Studies on the de novo Biosynthesis of NAD in Escherichia coli

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/66045/1/j.1432-1033.1975.tb04133.x.pd

Assessment of transparent and reproducible research practices in the psychiatry literature

Objective: Reproducibility is a cornerstone of scientific advancement; however, many published works may lack the core components needed for study reproducibility. In this study, we evaluate the state of transparency and reproducibility in the field of Psychiatry using specific indicators as proxies for these practices.Methods: An increasing number of publications have investigated indicators of reproducibility, including research by Harwicke et al., from which we based the methodology for our observational, cross-sectional study. From a random five-year sample of 300 publications in PubMed-indexed psychiatry journals, two researchers extracted data in a duplicate, blinded fashion using a piloted Google Form. The publications were examined for indicators of reproducibility and transparency, which included availability of: materials, data, protocol, analysis script, open-access, conflict of interest, funding, and online pre-registration.Results: This study ultimately evaluated 296 randomly-selected publications with a 3.20 median impact factor. Only 107 were available online. Most primary authors originated from the United States, United Kingdom, and Netherlands. The top three publication types were cohort studies, surveys, and clinical trials. Regarding indicators of reproducibility, 17 publications gave access to necessary materials, four provided in-depth protocol, and one contained raw data required to reproduce the outcomes. One publication offered its analysis script upon request; four provided a protocol availability statement. Only 107 publications were publicly available: 13 were registered in online repositories and four, ten, and eight publications included their hypothesis, methods, and analysis, respectively. Conflict of interest was addressed by 177 and reported by 31 publications. Of 185 publications with a funding statement, 153 were funded and 32 were unfunded.Conclusions: Currently, Psychiatry research has significant potential to improve adherence to reproducibility and transparency practices. Thus, this study presents a reference point for the state of reproducibility and transparency in Psychiatry literature. Future assessments are recommended to evaluate and encourage progress

Neurofibromin Deficiency Induces Endothelial Cell Proliferation and Retinal Neovascularization

Purpose: Neurofibromatosis type 1 (NF1) is the result of inherited mutations in the NF1 tumor suppressor gene, which encodes the protein neurofibromin. Eye manifestations are common in NF1 with recent reports describing a vascular dysplasia in the retina and choroid. Common features of NF1 retinopathy include tortuous and dilated feeder vessels that terminate in capillary tufts, increased endothelial permeability, and neovascularization. Given the retinal vascular phenotype observed in persons with NF1, we hypothesize that preserving neurofibromin may be a novel strategy to control pathologic retinal neovascularization. Methods: Nf1 expression in human endothelial cells (EC) was reduced using small hairpin (sh) RNA and EC proliferation, migration, and capacity to form vessel-like networks were assessed in response to VEGF and hypoxia. Wild-type (WT), Nf1 heterozygous (Nf1+/-), and Nf1flox/+;Tie2cre pups were subjected to hyperoxia/hypoxia using the oxygen-induced retinopathy model. Retinas were analyzed quantitatively for extent of retinal vessel dropout, neovascularization, and capillary branching. Results: Neurofibromin expression was suppressed in response to VEGF, which corresponded with activation of Mek-Erk and PI3-K-Akt signaling. Neurofibromin-deficient EC exhibited enhanced proliferation and network formation in response to VEGF and hypoxia via an Akt-dependent mechanism. In response to hyperoxia/hypoxia, Nf1+/- retinas exhibited increased vessel dropout and neovascularization when compared with WT retinas. Neovascularization was similar between Nf1+/- and Nf1flox/+;Tie2cre retinas, but capillary drop out in Nf1flox/+;Tie2cre retinas was significantly reduced when compared with Nf1+/- retinas. Conclusions: These data suggest that neurofibromin expression is essential for controlling endothelial cell proliferation and retinal neovascularization and therapies targeting neurofibromin-deficient EC may be beneficial

Diagnostic suite used for magnetohydrodynamics equilibrium reconstruction on the PEGASUS

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Disruptions, Disruptivity, and Safer Operating Windows in the High-β Spherical Torus NSTX

This paper discusses disruption rates, disruption causes, and disruptivity statistics in the high- βN National Spherical Torus Experiment (NSTX) [M. Ono, et al. Nuclear Fusion 40, 557 (2000)]. While the overall disruption rate is rather high, configurations with high βN , moderate q*, strong boundary shaping, sufficient rotation, and broad pressure and current profiles are found to have the lowest disruptivity; active n=1 control further reduces the disruptivity. The disruptivity increases rapidly for q*<2.7, which is substantially above the ideal MHD current limit. In quiescent conditions, qmin >1.25 is generally acceptable for avoiding the onset of core rotating n=1 kink/tearing modes; when EPM and ELM disturbances are present, the required qmin for avoiding those modes is raised to ~1.5. The current ramp and early flat-top phase of the discharges are prone to n=1 core rotating modes locking to the wall, leading to a disruption. Small changes to the discharge fueling during this phase can often mitigate the rotation damping associated with these modes and eliminate the disruption. The largest stored energy disruptions are those that occur at high current when a plasma current rampdown is initiated incorrectly

Three-dimensional distortions of the tokamak plasma boundary: boundary displacements in the presence of saturated MHD instabilities

The three-dimensional plasma boundary displacement induced by long-lasting core magnetohydrodynamic (MHD) instabilities has been measured in JET, MAST and NSTX. Only saturated instabilities are considered here since transient rapidly growing modes which degrade confinement and act as potential triggers for disruptions bring more fundamental concerns than boundary displacements. The measured displacements are usually small, although in extreme cases in MAST when the rotation braking is strong, a significant global displacement can be observed. The instability most likely to saturate and exist for many energy confinement times whilst distorting the boundary of ITER is the saturated internal kink, or helical core, which can be found in plasmas with a wide region of low magnetic shear such as the hybrid scenario. This mode can lead to non-negligible boundary displacements. Nonetheless, the boundary displacement resultant from core MHD instabilities in ITER is predicted to be less than ±1.5% of the minor radius, well within tolerable limits for heat loads to plasma-facing components

Optimization of negative central shear discharges in shaped cross sections

Magnetohydrodynamic (MHD) stability analyses of Negative Central Shear (NCS) equilibria have revealed a new understanding of the limiting MHD instabilities in NCS experiments. Ideal stability calculations show a synergistic effect between cross section shape and pressure profile optimization; strong shaping and broader pressure independently lead to moderately higher {Beta} limits, but broadening of the pressure profile in a strongly dee-shaped cross- section leads to a dramatic increase in the ideal {Beta} limit. Localized resistive interchange (RI) modes can be unstable in the negative shear region and are most restrictive for peaked pressure profiles. Resistive global modes can also be destabilized significantly below the ideal P limit. Experiments largely confirm the general trends, and diagnostic measurements and numerical stability calculations are found to be in good qualitative agreement. Observed disruptions in NCS discharges with L-mode edge and strongly peaked pressure, appear to be initiated by interactions between the RI, and the global ideal and resistive modes

Gelatin microparticles aggregates as three-dimensional scaffolding system in cartilage engineering

A three-dimensional (3D) scaffolding system for chondrocytes culture has been produced by agglomeration of cells and gelatin microparticles with a mild centrifuging process. The diameter of the microparticles, around 10 μ, was selected to be in the order of magnitude of the chondrocytes. No gel was used to stabilize the construct that maintained consistency just because of cell and extracellular matrix (ECM) adhesion to the substrate. In one series of samples the microparticles were charged with transforming growth factor, TGF-β1. The kinetics of growth factor delivery was assessed. The initial delivery was approximately 48 % of the total amount delivered up to day 14. Chondrocytes that had been previously expanded in monolayer culture, and thus dedifferentiated, adopted in this 3D environment a round morphology, both with presence or absence of growth factor delivery, with production of ECM that intermingles with gelatin particles. The pellet was stable from the first day of culture. Cell viability was assessed by MTS assay, showing higher absorption values in the cell/unloaded gelatin microparticle pellets than in cell pellets up to day 7. Nevertheless the absorption drops in the following culture times. On the contrary the cell viability of cell/TGF-β1 loaded gelatin microparticle pellets was constant during the 21 days of culture. The formation of actin stress fibres in the cytoskeleton and type I collagen expression was significantly reduced in both cell/gelatin microparticle pellets (with and without TGF-β1) with respect to cell pellet controls. Total type II collagen and sulphated glycosaminoglycans quantification show an enhancement of the production of ECM when TGF-β1 is delivered, as expected because this growth factor stimulate the chondrocyte proliferation and improve the functionality of the tissue.JLGR acknowledge the support of the Spanish Ministry of Education through project No. MAT2010-21611-C03-01 (including the FEDER financial support). The support of the Instituto de Salud Carlos III (ISCIII) through the CIBER initiative of the Networking Research Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN) is also acknowledged

Progress towards Steady State at Low Aspect Ratio on the National Spherical Torus Experiment (NSTX)

Modifications to the plasma control capabilities and poloidal field coils of the National Spherical Torus Experiment (NSTX) have enabled a significant enhancement in shaping capability which has led to the transient achievement of a record shape factor (S ≡ q95 (Iρ⁄ αΒτ)) of ∼41 (MA m−1 Τ−1) simultaneous with a record plasma elongation of κ ≡ β ⁄ α ∼ 3. This result was obtained using isoflux control and real-time equilibrium reconstruction. Achieving high shape factor together with tolerable divertor loading is an important result for future ST burning plasma experiments as exemplified by studies for future ST reactor concepts, as well as neutron producing devices, which rely on achieving high shape factors in order to achieve steady state operation while maintaining MHD stability. Statistical evidence is presented which demonstrates the expected correlation between increased shaping and improved plasma performance

Effect of plasma shaping on performance in the National Spherical Torus Experiment

The National Spherical Torus Experiment (NSTX) has explored the effects of shaping on plasma performance as determined by many diverse topics including the stability of global magnetohydrodynamic (MHD) modes (e.g., ideal external kinks and resistive wall modes), edge localized modes (ELMs), bootstrap current drive, divertor flux expansion, and heat transport. Improved shaping capability has been crucial to achieving Βt ∼40%. Precise plasma shape control has been achieved on NSTX using real-time equilibrium reconstruction. NSTX has simultaneously achieved elongation κ∼2.8 and triangularity δ∼0.8. Ideal MHD theory predicts increased stability at high values of shaping factor S≡ q95 Ip (a Bt), which has been observed at large values of the S∼37 [MA (m·T)] on NSTX. The behavior of ELMs is observed to depend on plasma shape. A description of the ELM regimes attained as shape is varied will be presented. Increased shaping is predicted to increase the bootstrap fraction at fixed Ip. The achievement of strong shaping has enabled operation with 1 s pulses with Ip =1 MA, and for 1.6 s for Ip =700 kA. Analysis of the noninductive current fraction as well as empirical analysis of the achievable plasma pulse length as elongation is varied will be presented. Data are presented showing a reduction in peak divertor heat load due to increasing in flux expansion. © 2006 American Institute of Physics