Shuffling and Unshuffling

We consider various shuffling and unshuffling operations on languages and words, and examine their closure properties. Although the main goal is to provide some good and novel exercises and examples for undergraduate formal language theory classes, we also provide some new results and some open problems

The role of c-Jun in controlling the EPAC1-dependent induction of the SOCS3 gene in HUVECs

The cyclic AMP sensor, EPAC1, activates AP1-mediated transcription in HUVECs. Correspondingly, induction of the SOCS3 minimal promoter by EPAC1 requires a single AP1 site that constitutively binds phosphorylated (Ser63) c-Jun in DNA-pull-down assays. c-Jun (Ser63) becomes further phosphorylated following cyclic AMP stimulation and specific activation of protein kinase A (PKA), but not through selective activation of EPAC1. Moreover, despite a requirement for c-Jun for SOCS3 induction in fibroblasts, phospho-null c-Jun (Ser63/73Ala) had little effect on SOCS3 induction by cyclic AMP in HUVECs. AP1 activation and SOCS3 induction by EPAC1 in HUVECs therefore occur independently of c-Jun phosphorylation on Ser63

Fife's Theorem for 7/3-powers

We prove a Fife-like characterization of the infinite binary 7/3-power-free words, by giving a finite automaton of 15 states that encodes all such words. As a consequence, we characterize all such words that are 2-automatic. © 2011 N. Rampersad

Repetitions in infinite palindrome-rich words

Rich words are characterized by containing the maximum possible number of distinct palindromes. Several characteristic properties of rich words have been studied; yet the analysis of repetitions in rich words still involves some interesting open problems. We address lower bounds on the repetition threshold of infinite rich words over 2 and 3-letter alphabets, and construct a candidate infinite rich word over the alphabet $\Sigma_2=\{0,1\}$ with a small critical exponent of $2+\sqrt{2}/2$. This represents the first progress on an open problem of Vesti from 2017.Comment: 12 page

A Sensitive Branched DNA HIV-1 Signal Amplification Viral Load Assay with Single Day Turnaround

Branched DNA (bDNA) is a signal amplification technology used in clinical and research laboratories to quantitatively detect nucleic acids. An overnight incubation is a significant drawback of highly sensitive bDNA assays. The VERSANT® HIV-1 RNA 3.0 Assay (bDNA) (“Versant Assay”) currently used in clinical laboratories was modified to allow shorter target incubation, enabling the viral load assay to be run in a single day. To dramatically reduce the target incubation from 16–18 h to 2.5 h, composition of only the “Lysis Diluent” solution was modified. Nucleic acid probes in the assay were unchanged. Performance of the modified assay (assay in development; not commercially available) was evaluated and compared to the Versant Assay. Dilution series replicates (>950 results) were used to demonstrate that analytical sensitivity, linearity, accuracy, and precision for the shorter modified assay are comparable to the Versant Assay. HIV RNA-positive clinical specimens (n = 135) showed no significant difference in quantification between the modified assay and the Versant Assay. Equivalent relative quantification of samples of eight genotypes was demonstrated for the two assays. Elevated levels of several potentially interfering endogenous substances had no effect on quantification or specificity of the modified assay. The modified assay with drastically improved turnaround time demonstrates the viability of signal-amplifying technology, such as bDNA, as an alternative to the PCR-based assays dominating viral load monitoring in clinical laboratories. Highly sensitive bDNA assays with a single day turnaround may be ideal for laboratories with especially stringent cost, contamination, or reliability requirements

A Ni(I)Fe(II) analogue of the Ni-L state of the active site of the [NiFe] hydrogenases

Ni(L1)Fe(tBuNC)4](PF6)2 is a robust NiIIFeII complex that undergoes a reversible one-electron reduction. Spectroscopic and theoretical studies show that [Ni(L1)Fe(tBuNC)4]+ is an unprecedented NiIFeII species that reproduces the electronic configuration of the Ni-L state of the [NiFe] hydrogenases

A Novel Quantification Method for Determining Previously Undetected Silent Infarcts on MR-perfusion in Patients Following Carotid Endarterectomy

The purpose of this paper is to evaluate the post-operative Magnetic Resonance Perfusion (MRP) scans of patients undergoing carotid endarterectomy (CEA), using a novel image-analysis algorithm, to determine if post-operative neurocognitive decline is associated with cerebral blood flow changes. CEA procedure reduces the risk of stroke in appropriately selected patients with significant carotid artery stenosis. However, 25% of patients experience subtle cognitive deficits after CEA compared to a control group. It was hypothesized that abnormalities in cerebral blood flow (CBF) are responsible for these cognitive deficits. A novel algorithm for analyzing MRperfusion (MRP) scans to identify and quantify the amount of CBF asymmetry in each hemisphere was developed and to quantify the degree of relative difference between three corresponding vascular regions in the ipsilateral and contralateral hemispheres, the Relative Difference Map (RDM). Patients undergoing CEA and spine surgery (controls) were examined preoperatively, and one day postoperatively with a battery of neuropsychometric (NPM) tests, and labeled “injured” patients with significant cognitive deficits, and “normal” if they demonstrated no decline in neurocognitive function. There are apparently significant RDM differences with MRP scans between the two hemispheres in patients with cognitive deficits which can be used to guide expert reviews of the imagery. The proposed methodology aids in the analysis of MRP parameters in patients with cognitive impairment