Using competition assays to quantitatively model cooperative binding by transcription factors and other ligands.

BACKGROUND: The affinities of DNA binding proteins for target sites can be used to model the regulation of gene expression. These proteins can bind to DNA cooperatively, strongly impacting their affinity and specificity. However, current methods for measuring cooperativity do not provide the means to accurately predict binding behavior over a wide range of concentrations. METHODS: We use standard computational and mathematical methods, and develop novel methods as described in Results. RESULTS: We explore some complexities of cooperative binding, and develop an improved method for relating in vitro measurements to in vivo function, based on ternary complex formation. We derive expressions for the equilibria among the various complexes, and explore the limitations of binding experiments that model the system using a single parameter. We describe how to use single-ligand binding and ternary complex formation in tandem to determine parameters that have thermodynamic relevance. We develop an improved method for finding both single-ligand dissociation constants and concentrations simultaneously. We show how the cooperativity factor can be found when only one of the single-ligand dissociation constants can be measured. CONCLUSIONS: The methods that we develop constitute an optimized approach to accurately model cooperative binding. GENERAL SIGNIFICANCE: The expressions and methods we develop for modeling and analyzing DNA binding and cooperativity are applicable to most cases where multiple ligands bind to distinct sites on a common substrate. The parameters determined using these methods can be fed into models of higher-order cooperativity to increase their predictive power

Peak Speeds of Professional Football Players During Bouts of Non-curved, Manual Treadmill Sprints

Purpose: Speed training and short distance sprints have become an essential component of preparation for professional football players. Current trends in speed training have included the application of non-curved, manual treadmills, as they may enhance peak speeds with less biomechanical stress. A lack of data currently exists in regards to the effectiveness of different settings and peak speed response. Therefore, we proposed to compare peak speeds during different settings of non-curved, manual treadmills. It was hypothesized that as resistance/incline increased, peak sprinting speeds would decrease and vice versa. Methods: Fourteen male professional football players (27.14 ± 3.11 yrs., 183.93 ± 8.52 cm, 100.36 ± 15.60 kg) sprinted at peak speeds during four different incline/resistance bouts. Paired samples T-tests examined differences between bouts, and significance was set at p ≤ 0.008. Results: A significant difference (p \u3c 0.001) existed for peak speeds between each incline/resistance bout (i.e. INC15R8, INC15R5, INC20R3, INC20R1). Conclusions: The observed data differences existed between all bouts, indicating that as resistance and/or incline increased, peak speed decreased. This also indicated that as resistance and/or incline decreased, peak speed increased during sprint bouts in professional football players

Medical Manikin Augmented Reality Simulation (M2ARS)

The Medical Manikin Augmented Reality Simulation (M2ARS) is an augmented reality simulation application built for the Microsoft HoloLens 2 that uses the principles of anatomy transfer to overlay human anatomical structures onto a medical manikin digitally. These structures currently consist of the skeletal, muscular, and circulatory systems. In addition, a model of the lungs and an animated heart are also available within the simulation. M2ARS allows the user to view these structures in a manner that is both visually and spatially accurate to the human body. This application contains two modes; an augmented reality mode, which uses a manikin, and a standalone virtual environment, which does not require a manikin. M2ARS aims to assist medical students and practitioners in their studies by providing an interactive method to better understand anatomical structures

Amino acid-dependent stability of the acyl linkage in aminoacyl-tRNA.

Aminoacyl-tRNAs are the biologically active substrates for peptide bond formation in protein synthesis. The stability of the acyl linkage in each aminoacyl-tRNA, formed through an ester bond that connects the amino acid carboxyl group with the tRNA terminal 3\u27-OH group, is thus important. While the ester linkage is the same for all aminoacyl-tRNAs, the stability of each is not well characterized, thus limiting insight into the fundamental process of peptide bond formation. Here, we show, by analysis of the half-lives of 12 of the 22 natural aminoacyl-tRNAs used in peptide bond formation, that the stability of the acyl linkage is effectively determined only by the chemical nature of the amino acid side chain. Even the chirality of the side chain exhibits little influence. Proline confers the lowest stability to the linkage, while isoleucine and valine confer the highest, whereas the nucleotide sequence in the tRNA provides negligible contribution to the stability. We find that, among the variables tested, the protein translation factor EF-Tu is the only one that can protect a weak acyl linkage from hydrolysis. These results suggest that each amino acid plays an active role in determining its own stability in the acyl linkage to tRNA, but that EF-Tu overrides this individuality and protects the acyl linkage stability for protein synthesis on the ribosome

The Physiologic and Behavioral Implications of Playing Active and Sedentary Video Games in a Seated and Standing Position

International Journal of Exercise Science 7(3) : 194-201, 2014. Previous studies have assessed physiologic response while playing video games per manufacturer instructions with participants standing during active video game play and seated during sedentary game play. It is not known whether an assigned seated or standing position affects positional preference and oxygen consumption (VO2) while gaming. The purpose of the study was to assess VO2 and preference of playing active and sedentary video games in a seated and standing position. VO2 was assessed in 25 participants during four, 20-minute conditions; resting, PlayStation 2 Madden NFL Football 2011, Nintendo Wii-Sports Boxing and Nintendo Wii Madden NFL Football 2011. Each condition was divided into two positional conditions (10 minutes seated, 10 minutes standing) and each participant indicated their positional preference after each 20-minute condition. Standing VO2 (4.4 ± 0.2 ml•kg-1•min-1 PS2, 4.6 ± 0.1 ml•kg-1•min-1 Wii Madden, 6.8 ± 0.3 ml•kg-1•min-1Wii Boxing) was significantly (p ≤ 0.001) greater than seated VO2 (4.0 ± 0.1 ml•kg-1•min-1 PS2, 4.2 ± 0.1 ml•kg-1•min-1 Wii Madden, 6.1 ± 0.3 ml•kg-1•min-1Wii Boxing) for each gaming condition. Participants preferred (p ≤ 0.001) to sit for all gaming conditions except Wii Boxing. Playing video games while standing increases VO2 to a greater extent than playing the same games in a seated position. Standing was only preferred for the most physiologically challenging game, Wii Boxing. Gaming position should be considered when assessing the physiologic and behavioral outcomes of playing video games

Neck movement during cervical transforaminal epidural injections and the position of the vertebral artery: an anatomical study.

Background: Cervical transforaminal epidural steroid injections (CTFESIs) are sometimes performed in patients with cervical radiculopathy secondary to nerve-root compression. Neck movements for patient positioning may include rotation, flexion, and extension. As physicians performing such procedures do not move the neck for fear of injuring the vertebral artery, we performed fluoroscopy and cadaveric dissection to analyze any movement of the vertebral artery during head movement and its relation to the foramina in the setting of CTFESI. Purpose: To determine cervical rotational positioning for optimized vertebral artery location in the setting of cervical transforaminal epidural steroid injections. Material and Methods: Four sides from two Caucasian whole cadavers (all fresh-frozen) were used. Using a guide wire and digital subtraction fluoroscopy, we evaluated the vertebral artery mimicking a CTFESI, then we removed the transverse processes and evaluated the vertebral artery by direct observation. Results: After performing such maneuvers, no displacement of the vertebral artery was seen throughout its course from the C6 to the C2 intervertebral foramina. To our knowledge, this is the first anatomical observation of its kind that evaluates the position of the vertebral artery inside the foramina during movement of the neck. Conclusion: Special caution should be given to the medial border of the intervertebral foramina when adjusting the target site and needle penetration for the injection. This is especially true for C6-C4 levels, whereas for the remaining upper vertebrae, the attention should be focused on the anterior aspect of the foramen. Since our study was centered on the vertebral artery, we do not discard the need for contrast injection and real-time digital subtraction fluoroscopy while performing the transforaminal epidural injection in order to prevent other vascular injuries

Physiologic Responses, Liking and Motivation for Playing the Same Video Game on an Active Versus a Traditional, Non-Active Gaming System.

Int J Exerc Sci 5(2) : 160-169, 2012. Evidence suggests that individuals playing certain video games on the Nintendo Wii® (Wii) exhibit increased energy expenditure versus traditional video games, although little research examines non-Wii Sports/Fit games. The purpose of this study is to assess physiologic responses, liking, and the relative reinforcing value (RRV) of a popular, non-Wii sports video game for the Wii relative to the same game played on a traditional, non-active system. Twenty-four college-aged students participated. Heart rate and oxygen consumption (O2) was assessed during rest and when playing the following games: Madden NFL 2011® for Playstation 2 (PS2 Madden) and the Wii (Wii Madden), and Wii Sports Boxing. The RRV was assessed for Wii Madden versus PS2 Madden. Analysis of variance demonstrated a main effect for condition (p ≤ 0.01) as O2 (5.2 ± 0.2 ml·kg-1·min-1 Wii, 4.1 ± 0.1 ml·kg-1·min-1 PS2, 3.7 ± 0.1 ml·kg-1·min-1, rest) and heart rate (89.2 ± 2.7 bpm Wii, 79.7 ± 2.5 bpm PS2, 79.1 ± 2.5 bpm, rest) was greater for Wii Madden than PS2 Madden and rest. Heart Rate (105.4 ± 5.3 bpm) and O2 (10.4 ml·kg-1·min-1) for Wii Sports Boxing was significantly greater than all other conditions (p ≤ 0.003). The RRV was not significantly different between Wii Madden and PS2 Madden (p = 0.50). Compared to the same game on a traditional system, Wii Madden is more physiologically challenging and equally reinforcing. However, Wii Madden would not be categorized as moderate-intensity physical activity

U.S. Strategic Options towards Iran: Understanding the U.S.–Iranian Relations through Iranian Domestic Politics

The ongoing nuclear negotiations between the P5+1 and Iran have made greater progress on more substantial issues than any previous talks. This report argues that Iran’s unprecedented willingness to negotiate is strongly influenced by two factors: a united P5+1 and more importantly, a convergence of interests among Iran’s domestic factions. While there has long been knowledge of the challenges posed by Iran’s often-competing factions, no other study pinpoints them as a primary variable in the nuclear negotiations. Based on 50 interviews with high-level Iran experts and government officials and independent research, our study provides a unique framework for understanding the dynamics of Iranian domestic politics and its impact on the efficacy of U.S. policies. This study considers three scenarios the U.S. could encounter on July 20, 2014, when the current Joint Plan of Action (JPOA) expires: the P5+1 and Iran could sign a comprehensive deal; another interim deal could be reached; or negotiations could break down. The common thread throughout these recommendations is that the U.S. must find a way to capitalize on the factional convergence and avoid undermining it. The U.S. should always negotiate with Iran as a unitary actor, rather than favor certain factions; avoid measures that prompt one faction to undercut another faction; and understand that while not unique in having domestic competition, Iran’s political factions have a stronger effect on the success of negotiations than many have realized. If a comprehensive agreement is reached, we recommend pursuing limited engagement that seeks to broaden cooperation with Iran by working on issues that interest all Iranian factions, while also having deterrent threats in place should Iran renege. In the case of another interim deal, we recommend that the U.S. embrace balanced diplomacy, which increases the level of positive and negative inducements meant to persuade Iran to reach a comprehensive agreement. This recommendation, which mimics current U.S. policy, should focus solely on nuclear issues, unlike the first scenario. If nuclear negotiations break down, we recommend coercive diplomacy that involves gradual pressure, ranging from increased sanctions to authorizing the use of force. The challenge here is credibly threatening Iran without alienating the other P5+1 members or pushing Iran’s factions to unite against the United States. In all future negotiations, the U.S. should capitalize on Iranian domestic convergences and engage Iran as a whole.United States State Departmen

Morphine Use in the ED and Outcomes of Patients With Acute Heart Failure A Propensity Score-Matching Analysis Based on the EAHFE Registry

OBJECTIVE: The objective was to determine the relationship between short-term mortality and intravenous morphine use in ED patients who received a diagnosis of acute heart failure (AHF). METHODS: Consecutive patients with AHF presenting to 34 Spanish EDs from 2011 to 2014 were eligible for inclusion. The subjects were divided into those with (M) or without IV morphine treatment (WOM) groups during ED stay. The primary outcome was 30-day all-cause mortality, and secondary outcomes were mortality at different intermediate time points, in-hospital mortality, and length of hospital stay. We generated a propensity score to match the M and WOM groups that were 1:1 according to 46 different epidemiological, baseline, clinical, and therapeutic factors. We investigated independent risk factors for 30-day mortality in patients receiving morphine. RESULTS: We included 6,516 patients (mean age, 81 [SD, 10] years; 56% women): 416 (6.4%) in the M and 6,100 (93.6%) in the WOM group. Overall, 635 (9.7%; M, 26.7%; WOM, 8.6%) died by day 30. After propensity score matching, 275 paired patients constituted each group. Patients receiving morphine had a higher 30-day mortality (55 [20.0%] vs 35 [12.7%] deaths; hazard ratio, 1.66; 95% CI, 1.09-2.54; P=.017). In patients receiving morphine, death was directly related to glycemia (P=.013) and inversely related to the baseline Barthel index and systolic BP (P=.021) at ED arrival (P=.021). Mortality was increased at every intermediate time point, although the greatest risk was at the shortest time (at 3 days: 22 [8.0%] vs 7 [2.5%] deaths; OR, 3.33; 95% CI, 1.40-7.93; P=.014). In-hospital mortality did not increase (39 [14.2%] vs 26 [9.1%] deaths; OR, 1.65; 95% CI, 0.97-2.82; P=.083) and LOS did not differ between groups (median [interquartile range] in M, 8 [7]; WOM, 8 [6]; P=.79). CONCLUSIONS: This propensity score-matched analysis suggests that the use of IV morphine in AHF could be associated with increased 30-day mortality.Peer reviewe

Room Temperature Electrochemical Synthesis of Hg-1212 Superconducting Thin Films

In the present investigation, the novel two-step electrochemical process of room temperature synthesis of Hg-1212 superconducting films has been developed and reported first time. Electrochemical parameters were optimized by studying cyclic voltammetry (CV), linear sweep voltammetry (LSV) and chronoamperometry (CA) for the deposition of Hg-Ba-Ca-Cu alloy at room temperature. Current time transient showed progressive growth with hemispheriodal granules, which were then revealed by scanning electron microscopy (SEM). Stoichiometric electrocrystallization to get Hg1Ba2Ca1Cu2O6+x (Hg-1212) was completed by electrochemically intercalating oxygen species into Hg-Ba-Ca-Cu alloy at room temperature. The oxygen content in the samples was varied by varying the electrochemical oxidation period and the changes in the crystal structure, microstructure, and superconducting transition temperature (Tc) and critical current density (Jc) were recorded. The films oxidized for 28 min showed Tc = 104.7 K with Jc = 1.437 x 103 A/cm2. The dependence of superconducting parameters on oxygen content is correlated with structure property relations and reported in this paper.Comment: 39 pages, 17 figures. Submitted to Physica