bluuebunny/crossref_metadata_2025_split huggingface dataset:
Recombinant production of Streptococcus equisimilis streptokinase by Streptomyces lividans
Authors: Pimienta Elsa , Ayala Julio C , Rodríguez Caridad , Ramos Astrid , Van Mellaert Lieve , Vallín Carlos , Anné Jozef 
Published: July 2007

Abstract

Background
Streptokinase (SK) is a potent plasminogen activator with widespread clinical use as a thrombolytic agent. It is naturally secreted by several strains of beta-haemolytic streptococci. The low yields obtained in SK production, lack of developed gene transfer methodology and the pathogenesis of its natural host have been the principal reasons to search for a recombinant source for this important therapeutic protein. We report here the expression and secretion of SK by the Gram-positive bacterium Streptomyces lividans. The structural gene encoding SK was fused to the Streptomyces venezuelae CBS762.70 subtilisin inhibitor (vsi) signal sequence or to the Streptomyces lividans xylanase C (xlnC) signal sequence. The native Vsi protein is translocated via the Sec pathway while the native XlnC protein uses the twin-arginine translocation (Tat) pathway.

Results
SK yield in the spent culture medium of S. lividans was higher when the Sec-dependent signal peptide mediates the SK translocation. Using a 1.5 L fermentor, the secretory production of the Vsi-SK fusion protein reached up to 15 mg SK/l. SK was partially purified from the culture supernatant by DEAE-Sephacel chromatography. A 44-kDa degradation product co-eluted with the 47-kDa mature SK. The first amino acid residues of the S. lividans-produced SK were identical with those of the expected N-terminal sequence. The Vsi signal peptide was thus correctly cleaved off and the N-terminus of mature Vsi-SK fusion protein released by S. lividans remained intact. This result also implicates that the processing of the recombinant SK secreted by Streptomyces probably occurred at its C-terminal end, as in its native host Streptococcus equisimilis. The specific activity of the partially purified Streptomyces-derived SK was determined at 2661 IU/mg protein.

Conclusion
Heterologous expression of Streptococcus equisimilis ATCC9542 skc-2 in Streptomyces lividans was successfully achieved. SK can be translocated via both the Sec and the Tat pathway in S. lividans, but yield was about 30 times higher when the SK was fused to the Sec-dependent Vsi signal peptide compared to the fusion with the Tat-dependent signal peptide of S. lividans xylanase C. Small-scale fermentation led to a fourfold improvement of secretory SK yield in S. lividans compared to lab-scale conditions. The partially purified SK showed biological activity. Streptomyces lividans was shown to be a valuable host for the production of a world-wide important, biopharmaceutical product in a bio-active form.
Transcriptional recapitulation and subversion of embryonic colon development by mouse colon tumor models and human colon cancer
Authors: Kaiser Sergio , Park Young-Kyu , Franklin Jeffrey L , Halberg Richard B , Yu Ming , Jessen Walter J , Freudenberg Johannes , Chen Xiaodi , Haigis Kevin , Jegga Anil G , Kong Sue , Sakthivel Bhuvaneswari , Xu Huan , Reichling Timothy , Azhar Mohammad , Boivin Gregory P , Roberts Reade B , Bissahoyo Anika C , Gonzales Fausto , Bloom Greg C , Eschrich Steven , Carter Scott L , Aronow Jeremy E , Kleimeyer John , Kleimeyer Michael , Ramaswamy Vivek , Settle Stephen H , Boone Braden , Levy Shawn , Graff Jonathan M , Doetschman Thomas , Groden Joanna , Dove William F , Threadgill David W , Yeatman Timothy J , Coffey Robert J , Aronow Bruce J 
Published: July 2007

Abstract
Background
The expression of carcino-embryonic antigen by colorectal cancer is an example of oncogenic activation of embryonic gene expression. Hypothesizing that oncogenesis-recapitulating-ontogenesis may represent a broad programmatic commitment, we compared gene expression patterns of human colorectal cancers (CRCs) and mouse colon tumor models to those of mouse colon development embryonic days 13.5-18.5.

Results
We report here that 39 colon tumors from four independent mouse models and 100 human CRCs encompassing all clinical stages shared a striking recapitulation of embryonic colon gene expression. Compared to normal adult colon, all mouse and human tumors over-expressed a large cluster of genes highly enriched for functional association to the control of cell cycle progression, proliferation, and migration, including those encoding MYC, AKT2, PLK1 and SPARC. Mouse tumors positive for nuclear β-catenin shifted the shared embryonic pattern to that of early development. Human and mouse tumors differed from normal embryonic colon by their loss of expression modules enriched for tumor suppressors (EDNRB, HSPE, KIT and LSP1). Human CRC adenocarcinomas lost an additional suppressor module (IGFBP4, MAP4K1, PDGFRA, STAB1 and WNT4). Many human tumor samples also gained expression of a coordinately regulated module associated with advanced malignancy (ABCC1, FOXO3A, LIF, PIK3R1, PRNP, TNC, TIMP3 and VEGF).

Conclusion
Cross-species, developmental, and multi-model gene expression patterning comparisons provide an integrated and versatile framework for definition of transcriptional programs associated with oncogenesis. This approach also provides a general method for identifying pattern-specific biomarkers and therapeutic targets. This delineation and categorization of developmental and non-developmental activator and suppressor gene modules can thus facilitate the formulation of sophisticated hypotheses to evaluate potential synergistic effects of targeting within- and between-modules for next-generation combinatorial therapeutics and improved mouse models.
An investigation into the non-elastic behaviour of turbine rotor discs at high temperatures
Authors: Chubb E J 
Published: July 2007

A simplified geometry has been used in the examination of the effects of temperature on a turbine rotor disc for steady and cyclic loading. For steady loading creep solutions have been obtained which show the effect of non-isothermal conditions and various commonly applied approximations. For cyclic loading the effects of high transient stress during start-up and shutdown on the creep strain have been examined. The development of plastic strain and its effect on rotor creep are also considered.
Stress-concentration factors for shoulder fillets and grooves in plates
Authors: Wilson I H , White D J 
Published: July 2007

Stress-concentration factors have been determined photoelastically for shoulder fillets and grooves in plates subjected to tension and bending. The parameters were mainly outside the range of previously published work which is also critically examined. The validity of Neuber's analysis for grooved plates is confirmed. The new results on shouldered plates provide a useful extension to Engineering Sciences Data Unit item no. 69020 for small values of r/d and values of D/d from 1.01 to 1.5, where r is the fillet radius, D is the greater width, and d the smaller width of the plate. These results for plates may be applied to shouldered shafts without the incurring of serious error.
Experimental methods for fracture toughness measurement
Authors: Priest A H 
Published: July 2007

Recommended methods for measuring fracture toughness parameters are discussed. The relevant Draft British Standards are: (a) Draft for Development 3:1971 ‘Methods for Plane Strain Fracture Toughness ( KI c) Testing’. (b) Draft for Development 19:1972 ‘Methods for Crack Opening Displacement (COD) Testing’. These documents are being revized and updated for publishing as full British Standards and any significant additions and alterations are noted. The situation with respect to non-standard tests is reviewed. The fracture toughness parameters under this heading include JI c, equivalent energy values, fracture propagation energy values and R-curve analysis. Particular attention is paid to the influence of strain rate on testing procedures and a crack monitoring technique is discussed.
Comparison of finite element predictions of creep crack growth with experimental data
Authors: Hyde T H , Low K C , Webster J J 
Published: July 2007

Five, pre-fatigued, compact tension specimens made from a model material, which exhibits similar macroscopic behaviour to some high temperature materials, have been subjected to steady loads. The results of these tests indicate that the ‘crack tip opening displacement’ governs the intiation of crack propagation. The subsequent creep crack growth rates are accurately predicted by the C∗ parameter. ‘Moving crack’ finite element calculations have shown that accurate predictions of creep crack growth rates are possible even with relatively coarse meshes. However, the predictions are very sensitive to both the critical crack tip opening displacement used for initiation and to the magnitude of the load. Also, although the C∗ parameter is strictly only applicable to stationary state stresses at stationary cracks, predictions of crack growth were found to be accurate when using C∗ under non-stationary stress and moving crack situations.
Cloud microphysics, radiation and vertical velocities in two‐ and three‐dimensional simulations of deep convection
Authors: Phillips Vaughan T. J. , Donner Leo J. 
Published: July 2007

AbstractThis study investigates the importance of dimensionality for the characteristics of simulations performed with cloud‐system resolving models (CSRMs). In addition to intrinsic questions related to dimensionality in CSRMs, the issue has gained added interest since CSRMs can be utilized instead of conventional cloud parametrizations to represent deep convection within global climate models. Such CSRMs may be either two‐ or three‐dimensional.CSRM simulations of five observed cases of deep convection are performed in both two and three dimensions (2D and 3D) with the aim of elucidating the impact of dimensionality on overall cloud statistics. Observed profiles of the large‐scale average of advection of temperature and humidity are applied to initiate and maintain the convection. Two of the cases are from tropical oceanic regions. The other three cases are continental.The average ascent rate in deep convective, cloudy updraughts is about 20–50% higher at mid‐levels of the troposphere in 3D than in 2D, for all cases. This corresponds to an increase by a similar percentage in the vertical mass flux of deep updraughts in the oceanic cases. Furthermore, the weak ascent (0.1<w<1 m s−1) outside the deep convective updraughts is much less prevalent in 3D than in 2D, with vertical velocities being about 20% lower for a given cumulative frequency and a lower vertical mass flux. Downdraughts are weaker in 3D, for most cases.There is a substantial sensitivity of the vertical profiles of cloud liquid and cloud ice, and of other microphysical species, to dimensionality. This is consistent with the sensitivity of the dynamics of convection. Corresponding changes in radiative transfer, especially in the short‐wave band, result from the cloud–radiative interactions. In particular, the peak in domain‐averaged cloud liquid content in the melting layer is about 50% higher in most of the 2D simulations. The land cases display more sensitivity of the short‐wave radiative flux to the choice of orientation of the vertical plane of 2D simulations. Copyright © 2006 Royal Meteorological Society
Background error covariance functions for vector wind analyses using Doppler‐radar radial‐velocity observations
Authors: Xu Qin , Liu Shun , Xue Ming 
Published: July 2007

AbstractA two‐dimensional form of cross‐covariance function between the radar radial‐ and tangential‐components (with respect to the direction of radar beam) of background wind errors is derived. Like the previously derived auto‐covariance function for the radial component, this cross‐covariance function is homogeneous but non‐isotropic in the horizontal. The auto‐ and cross‐covariance functions are used with the statistical interpolation technique to perform a vector wind analysis from Doppler radial‐velocity observations on a conical surface of low‐elevation radar‐scans. The structures of the two covariance functions are compared and interpreted in terms of the influence of a single‐point radial‐velocity observation on the analysed vector wind field. The utility and value of these covariance functions are demonstrated through analysis experiments that use either simulated radial‐velocity data from idealized flows or real radar observations. The results of the statistical interpolation scheme utilizing the proposed covariance functions are shown to be superior to the results of traditional VAD technique. The proposed technique can actually be considered a generalization of the traditional VAD technique. Copyright © 2006 Royal Meteorological Society
Modelling the influence of rimer surface temperature on the glaciation of intense thunderstorms: The rime–splinter mechanism of ice multiplication
Authors: Connolly Paul J. , Heymsfield Andrew J. , Choularton Thomas W. 
Published: July 2007

AbstractA modelling study is presented to look at the potential importance of ice multiplication in a deep Cb cloud observed during the second Egrett Microphysics Experiment with Radiation, Lidar and Dynamics (EMERALD‐II). Simulations with both a cloud‐resolving model (CRM) and an explicit‐microphysics model (EMM) are used. The CRM has a two‐moment bulk microphysics scheme and resolved cloud dynamics, while the EMM has detailed size‐resolved microphysics, but is driven by the CRM cloud dynamics. The simulations consider the sensitivity of the storms to the rime‐splinter, secondary ice production mechanism (or Hallett–Mossop process).Recent literature on modelling this process in Cb clouds suggests that it is of low importance to the cloud glaciation in intense storms. However, until now, numerical simulations in the literature have investigated this process by either switching it on or off in the model microphysics scheme. We show that if the rate of splinter production is doubled from that proposed by Hallett and Mossop's experiment—a reasonable factor—then for this simulated model cloud, there is a large direct impact on anvil glaciation. The approximate net radiative impact of this calculated with the CRM is 10 W m−2. Similar, ‘nonlinear’ results can also be expected from other ice nucleating mechanisms. Simulations are performed for both continental and maritime cloud condensation nuclei concentrations. In stark contrast to previous literature, we find that the Hallett–Mossop process is more important in the continental (‘polluted’) case than in the maritime (‘clean’) case. This is because of the extremely warm cloud base for this particular storm and consequently—because of the rapid production of rain—the scarcity of small cloud droplets for riming in the clean case. Copyright © 2006 Royal Meteorological Society
Measuring forecast skill: is it real skill or is it the varying climatology?
Authors: Hamill Thomas M. , Juras Josip 
Published: July 2007

AbstractIt is common practice to summarize the skill of weather forecasts from an accumulation of samples spanning many locations and dates. In calculating many of these scores, there is an implicit assumption that the climatological frequency of event occurrence is approximately invariant over all samples. If the event frequency actually varies among the samples, the metrics may report a skill that is different from that expected. Many common deterministic verification metrics, such as threat scores, are prone to mis‐reporting skill, and probabilistic forecast metrics such as the Brier skill score and relative operating characteristic skill score can also be affected.Three examples are provided that demonstrate unexpected skill, two from synthetic data and one with actual forecast data. In the first example, positive skill was reported in a situation where metrics were calculated from a composite of forecasts that were comprised of random draws from the climatology of two distinct locations. As the difference in climatological event frequency between the two locations was increased, the reported skill also increased. A second example demonstrates that when the climatological event frequency varies among samples, the metrics may excessively weight samples with the greatest observational uncertainty. A final example demonstrates unexpectedly large skill in the equitable threat score of deterministic precipitation forecasts.Guidelines are suggested for how to adjust skill computations to minimize these effects. Copyright © 2006 Royal Meteorological Society
A time‐staggered semi‐Lagrangian discretization of the rotating shallow‐water equations
Authors: Staniforth Andrew , Wood Nigel , Reich Sebastian 
Published: July 2007

AbstractA time‐staggered semi‐Lagrangian discretization of the rotating shallow‐water equations is proposed and analysed. Application of regularization to the geopotential field used in the momentum equations leads to an unconditionally stable scheme. The analysis, together with a fully nonlinear example application, suggests that this approach is a promising, efficient, and accurate alternative to traditional schemes. © Royal Meteorological Society, 2006. A. Staniforth's and N. Wood's contributions are Crown copyright material, reproduced with the permission of the Controller of Her Majesty's Stationery Office.
Föohn/cold‐pool interactions in the Rhine valley during MAP IOP 15
Authors: Flamant C. , Drobinski P. , Furger M. , Chimani B. , Tschannett S. , Steinacker R. , Protat A. , Richner H. , Gubser S. , Häberli C. 
Published: July 2007

AbstractThe föhn/cold‐pool interactions in the lower Alpine Rhine valley documented in the framework of the Intensive Observing Period (IOP) 15 of the Mesoscale Alpine Programme (MAP) on 5 November 1999 are analysed. The present study focuses on the water vapour mixing ratio measurements acquired with the airborne differential absorption lidar LEANDRE 2 which enabled detailed documentation of the along‐valley structure of the cold pool. LEANDRE 2 and microbarograph measurements revealed the presence of Kelvin–Helmholtz waves (KHW) at the top of the cold pool. The characteristics of the waves were different in the region of the cold‐ pool leading edge (the southernmost part of the cold pool) and in the vicinity of the Bodensee (Lake Constance), further to the north. Gravity waves were also observed above the cold pool in the in situ aircraft data acquired in the vicinity of the Bodensee. The gravity waves are suspected to be triggered by the KHW at the top of the cold pool. We also investigate the respective role of the three known processes likely to control the structure of the cold pool and its erosion along the Rhine valley, namely (i) convection within the cold pool, (ii) turbulent erosion at the top of the cold pool due to the presence of KHW, and (iii) dynamic displacement of the cold pool by föhn air. The former two processes are likely not to play a role in the erosion of the cold pool observed in the course of this IOP. Finally, the temporal evolution of the heat budget advection term in the lower Rhine valley was investigated using temperature profiles derived from balloon soundings acquired at two sites which were overpassed by the cold‐pool edge in the course of its displacement northwards during the early afternoon as the result of the action of the föhn, and then southwards in the late afternoon as the föhn weakened and cold air from the Bodensee area was filling the lower Rhine Valley. Copyright © 2006 Royal Meteorological Society
A study of the Elite Plus femoral component using radiostereometric analysis
Authors: Derbyshire B. , Porter M. L. 
Published: July 2007

We performed a three-year radiostereometric analysis (RSA) study of the Elite Plus femoral component on 25 patients undergoing primary total hip replacement. Additional assessments and measurements from standard radiographs were also made. Subsidence of the stem occurred at the cement-stem interface. At 36 months the subsidence of the stem centroid was a mean of 0.30 mm (0.02 to 1.28), and was continuing at a slow rate. At the same time point, internal rotation and posterior migration of the femoral head had ceased. One stem migrated excessively and additional assessments suggested that this was probably due to high patient demand. The failure rate of 4% in our study is consistent with data from arthroplasty registers but contrasts with poor results from another RSA study, and from some clinical studies. We believe that the surgical technique, particularly the use of high-viscosity cement, may have been an important factor contributing to our results.
Effect of progesterone on recovery from nerve injury during leg lengthening in rats
Authors: Hara Y. , Ochiai N. , Abe I. , Ichimura H. , Saijilafu  , Nishiura Y. 
Published: July 2007

We investigated the effect of progesterone on the nerve during lengthening of the limb in rats. The sciatic nerves of rats were elongated by leg lengthening for ten days at 3 mm per day. On alternate days between the day after the operation and nerve dissection, the progesterone-treated group received subcutaneous injections of 1 mg progesterone in sesame oil and the control group received oil only. On the fifth, tenth and 17th day, the sciatic nerves were excised at the midpoint of the femur and the mRNA expression level of myelin protein P0 was analysed by quantitative real time polymerase chain reaction. On day 52 nodal length was examined by electron microscopy, followed by an examination of the compound muscle action potential (C-MAP) amplitude and the motor conduction velocity (MCV) of the tibial nerve on days 17 and 52. The P0 (a major myelin glycoprotein) mRNA expression level in the progesterone-treated group increased by 46.6% and 38.7% on days five and ten, respectively. On day 52, the nodal length in the progesterone-treated group was smaller than that in the control group, and the MCV of the progesterone-treated group had been restored to normal. Progesterone might accelerate the restoration of demyelination caused by nerve elongation by activating myelin synthesis.
A computer model of the position of the combined component in the prevention of impingement in total hip replacement
Authors: Barsoum W. K. , Patterson R. W. , Higuera C. , Klika A. K. , Krebs V. E. , Molloy R. 
Published: July 2007

Dislocation remains a major concern after total hip replacement, and is often attributed to malposition of the components. The optimum position for placement of the components remains uncertain. We have attempted to identify a relatively safe zone in which movement of the hip will occur without impingement, even if one component is positioned incorrectly. A three-dimensional computer model was designed to simulate impingement and used to examine 125 combinations of positioning of the components in order to allow maximum movement without impingement. Increase in acetabular and/or femoral anteversion allowed greater internal rotation before impingement occurred, but decreases the amount of external rotation. A decrease in abduction of the acetabular components increased internal rotation while decreasing external rotation. Although some correction for malposition was allowable on the opposite side of the joint, extreme degrees could not be corrected because of bony impingement. We introduce the concept of combined component position, in which anteversion and abduction of the acetabular component, along with femoral anteversion, are all defined as critical elements for stability.