bluuebunny/crossref_metadata_2025_split huggingface dataset:
Biosynthesis of Active
Bacillus subtilis
Urease in the Absence of Known Urease Accessory Proteins
Authors: Kim Jong Kyong , Mulrooney Scott B. , Hausinger Robert P. 
Published: September 2005

ABSTRACT

Bacillus subtilis
contains urease structural genes but lacks the accessory genes typically required for GTP-dependent incorporation of nickel. Nevertheless,
B. subtilis
was shown to possess a functional urease, and the recombinant enzyme conferred low levels of nickel-dependent activity to
Escherichia coli
. Additional investigations of the system lead to the suggestion that
B. subtilis
may use unidentified accessory proteins for in vivo urease activation.
YrxA Is the Transcriptional Regulator That Represses De Novo NAD Biosynthesis inBacillus subtilis
Authors: Rossolillo Paola , Marinoni Ilaria , Galli Elisa , Colosimo Anna , Albertini Alessandra M. 
Published: September 2005

ABSTRACTThe first genetic, in vivo, and in vitro evidences that YrxA is the regulator of NAD de novo biosynthesis inBacillus subtilisare hereby reported. The protein is essential to the transcription repression of the divergent operonsnadBCAandnifS-yrxAin the presence of nicotinic acid and binds to their shared operator-promoter region.
The Recombinant Phage Lysin LysK Has a Broad Spectrum of Lytic Activity against Clinically Relevant Staphylococci, Including Methicillin-Resistant
Staphylococcus aureus
Authors: O'Flaherty S. , Coffey A. , Meaney W. , Fitzgerald G. F. , Ross R. P. 
Published: September 2005

ABSTRACT

This study concerns the cloning, characterization, and expression of the lysin (LysK) from staphylococcal phage K in
Lactococcus lactis
. Lactococcal lysates containing recombinant LysK were found to inhibit a range of different species of staphylococci isolated from bovine and human infection sources, including methicillin-resistant
Staphylococcus aureus
. LysK thus has potential as an antimicrobial for applications in the prevention and/or treatment of infections caused by staphylococci.
Practical virtue ethics: healthcare whistleblowing and portable digital technology
Authors: Bolsin S , Faunce T , Oakley J 
Published: September 2005

Medical school curricula and postgraduate education programmes expend considerable resources teaching medical ethics. Simultaneously, whistleblowers’ agitation continues, at great personal cost, to prompt major intrainstitutional and public inquiries that reveal problems with the application of medical ethics at particular clinical “coalfaces”.Virtue ethics, emphasising techniques promoting an agent’s character and instructing their conscience, has become a significant mode of discourse in modern medical ethics. Healthcare whistleblowers, whose complaints are reasonable, made in good faith, in the public interest, and not vexatious, we argue, are practising those obligations of professional conscience foundational to virtue based medical ethics. Yet, little extant virtue ethics scholarship seriously considers the theoretical foundations of healthcare whistleblowing.The authors examine whether healthcare whistleblowing should be considered central to any medical ethics emphasising professional virtues and conscience. They consider possible causes for the paucity of professional or academic interest in this area and examine the counterinfluence of a continuing historical tradition of guild mentality professionalism that routinely places relationships with colleagues ahead of patient safety.Finally, it is proposed that a virtue based ethos of medical professionalism, exhibiting transparency and sincerity with regard to achieving uniform quality and safety of health care, may be facilitated by introducing a technological imperative using portable computing devices. Their use by trainees, focused on ethical competence, provides the practical face of virtue ethics in medical education and practice. Indeed, it assists in transforming the professional conscience of whistleblowing into a practical, virtue based culture of self reporting and personal development.
Robust stabilization of nonlinear systems: The LMI approach
Authors: Šiljak D. D. , Stipanović D. M. 
Published: September 2005

This paper presents a new approach to robust quadratic stabilization of nonlinear systems within the framework of Linear Matrix Inequalities (LMI). The systems are composed of a linear constant part perturbed by an additive nonlinearity which depends discontinuously on both time and state. The only information about the nonlinearity is that it satisfies a quadratic constraint. Our major objective is to show how linear constant feedback laws can be formulated to stabilize this type of systems and, at the same time, maximize the bounds on the nonlinearity which the system can tolerate without going unstable.We shall broaden the new setting to include design of decentralized control laws for robust stabilization of interconnected systems. Again, the LMI methods will be used to maximize the class of uncertain interconnections which leave the overall system connectively stable. It is useful to learn that the proposed LMI formulation “recognizes” the matching conditions by returning a feedback gain matrix for any prescribed bound on the interconnection terms. More importantly, the new formulation provides a suitable setting for robust stabilization of nonlinear systems where the nonlinear perturbations satisfy the generalized matching conditions.
Identification of an unstable ARMA equation
Authors: Gel Yulia R. , Fomin Vladimir N. 
Published: September 2005

Usually the coefficients in a stochastic time series model are partially or entirely unknown when the realization of the time series is observed. Sometimes the unknown coefficients can be estimated from the realization with the required accuracy. That will eventually allow optimizing the data handling of the stochastic time series.Here it is shown that the recurrent least‐squares (LS) procedure provides strongly consistent estimates for a linear autoregressive (AR) equation of infinite order obtained from a minimal phase regressive (ARMA) equation. The LS identification algorithm is accomplished by the Padé approximation used for the estimation of the unknown ARMA parameters.
M/G/1 vacation model with limited service discipline and hybrid switching‐on policy
Authors: Babitsky Alexander V. 
Published: September 2005

The author studies an M/G/1 queueing system with multiple vacations. The server is turned off in accordance with the K‐limited discipline, and is turned on in accordance with the T‐N‐hybrid policy. This is to say that the server will begin a vacation from the system if either the queue is empty or K
customers were served during a busy period. The server idles until it finds at least N waiting units upon return from a vacation.Formulas for the distribution generating function and some characteristics of the queueing process are derived. An optimization problem is discussed.
On a numerical model for diffusion‐controlled growth and dissolution of spherical precipitates
Authors: Van Keer R. , Kačur J. 
Published: September 2005

This paper deals with a numerical model for the kinetics of some diffusion‐limited phase transformations. For the growth and dissolution processes in 3D we consider a single spherical precipitate at a constant and uniform concentration, centered in a finite spherical cell of a matrix, at the boundary of which there is no mass transfer, see also Asthana and Pabi [1] and Caers [2].The governing equations are the diffusion equation (2nd Fick′s law) for the concentration of dissolved element in the matrix, with a known value at the precipitate‐matrix interface, and the flux balans (1st Fick′s law) at this interface. The numerical method, outlined for this free boundary value problem (FBP), is based upon a fixed domain transformation and a suitably adapted nonconforming finite element technique for the space discretization. The algorithm can be implemented on a PC. By numerous experiments the method is shown to give accurate numerical results.
A model of frontal polymerization using complex initiation
Authors: Goldfeder P. M. , Volpert V. A. 
Published: September 2005

Frontal polymerization is a process in which a spatially localized reaction zone propagates into a monomer, converting it into a polymer. In the simplest case of free‐radical polymerization, a mixture of monomer and initiator is placed in a test tube. A reaction is then initiated at one end of the tube. Over time, a self‐sustained thermal wave, in which chemical conversion occurs, is produced. This phenomenon is possible because of the highly exothermic nature of the polymerization reactions.Though there are certain advantages to this polymerization process over the more traditional methods, one of the drawbacks is that conversion tends to be incomplete. One way to increase conversion is by using greater amounts of initiator. The disadvantage to using this method is that more initiator results in the production of more free radicals, leading to large numbers of undesirably short polymer chains. A second method is to use a mixture of unstable and stable initiators. In this paper we develop and study a mathematical model of the propagation of free‐radical polymerization fronts using such a complex initiation. We compare the propagation velocity, maximum temperature and degree of conversion of fronts with a stable initiator, an unstable initiator and a mixture of the two. In addition, we examine how altering the stability of the stable initiator affects these quantities. We show that it is indeed the case that a mixture of unstable and stable initiators does have many advantages over using either type of initiator individually, in agreement with the existing experimental data.
Analysis of a production system with a feedback buffer and ageneral dispatching time
Authors: Lee Ho Woo , Ahn Boo Yong 
Published: September 2005

In this paper, we analyze a production system with a finite feedback buffer and dispatching time. Parts enter a “main buffer” before they are processed. Processed parts leave the system with probability 1 − p or are fed back to a “feedback buffer” with probability p. As soon as the feedback buffer becomes full, the parts in the
feedback buffer are dispatched, all at once, to the main buffer by the server for
reprocessing. The dispatching time follows a general distribution. Thus the server is
engaged either in one of the following states: idle, processing, dispatching.We derive various performance measures such as the mean number of parts in each buffer, the mean system sojourn time and the dispatching rate. We also discuss the effects of the dispatching time on the performance measures. We finally derive the procedure to obtain the optimal buffer size that minimizes the overall operating cost.
Evaluation of Atmospheric Fields from the ECMWF Seasonal Forecasts over a 15-Year Period
Authors: Jan van Oldenborgh Geert , Balmaseda Magdalena A. , Ferranti Laura , Stockdale Timothy N. , Anderson David L. T. 
Published: September 2005

Abstract
Since 1997, the European Centre for Medium-Range Weather Forecasts (ECMWF) has made seasonal forecasts with ensembles of a coupled ocean–atmosphere model, System-1 (S1). In January 2002, a new version, System-2 (S2), was introduced. For the calibration of these models, hindcasts have been performed starting in 1987, so that 15 yr of hindcasts and forecasts are now available for verification.
The main cause of seasonal predictability is El Niño and La Niña perturbing the average weather in many regions and seasons throughout the world. As a baseline to compare the dynamical models with, a set of simple statistical models (STAT) is constructed. These are based on persistence and a lagged regression with the first few EOFs of SST from 1901 to 1986 wherever the correlations are significant. The first EOF corresponds to ENSO, and the second corresponds to decadal ENSO. The temperature model uses one EOF, the sea level pressure (SLP) model uses five EOFs, and the precipitation model uses two EOFs but excludes persistence.
As the number of verification data points is very low (15), the simplest measure of skill is used: the correlation coefficient of the ensemble mean. To further reduce the sampling uncertainties, we restrict ourselves to areas and seasons of known ENSO teleconnections.
The dynamical ECMWF models show better skill in 2-m temperature forecasts over sea and the tropical land areas than STAT, but the modeled ENSO teleconnection pattern to North America is shifted relative to observations, leading to little pointwise skill. Precipitation forecasts of the ECMWF models are very good, better than those of the statistical model, in southeast Asia, the equatorial Pacific, and the Americas in December–February. In March–May the skill is lower. Overall, S1 (S2) shows better skill than STAT at lead time of 2 months in 29 (32) out of 40 regions and seasons of known ENSO teleconnections.
Atlantic Thermohaline Circulation in a Coupled General Circulation Model: Unforced Variations versus Forced Changes
Authors: Dai Aiguo , Hu A. , Meehl G. A. , Washington W. M. , Strand W. G. 
Published: September 2005

Abstract
A 1200-yr unforced control run and future climate change simulations using the Parallel Climate Model (PCM), a coupled atmosphere–ocean–land–sea ice global model with no flux adjustments and relatively high resolution (∼2.8° for the atmosphere and 2/3° for the oceans) are analyzed for changes in Atlantic Ocean circulations. For the forced simulations, historical greenhouse gas and sulfate forcing of the twentieth century and projected forcing for the next two centuries are used. The Atlantic thermohaline circulation (THC) shows large multidecadal (15–40 yr) variations with mean-peak amplitudes of 1.5–3.0 Sv (1 Sv ≡ 106 m3 s−1) and a sharp peak of power around a 24-yr period in the control run. Associated with the THC oscillations, there are large variations in North Atlantic Ocean heat transport, sea surface temperature (SST) and salinity (SSS), sea ice fraction, and net surface water and energy fluxes, which all lag the variations in THC strength by 2–3 yr. However, the net effect of the SST and SSS variations on upper-ocean density in the midlatitude North Atlantic leads the THC variations by about 6 yr, which results in the 24-yr period. The simulated SST and sea ice spatial patterns associated with the THC oscillations resemble those in observed SST and sea ice concentrations that are associated with the North Atlantic Oscillation (NAO). The results suggest a dominant role of the advective mechanism and strong coupling between the THC and the NAO, whose index also shows a sharp peak around the 24-yr time scale in the control run. In the forced simulations, the THC weakens by ∼12% in the twenty-first century and continues to weaken by an additional ∼10% in the twenty-second century if CO2 keeps rising, but the THC stabilizes if CO2 levels off. The THC weakening results from stabilizing temperature increases that are larger in the upper and northern Atlantic Ocean than in the deep and southern parts of the basin. In both the control and forced simulations, as the THC gains (loses) strength and depth, the separated Gulf Stream (GS) moves southward (northward) while the subpolar gyre centered at the Labrador Sea contracts from (expands to) the east with the North Atlantic Current (NAC) being shifted westward (eastward). These horizontal circulation changes, which are dynamically linked to the THC changes, induce large temperature and salinity variations around the GS and NAC paths.
CD163 is the macrophage scavenger receptor for native and chemically modified hemoglobins in the absence of haptoglobin
Authors: Schaer Dominik J. , Schaer Christian A. , Buehler Paul W. , Boykins Robert A. , Schoedon Gabriele , Alayash Abdu I. , Schaffner Andreas 
Published: September 2005

AbstractCD163 mediates the internalization of hemoglobin-haptoglobin (Hb-Hp) complexes by macrophages. Because Hp binding capacity is exhausted during severe hemolysis, an Hp-independent Hb-clearance pathway is presumed to exist. We demonstrate that Hb interacts efficiently with CD163 in the absence of Hp. Not only is Hb internalized into an endosomal compartment by CD163 as a result of active receptor-dependent endocytosis; it also inhibits the uptake of Hb-Hp complexes, suggesting a common receptor-binding site. Free Hb further induces heme oxygenase mRNA expression in CD163+ HEK293 cells, but not in CD163- cells. Additional evidence for Hp-independent Hb-CD163 interaction is provided by the demonstration that CD163 mediates the uptake of αα-DBBF crosslinked Hb, a chemically modified Hb that forms minimal Hp complexes. Moreover, certain modifications to Hb, such as polymerization or the attachment of specific functional groups (3 lysyl residues) to the β-Cys93 can reduce or enhance this pathway of uptake. In human macrophages, Hp-complex formation critically enhances Hb uptake at low (1 μg/mL), but not at high (greater than 100 μg/mL), ligand concentrations, lending support for a concentration-dependent biphasic model of macrophage Hb-clearance. These results identify CD163 as a scavenger receptor for native Hb and small-molecular-weight Hb-based blood substitutes after Hp depletion.
Severe secondary deficiency of von Willebrand factor–cleaving protease (ADAMTS13) in patients with sepsis-induced disseminated intravascular coagulation: its correlation with development of renal failure
Authors: Ono Tomoko , Mimuro Jun , Madoiwa Seiji , Soejima Kenji , Kashiwakura Yuji , Ishiwata Akira , Takano Katsuhiro , Ohmori Tsukasa , Sakata Yoichi 
Published: September 2005

AbstractDeficiency of ADAMTS13 is found in patients with thrombotic thrombocytopenic purpura (TTP), and the genetic defects in the ADAMTS13 gene or the autoantibody against ADAMTS13 is thought to be responsible for the development of TTP. The clinical correlation and mechanisms of secondary ADAMTS13 deficiency in other disease states were investigated. In addition to TTP, ADAMTS13 levels were severely decreased in patients with sepsis-induced disseminated intravascular coagulation (DIC). The incidence of acute renal failure and serum creatinine levels in patients with ADAMTS13 activity levels lower than 20% (incidence, 41.2%; creatinine, 160 ± 150 μM [1.81 ± 1.70 mg/dL]) (P < .05) were significantly higher than they were in patients with ADAMTS13 activity levels higher than 20% (incidence, 15.4%; creatinine, 84 ± 67 μM [0.95 ± 0.76 mg/dL]) (P < .01). Additionally, unusually large von Willebrand factor multimers were detected in 26 (51.0%) of 51 patients with ADAMTS13 activity levels lower than 20%. Lower molecular weight forms of ADAMTS13 were found in the plasma of patients with sepsis-induced DIC, suggesting that the deficiency of ADAMTS13 was partially caused by its cleavage by proteases in addition to decreased synthesis in the liver. These data suggested that severe secondary ADAMTS13 deficiency can be associated with sepsis-induced DIC and may contribute to the development of renal failure.
Ablation of oncogenic ALK is a viable therapeutic approach for anaplastic large-cell lymphomas
Authors: Piva Roberto , Chiarle Roberto , Manazza Andrea D. , Taulli Riccardo , Simmons William , Ambrogio Chiara , D'Escamard Valentina , Pellegrino Elisa , Ponzetto Carola , Palestro Giorgio , Inghirami Giorgio 
Published: September 2005

AbstractAnaplastic large-cell lymphomas (ALCLs) carry chromosome translocations in which the anaplastic lymphoma kinase (ALK) gene is fused to several partners, most frequently, the NPM1 gene. We have demonstrated that the constitutive activation of ALK fusion proteins results in cellular transformation and lymphoid neoplasia. Herein, we specifically down-regulated ALK protein expression by using small hairpin RNA (shRNA) targeting a sequence coding for the catalytic domain of ALK. The ablation of ALK leads to the down-modulation of known ALK downstream effectors, cell growth arrest, and reversion of the transformed phenotype of ALK+ mouse embryonic fibroblasts in vitro and in vivo. In human ALCL cells lentiviral-mediated ALK knock-down leads to G1 cell-cycle arrest and apoptosis in vitro and tumor growth inhibition and regression in vivo. Using a specific approach we have demonstrated that the survival and growth of ALK+ ALCLs are strictly dependent on ALK activation and signaling. Therefore, ALK is a viable target for therapeutic intervention and its inactivation might represent a pivotal approach for the treatment of ALK lymphomas and other ALK-dependent human tumors.
Stable gene transfer and expression in human primary T cells by the Sleeping Beauty transposon system
Authors: Huang Xin , Wilber Andrew C. , Bao Lei , Tuong Dong , Tolar Jakub , Orchard Paul J. , Levine Bruce L. , June Carl H. , McIvor R. Scott , Blazar Bruce R. , Zhou Xianzheng 
Published: September 2005

AbstractThe Sleeping Beauty (SB) transposon system is a nonviral DNA delivery system in which a transposase directs integration of an SB transposon into TA-dinucleotide sites in the genome. To determine whether the SB transposon system can mediate stable gene expression in human T cells, primary peripheral blood lymphocytes (PBLs) were nucleofected with SB vectors carrying a DsRed reporter gene. Plasmids containing the SB transposase on the same molecule as (cis) or on a molecule separate from (trans) the SB transposon mediated long-term and stable reporter gene expression in human primary T cells. Sequencing of transposon:chromosome junctions confirmed that stable gene expression was due to SB-mediated transposition. In other studies, PBLs were successfully transfected using the SB transposon system and shown to stably express a fusion protein consisting of (1) a surface receptor useful for positive T-cell selection and (2) a “suicide” gene useful for elimination of transfected T cells after chemotherapy. This study is the first report demonstrating that the SB transposon system can mediate stable gene transfer in human primary PBLs, which may be advantageous for T-cell–based gene therapies.
A model of oncogenic rearrangements: differences between chromosomal translocation mechanisms and simple double-strand break repair
Authors: Weinstock David M. , Elliott Beth , Jasin Maria 
Published: September 2005

AbstractRecurrent reciprocal translocations are present in many hematologic and mesenchymal malignancies. Because significant sequence homology is absent from translocation breakpoint junctions, non-homologous end-joining (NHEJ) pathways of DNA repair are presumed to catalyze their formation. We developed translocation reporters for use in mammalian cells from which NHEJ events can be selected after precise chromosomal breakage. Translocations were efficiently recovered with these reporters using mouse cells, and their breakpoint junctions recapitulated findings from oncogenic translocations. Small deletions and microhomology were present in most junctions; insertions and more complex events also were observed. Thus, our reporters model features of oncogenic rearrangements in human cancer cells. A homologous sequence at a distance from the break site affected the translocation junction without substantially altering translocation frequency. Interestingly, in a direct comparison, the spectrum of translocation breakpoint junctions differed from junctions derived from repair at a single chromosomal break, providing mechanistic insight into translocation formation. (Blood. 2006;107:777-780)