vapour continuum and High Resolution Transmission Molecular Absorption 2000 spectral database. Zenith observations from low altitude indicate that the continuum requires reducing by between 6% and 15% depending on the frequency, which is in good agreement with recent laboratory data. A modified continuum is presented and used in modelling to compare against upper‐troposphere nadir measurements obtained in tropical and sub‐arctic atmospheres. Copyright © Crown copyright, 2003
The Reverberation Time and Equivalent Sound Absorption Area of Rooms in Dwellings
Authors: Díaz César , Pedrero Antonio
Published: August 2007

The study gives the results of the measurements of the reverberation time in 11,687 rooms, of which 11,457 are furnished (8,246 bedrooms, 3,211 living rooms), and 230 unfurnished. All the rooms have thick walls and ceilings, and a heavy floor covering. The reverberation times measured are quite similar in bedrooms and living rooms within the same size range, and decrease fairly uniformly as the frequency increases. Moreover, in each frequency band the greater the volume of the room, the greater the reverberation time.

The results of this extensive fieldwork allow us to predict accurately the reverberation time in these kinds of spaces as a function of their size and the frequency. These data may be useful for improving the accuracy of calculation models to estimate the reverberation time of enclosed spaces. The equivalent sound absorption area of these rooms was also calculated.
Alternative splicing of the ADAR1 transcript in a region that functions either as a 5′-UTR or an ORF
Authors: Lykke-Andersen Søren , Piñol-Roma Serafín , Kjems Jørgen
Published: August 2007

The ADAR enzymes mediate the hydrolytic deamination of adenosines in specific RNA substrates and thereby diversify both the transcriptome and the proteome in metazoan species. Three promoters drive the transcription from the ADAR1 gene yielding the ADAR1-A, -B, and -C transcripts, which, in turn, lead to the production of two protein isoforms, namely, iADAR1 and cADAR1. In this study, we establish the presence of a previously unidentified alternative intron within the 5′-end of the common second exon of mRNAs encoding ADAR1 in primate species—a region that can function either as a 5′-UTR or an ORF. In addition, it is shown that the relative expression of the three promoter-specific ADAR1 transcripts is tissue specific and that the novel intron is excised from all transcripts, but at different relative levels indicating a specific regulation of the alternative splicing. Finally, possible functional consequences of the splicing are investigated. From these studies, we conclude that the alternatively spliced ADAR1-A transcript is immune to nonsense-mediated decay although it is a potential substrate. Moreover, this transcript is associated with translating ribosomes, which suggests that a truncated version of iADAR1 is expressed.
Defining the optimal parameters for hairpin-based knockdown constructs
Authors: Li Leiming , Lin Xiaoyu , Khvorova Anastasia , Fesik Stephen W. , Shen Yu
Published: August 2007

Induction of gene silencing using intracellularly expressed silencing triggers has been explored for large-scale loss-of-function screening, creation of knockdown cell lines or knockdown animals, and disease intervention. In all of these applications, the use of highly potent silencing constructs can maximize the possibility of obtaining target knockdown and thereby is intrinsically important for the chance of success. Several attempts have been made to improve the potency of a silencing construct. Results published in high profile journals such as Nature Biotechnology and Nature Genetics suggest that shRNAs with a 29-nucleotide (nt) stem is much more potent than shRNAs with a 19-nt stem, and miR30-based silencing constructs are much more potent than shRNA-based constructs. In this study, we systematically investigated several parameters, including the use of shRNA- or miR30-based scaffolds, the length of shRNA, and the selection of shRNA sequences for their impact on the knockdown efficiency of a silencing construct. Our studies revealed that the optimal configurations for a potent silencing trigger could be an shRNA with a 19-nt stem and a 9-nt loop. By comparing properties that favor the functional shRNAs and siRNAs using a set of 190 shRNAs against 19 targets and 360 siRNAs against four targets, we found that the functional shRNAs and siRNAs displayed similar but not identical nucleotide preferences. Based on the characteristic nucleotide preferences in the functional versus the nonfunctional shRNAs, we developed a computer program that outperforms an advanced siRNA selection algorithm for the enrichment of highly functional shRNAs.
A functional interaction of SmpB with tmRNA for determination of the resuming point of trans-translation
Authors: Konno Takayuki , Kurita Daisuke , Takada Kazuma , Muto Akira , Himeno Hyouta
Published: August 2007

In trans-translation, transfer-messenger RNA (tmRNA), possessing a dual function as a tRNA and an mRNA, relieves a stalled translation on the ribosome with the help of SmpB. Here, we established an in vitro system using Escherichia coli translation and trans-translation factors to evaluate two steps of trans-translation, peptidyl transfer from peptidyl-tRNA to alanyl-tmRNA and translation of the resume codon on tmRNA. Using this system, the effects of several mutations upstream of the tag-encoding region on tmRNA were examined. These mutations affected translation of the resume codon rather than peptidyl transfer, and one of them, A84U/U85G, caused a shift of the resume codon by −1. We also found that U85 is protected from chemical modification by SmpB. In the A84U/U85G mutant, the base of protection was shifted from 85 to 84. Another mutation, A86U, which caused a shift of the resume codon by +1, shifted the base of protection from 85 to 86. The protection at 85 was suppressed by a mutation in the tRNA-like domain critical to SmpB binding. These results suggest that SmpB serves to bridge two separate domains of tmRNA to determine the initial codon for tag-translation. A mutant SmpB with a truncation of the unstructured C-terminal tail failed to promote peptidyl transfer, although it still protected U85 from chemical modification.
Systematic analysis of microRNA expression of RNA extracted from fresh frozen and formalin-fixed paraffin-embedded samples
Authors: Xi Yaguang , Nakajima Go , Gavin Elaine , Morris Chris G. , Kudo Kenji , Hayashi Kazuhiko , Ju Jingfang
Published: August 2007

microRNAs (miRNAs) are noncoding small RNAs that regulate gene expression at the translational level by mainly interacting with 3′ UTRs of their target mRNAs. Archived formalin-fixed paraffin-embedded (FFPE) specimens represent excellent resources for biomarker discovery. Currently there is a lack of systematic analysis on the stability of miRNAs and optimized conditions for expression analysis using FFPE samples. In this study, the expression of miRNAs from FFPE samples was analyzed using high-throughput locked nucleic acid-based miRNA arrays. The effect of formalin fixation on the stability of miRNAs was also investigated using miRNA real-time quantitative reverse transcription-polymerase chain reaction (qRT-PCR) analysis. The stability of miRNAs of archived colorectal cancer FFPE specimens was characterized with samples dating back up to 10 yr. Our results showed that the expression profiles of miRNAs were in good correlation between 1 μg of fresh frozen and 1–5 μg of FFPE samples (correlation coefficient R2 = 0.86–0.89). Different formalin fixation times did not change the stability of miRNAs based on real-time qRT-PCR analysis. There are no significant differences of representative miRNA expression among 40 colorectal cancer FFPE specimens. This study provides a foundation for miRNA investigation using FFPE samples in cancer and other types of diseases.
Improved amber and opal suppressor tRNAs for incorporation of unnatural amino acids in vivo. Part 1: Minimizing misacylation
Authors: Rodriguez Erik A. , Lester Henry A. , Dougherty Dennis A.
Published: August 2007

The incorporation of unnatural amino acids site-specifically is a valuable technique for structure–function studies, incorporation of biophysical probes, and determining protein–protein interactions. THG73 is an amber suppressor tRNA used extensively for the incorporation of >100 different residues in over 20 proteins, but under certain conditions THG73 is aminoacylated in vivo by endogenous aminoacyl-tRNA synthetase. Similar aminoacylation is seen with the Escherichia coli Asn amber suppressor tRNA, which has also been used to incorporate UAAs in many studies. We now find that the natural amino acid placed on THG73 is Gln. Since the E. coli GlnRS recognizes positions in the acceptor stem, we made several acceptor stem mutations in the second to fourth positions on THG73. All mutations reduce aminoacylation in vivo and allow for the selection of highly orthogonal tRNAs. To show the generality of these mutations, we created opal suppressor tRNAs that show less aminoacylation in Xenopus oocytes relative to THG73. We have created a library of Tetrahymena thermophila Gln amber suppressor tRNAs that will be useful for determining optimal suppressor tRNAs for use in other eukaryotic cells.
Exploring psychological mechanisms of collective action: Does relevance of group identity influence how people cope with collective disadvantage?
Authors: van Zomeren Martijn , Spears Russell , Leach Colin Wayne
Published: August 2007

Two studies examined how the relevance of group identity influences two psychological mechanisms of collective action: Emotion‐ and problem‐focused coping with collective disadvantage. ExtendingVan Zomeren, Spears, Fischer, and Leach's (2004)integrative theoretical model of coping with collective disadvantage, we predicted that when group identity is more relevant to disadvantaged group members, it increases their collective action tendencies through their feelings ofgroup‐based angerabout their group's disadvantage. When group identity is less relevant and hence emotion‐focused coping processes are less likely,group‐efficacy beliefsbecome more predictive of disadvantaged group members' collective action tendencies because people focus more instrumentally on whether collective action will be effective (and benefit them) or not. A field study and a follow‐up experiment both showed that the relevance of group identity facilitated emotion‐focused coping and moderated problem‐focused coping with collective disadvantage. We discuss these results in terms of two distinct psychological mechanisms of collective action.
Interracial prison contact: The pros for (socially dominant) cons
Authors: Hodson Gordon
Published: August 2007

Individuals high in social dominance orientation (SDO; Sidanius & Pratto, 1999) endorse group hierarchies and social inequality. Surprisingly little research has addressed contextual factors associated with reduced intergroup biases among such individuals. The present investigation considers a Person × Situation approach to this question in two British prisons, exploring the contextual factors outlined in the Contact Hypothesis (Allport, 1954). White inmates scoring higher in SDO exhibited significantly less in‐group bias when reporting increased contact with Black inmates (Studies 1 & 2), when perceiving that favourable contact conditions are institutionally supported (Study 1), or when experiencing more pleasant personal interactions with Black inmates (Study 2). These SDO × Contact Condition moderation effects were mediated in Study 2: among high‐SDO individuals, increased empathy towards Black inmates mediated the relation between contact variables and lower in‐group bias. Implications for considering individual differences and empathy in contact settings are considered.
What do applicants want? Examining changes in attribute judgments over time
Authors: Harold Crystal M. , Ployhart Robert E.
Published: August 2007

Despite years of research examining the types of job and organizational attributes (e.g. pay, fit) that influence applicants' perceptions of organizational attractiveness, almost no research has examined how and why the weighting placed on these attributes may change across the stages of a recruitment and selection process. Using a longitudinal policy‐capturing methodology, doctoral applicants to a psychology graduate programme were surveyed at three points in time. Results revealed the weighting of fit and funding (pay) attributes increased over time, and there were individual differences in attribute weighting over time. Individual differences in applicant marketability partially explained these changes.
Josephin domain-containing proteins from a variety of species are active de-ubiquitination enzymes
Authors: Tzvetkov Nikolay , Breuer Peter
Published: August 2007

The neurodegenerative disease spinocerebellar ataxia type 3 (SCA3) is caused by the presence of an extended polyglutamine stretch (polyQ) in the unstructured C-terminus of the human ataxin-3 (AT3) protein. The structured N-terminal Josephin domain (JD) of AT3 is conserved within a novel family of potential ubiquitin proteases, the JD-containing proteins, which are sub-divided into two groups termed ataxins and Josephins. These AT3 orthologs are encoded by the genomes of organisms ranging from Plasmodium falciparum to humans, with most species possessing more than one homolog. While Josephins consist of JDs alone, ataxins contain additional functional domains that may influence their enzyme activity. Here, we show that the enzyme activity of human AT3 (hAT3) is not affected by the length of polyQ in its C-terminus, even when it is in the range associated with SCA3. We also show that JDs of all human proteins with homology to AT3 and its homologs from various species possess de-ubiquitination activity. These results establish JD-containing proteins as a novel family of active de-ubiquitination enzymes with wide phylogenic distribution.
Diversity of proteasomal missions: fine tuning of the immune response
Authors: Borissenko Ljudmila , Groll Michael
Published: August 2007

The majority of cellular proteins are degraded by proteasomes within the ubiquitin-proteasome ATP-dependent degradation pathway. Products of proteasomal activity are short peptides that are further hydrolysed by proteases to single amino acids. However, some peptides can escape this degradation, being selected and taken up by major histocompatibility complex (MHC) class I molecules for presentation to the immune system on the cell surface. MHC class I molecules are highly selective and specific in terms of ligand binding. Variability of peptides produced in living cells arises in a variety of ways, ensuring fast and efficient immune responses. Substitution of constitutive proteasomal subunits with immunosubunits leads to conformational changes in the substrate binding channels, resulting in a modified protein cleavage pattern and consequently in the generation of new antigenic peptides. The recently discovered event of proteasomal peptide splicing opens new horizons in the understanding of additional functions that proteasomes apparently possess. Whether peptide splicing is an occasional side product of proteasomal activity still needs to be clarified. Both γ-interferon-induced immunoproteasomes and peptide splicing represent two significant events providing increased diversity of antigenic peptides for flexible and fine-tuned immune response.
Cysteine protease inhibitors reduce brain β-amyloid and β-secretase activity in vivo and are potential Alzheimer's disease therapeutics
Authors: Hook Gregory , Hook Vivian Y.H. , Kindy Mark
Published: August 2007

β-Secretase inhibitors that lower brain β-amyloid peptides (Aβ) are likely to be effective for treating Alzheimer's disease (AD). Irreversible epoxysuccinyl cysteine protease inhibitors are known to reduce brain Aβ and β-secretase activity in the guinea pig model of human Aβ production. In this study, acetyl-l-leucyl-l-valyl-l-lysinal (Ac-LVK-CHO) is also shown to significantly reduce brain Aβ and β-secretase activity and brain Aβ in the same model. Ac-LVK-CHO is structurally distinct from the epoxysuccinyl inhibitors and is a reversible cysteine protease inhibitor. The results suggest that cysteine protease inhibitors generally, and reversible cysteine protease inhibitors specifically, have potential for development as AD therapeutics.
Chloroplast photorelocation movement mediated by phototropin family proteins in green plants
Authors: Suetsugu Noriyuki , Wada Masamitsu
Published: August 2007

Chloroplasts gather in areas irradiated with weak light to maximize photosynthesis (the accumulation response). They move away from areas irradiated with strong light to minimize damage of the photosynthetic apparatus (the avoidance response). The processes underlying these chloroplast movements can be divided into three parts: photoperception, signal transduction, and chloroplast movement. Photoreceptors for chloroplast movement have been identified recently in various plant species. A blue light receptor phototropin (phot) mediates chloroplast photorelocation movement in the seed plantArabidopsis thaliana, the fernAdiantum capillus-veneris, the mossPhyscomitrella patensand possibly the green algaMougeotia scalaris. A chimeric photoreceptor between phytochrome and phototropin, neochrome (neo), was found in some advanced ferns and in the green algaM. scalaris. While the mechanism of chloroplast movement is not well understood, it is known that actin filaments play an important role in this process. To understand the molecular mechanisms associated with chloroplast movement, several mutants were isolated inA.thaliana(jac1andchup1) and the corresponding genes were cloned. In this review, recent progress in photoreceptor research into chloroplast movement in various plant species and the possible factors functioning in signal transduction or the regulation of actin filaments identified inA. thalianais discussed.
Transport of nuclear-encoded proteins into secondarily evolved plastids
Authors: Hempel Franziska , Bozarth Andrew , Sommer Maik S. , Zauner Stefan , Przyborski Jude M. , Maier Uwe-G.
Published: August 2007

Many algal groups evolved by engulfment and intracellular reduction of a eukaryotic phototroph within a heterotrophic cell. Via this process, so-called secondary plastids evolved, surrounded by three or four membranes. In these organisms most of the genetic material encoding plastid functions is localized in the cell nucleus, with the result that many proteins have to pass three, four, or even five membranes to reach their final destination within the plastid. In this article, we review recent models and findings that help to explain important cellular mechanisms involved in the complex process of protein transport into secondary plastids.
Cross polarisation/magic angle spinning 13C-NMR spectroscopic studies of cellulose structural changes in hardwood dissolving pulp process
Authors: Nocanda Xolani , Larsson Per Tomas , Spark Andrew , Bush Tamara , Olsson Ann , Madikane Mzekelo , Bissessur Ajay , Iversen Tommy
Published: August 2007

Cross polarisation/magic angle spinning 13C NMR spectroscopy has been used to study structural changes in cellulose induced by the dissolving pulp process. The cellulose structure in several dissolving pulps was investigated for commercial and laboratory cooked Eucalyptus 92α and 96α. The average lateral dimension, or average thickness, of the cellulose fibril aggregates is related to the amount of surface area exposed and could be one controlling factor for the chemical reactivity of commercial dissolving pulps during modification reactions. The thickness of the cellulose fibril aggregates governs the amount of surface area present in the fibre wall, and cellulose surface material constitutes the part of the cellulose that is directly accessible to reagents. In all sample series investigated, the raw pulp was found to be less aggregated than the corresponding bleached final pulp. Furthermore, an irreversible increase in fibril aggregate width was observed on free drying for both laboratory cooked and commercial pulps. Upon rewetting with water, the freely dried 96α pulp was found to be more aggregated than the freely dried 92α pulp, although sugar analysis showed very similar carbohydrate compositions. As indicated by the molecular mass distribution, the commercial 92α pulp contained larger amounts of degraded cellulose; this may be a plausible explanation for the different behaviour of the 92α and 96α pulps during free drying.