Development of the wake behind a circular cylinder impulsively started into rotatory and rectilinear motion: Intermediate rotation rates

The temporal development of two-dimensional viscous incompressible flow generated by a circular cylinder started impulsively into steady rotatory and rectilinear motion is studied by integration of a velocity/vorticity formulation of the governing equations, using an explicit finite-difference/pseudo-spectral technique and an implementation of the Biot-Savart law. Results are presented for a Reynolds number of 200 (based on the cylinder diameter 2a and the magnitude U of the rectilinear velocity) for several values of the angular/rectilinear speed ratio alpha = (omega x a)/U (where omega is the angular speed) up to 3.25. Several aspects of the kinematics and dynamics of the flow not considered earlier are discussed. For higher values of alpha, the results indicate that for Re = 200, vortex shedding does indeed occur for alpha = 3.25. The shedding process is; however, very different from that which gives rise to the usual Karman vortex street for alpha = 0. In particular, consecutive vortices shed by the body can be shed from the same side and be of the same sense, in contrast to the nonrotating case, in which mirror-image vortices of opposite sense are shed alternately on opposite sides of the body. The implications of the results are discussed in relation to the possibility of suppressing vortex shedding by open or closed-loop control of the rotation rate

Bio-logic: gene expression and the laws of combinatorial logic

Original article can be found at: http://www.mitpressjournals.org/ Copyright MIT Press DOI: 10.1162/artl.2008.14.1.121At the heart of the development of fertilized eggs into fully formed organisms and the adaptation of cells to changed conditions are genetic regulatory networks (GRNs). In higher multi-cellular organisms, signal selection and multiplexing is performed at the cis-regulatory domains of genes, where combinations of transcription factors (TFs) regulate the rates at which the genes are transcribed into mRNA. To be able to act as activators or repressors of gene transcription, TFs must first bind to target sequences on the regulatory domains. Two TFs that act in concert may bind entirely independently of each other, but more often binding of the first one will alter the affinity of the other for its binding site. This paper presents a systematic investigation into the effect of TF binding dependencies on the predicted regulatory function of this “bio-logic”. Four extreme scenarios, commonly used to classify enzyme activation and inhibition patterns, for the binding of two TFs were explored: independent (the TFs bind without affecting each other’s affinities), competitive (the TFs compete for the same binding site), ordered (the TFs bind in a compulsory order), and joint binding (the TFs either bind as a preformed complex, or binding of one is virtually impossible in the absence of the other). The conclusions are: 1) the laws of combinatorial logic hold only for systems with independently binding TFs; 2) systems formed according to the other scenarios can mimic the functions of their Boolean logical counterparts, but cannot be combined or decomposed in the same way; and 3) the continuously scaled output of systems consisting of competitively binding activators and repressors can be more robustly controlled than that of single TF or (quasi-) logical multi-TF systems. Keywords: Transcription regulation, Genetic regulatory networks, Enzyme kinetics, Combinatorial logic, Non-Boolean continuous logic, Modelling.Peer reviewe

Glutathione and Glutaredoxin—Key Players in Cellular Redox Homeostasis and Signaling

This Special Issue of Antioxidants on Glutathione (GSH) and Glutaredoxin (Grx) was designed to collect review articles and original research studies focused on advancing the current understanding of the roles of the GSH/Grx system in cellular homeostasis and disease processes. The tripeptide glutathione (GSH) is the most abundant non-enzymatic antioxidant/nucleophilic molecule in cells. In addition to various metabolic reactions involving GSH and its oxidized counterpart GSSG, oxidative post-translational modification (PTM) of proteins has been a focal point of keen interest in the redox field over the last few decades. In particular, the S-glutathionylation of proteins (protein-SSG formation), i.e., mixed disulfides between GSH and protein thiols, has been studied extensively. This reversible PTM can act as a regulatory switch to interconvert inactive and active forms of proteins, thereby mediating cell signaling and redox homeostasis. The unique architecture of the GSH molecule enhances its relative abundance in cells and contributes to the glutathionyl specificity of the primary catalytic activity of the glutaredoxin enzymes, which play central roles in redox homeostasis and signaling, and in iron metabolism in eukaryotes and prokaryotes under physiological and pathophysiological conditions. The class-1 glutaredoxins are characterized as cytosolic GSH-dependent oxidoreductases that catalyze reversible protein S-glutathionylation specifically, thereby contributing to the regulation of redox signal transduction and/or the protection of protein thiols from irreversible oxidation. This Special Issue includes nine other articles: three original studies and six review papers. Together, these ten articles support the central theme that GSH/Grx is a unique system for regulating thiol-redox hemostasis and redox-signal transduction, and the dysregulation of the GSH/Grx system is implicated in the onset and progression of various diseases involving oxidative stress. Within this context, it is important to appreciate the complementary functions of the GSH/Grx and thioredoxin systems not only in thiol-disulfide regulation but also in reversible S-nitrosylation. Several potential clinical applications have emerged from a thorough understanding of the GSH/Grx redox regulatory system at the molecular level, and in various cell types in vitro and in vivo, including, among others, the concept that elevating Grx content/activity could serve as an anti-fibrotic intervention; and discovering small molecules that mimic the inhibitory effects of S-glutathionylation on dimer association could identify novel anti-viral agents that impact the key protease activities of the HIV and SARS-CoV-2 viruses. Thus, this Special Issue on Glutathione and Glutaredoxin has focused attention and advanced understanding of an important aspect of redox biology, as well as spawning questions worthy of future study

An Enhanced Nonlinear Critical Gradient for Electron Turbulent Transport due to Reversed Magnetic Shear

The first nonlinear gyrokinetic simulations of electron internal transport barriers (e-ITBs) in the National Spherical Torus Experiment show that reversed magnetic shear can suppress thermal transport by increasing the nonlinear critical gradient for electron-temperature-gradient-driven turbulence to three times its linear critical value. An interesting feature of this turbulence is nonlinearly driven off-midplane radial streamers. This work reinforces the experimental observation that magnetic shear is likely an effective way of triggering and sustaining e-ITBs in magnetic fusion devices.Comment: 4 pages, 5 figure

An Enhanced Nonlinear Critical Gradient for Electron Turbulent Transport due to Reversed Magnetic Shear

The first nonlinear gyrokinetic simulations of electron internal transport barriers (e-ITBs) in the National Spherical Torus Experiment show that reversed magnetic shear can suppress thermal transport by increasing the nonlinear critical gradient for electron-temperature-gradient-driven turbulence to three times its linear critical value. An interesting feature of this turbulence is nonlinearly driven off-midplane radial streamers. This work reinforces the experimental observation that magnetic shear is likely an effective way of triggering and sustaining e-ITBs in magnetic fusion devices.Comment: 4 pages, 5 figure

Influence of cysteine to cysteic acid oxidation on the collision-activated decomposition of protonated peptides: evidence for intraionic interactions

AbstractOxidation of cysteine residues to cysteic acids in C-terminal arginine-containing peptides (such as those derived by tryptic digestion of proteins) strongly promotes the formation of multiple members of the Y″ series of fragment ions following low energy collision-activated decomposition (CAD) of the protonated peptides. Removal of the arginine residue abolishes the effect, which is also attenuated by conversion of the arginine to dimethylpyrimidylornithine. The data indicate the importance of an intraionic interaction between the cysteic acid and arginine side-chains. Low energy CAD of peptides which include cysteic acid and histidine residues, also provides evidence for intraionic interactions. It is proposed that these findings are consistent with the general hypothesis that an increased heterogeneity (with respect to location of charge) of the protonated peptide precursor ion population is beneficial to the generation of a high yield of product ions via several charge-directed, low energy fragmentation pathways. Furthermore, these data emphasize the significance of gas-phase conformations of protonated peptides in determining fragmentation pathways

Determination of the microscopic quality of InGaAs‐InAlAs interfaces by photoluminescence—Role of interrupted molecular beam epitaxial growth

Photoluminescence (PL) studies have been carried out on 120 Å InGaAs/InAlAs single quantum well structures grown by molecular beam epitaxy. Three types of samples were grown with the growth being interrupted before interface formation. The interruption times were 0, 2, and 3 min. The corresponding linewidth of the main excitonic transition associated with the quantum well was found to be 20, 16, and 10 meV, respectively, while the PL intensity changed by the ratio 1:0.4:0.1. We believe this behavior is due to a steady improvement in the interface quality due to interruption accompanied by impurity accumulation during the interruption. Analysis of the 10 meV linewidth, which is among the smallest ever reported, suggests that the InAlAs/InGaAs interface can be described by two‐dimensional InAlAs and InGaAs islands which have a height of two monolayers and a lateral extent of about 100 Å.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/70980/2/APPLAB-48-4-290-1.pd

Internal transport barriers in the National Spherical Torus Experiment

In the National Spherical Torus Experiment [M. Ono , Nucl. Fusion 41, 1435 (2001)], internal transport barriers (ITBs) are observed in reversed (negative) shear discharges where diffusivities for electron and ion thermal channels and momentum are reduced. While neutral beam heating can produce ITBs in both electron and ion channels, high harmonic fast wave heating can also produce electron ITBs (e-ITBs) under reversed magnetic shear conditions without momentum input. Interestingly, the location of the e-ITB does not necessarily match that of the ion ITB (i-ITB). The e-ITB location correlates best with the magnetic shear minima location determined by motional Stark effect constrained equilibria, whereas the i-ITB location better correlates with the location of maximum ExB shearing rate. Measured electron temperature gradients in the e-ITB can exceed critical gradients for the onset of electron thermal gradient microinstabilities calculated by linear gyrokinetic codes. A high-k microwave scattering diagnostic shows locally reduced density fluctuations at wave numbers characteristic of electron turbulence for discharges with strongly negative magnetic shear versus weakly negative or positive magnetic shear. Reductions in fluctuation amplitude are found to be correlated with the local value of magnetic shear. These results are consistent with nonlinear gyrokinetic simulations predicting a reduction in electron turbulence under negative magnetic shear conditions despite exceeding critical gradients.X1128sciescopu

Angle-resolved photoemission study of insulating and metallic Cu-O chains in PrBa2_2Cu3_3O7_7 and PrBa2_2Cu4_4O8_8

We compare the angle-resolved photoemission spectra of the hole-doped Cu-O chains in PrBa$_2$Cu$_3$O$_7$ (Pr123) and in PrBa$_2$Cu$_4$O$_8$ (Pr124). While, in Pr123, a dispersive feature from the chain takes a band maximum at $k_b$ (momentum along the chain) $\sim$ $\pi/4$ and loses its spectral weight around the Fermi level, it reaches the Fermi level at $k_b$ $\sim$ $\pi/4$ in Pr124. Although the chains in Pr123 and Pr124 are approximately 1/4-filled, they show contrasting behaviors: While the chains in Pr123 have an instability to charge ordering, those in Pr124 avoid it and show an interesting spectral feature of a metallic coupled-chain system.Comment: 4 pages, 5 figures, to be published in PR

Multi-institution analysis of racial disparity among African- American men eligible for prostate cancer active surveillance

There is a significant controversy on whether race should be a factor in considering active surveillance for low-risk prostate cancer. To address this question, we analyzed a multi-institution database to assess racial disparity between African-American and White-American men with low risk prostate cancer who were eligible for active surveillance but underwent radical prostatectomy. A retrospective analysis of prospectively collected clinical, pathologic and oncologic outcomes of men with low-risk prostate cancer from seven tertiary care institutions that underwent radical prostatectomy from 2003–2014 were used to assess potential racial disparity. Of the 333 (14.8%) African-American and 1923 (85.2%) White-American men meeting active surveillance criteria, African-American men were found to be slightly younger (57.5 vs 58.5 years old; p = 0.01) and have higher BMI (29.3 v 27.9; p \u3c 0.01), pre-op PSA (5.2 v 4.7; p \u3c 0.01), and maximum percentage cancer on biopsy (15.1% v 13.6%; p \u3c 0.01) compared to White-American men. Univariate and multivariate analysis demonstrated similar rates of upgrading, upstaging, positive surgical margin, and biochemical recurrence between races. These results suggest that single institution studies recommending more stringent AS enrollment criteria for AA men with a low-risk prostate cancer may not capture the complete oncologic landscape due to institutional variability in cancer outcomes. Since all seven institutions demonstrated no significant racial disparity, current active surveillance eligibility should not be modified based upon race until a prospective study has been completed. © Dinizo et al