Quantitative analysis of DNA-protein interactions using double-labeled native gel electrophoresis and fluorescence-based imaging

We have developed a sensitive, non-radioactive method to assess the interaction of transcription factors/DNA-binding proteins with DNA. We have modified the traditional radiolabeled DNA gel mobility shift assay to incorporate a DNA probe end-labeled with a Texas-red fluorophore and a DNA-binding protein tagged with the green fluorescent protein to monitor precisely DNA-protein complexation by native gel electrophoresis. We have applied this method to the DNA-binding proteins telomere release factor-1 and the sex-determining region-Y, demonstrating that the method is sensitive (able to detect 100 fmol of fluorescently labeled DNA), permits direct visualization of both the DNA probe and the DNA-binding protein, and enables quantitative analysis of DNA and protein complexation, and thereby an estimation of the stoichiometry of protein-DNA binding.

Decentralized supply chain formation using max-sum loopy belief propagation

Supply chain formation is the process by which a set of producers within a network determine the subset of these producers able to form a chain to supply goods to one or more consumers at the lowest cost. This problem has been tackled in a number of ways, including auctions, negotiations, and argumentation-based approaches. In this paper we show how this problem can be cast as an optimization of a pairwise cost function. Optimizing this class of energy functions is NP-hard but efficient approximations to the global minimum can be obtained using loopy belief propagation (LBP). Here we detail a max-sum LBP-based approach to the supply chain formation problem, involving decentralized message-passing between supply chain participants. Our approach is evaluated against a well-known decentralized double-auction method and an optimal centralized technique, showing several improvements on the auction method: it obtains better solutions for most network instances which allow for competitive equilibrium (Competitive equilibrium in Walsh and Wellman is a set of producer costs which permits a Pareto optimal state in which agents in the allocation receive non-negative surplus and agents not in the allocation would acquire non-positive surplus by participating in the supply chain) while also optimally solving problems where no competitive equilibrium exists, for which the double-auction method frequently produces inefficient solutions. © 2012 Wiley Periodicals, Inc.

Spectrum redistribution for cognitive radios using discriminatory spectrum double auction

With the reformation of spectrum policy and the development of cognitive radio, secondary users will be allowed to access spectrums licensed to primary users. Spectrum auctions can facilitate this secondary spectrum access in a market-driven way. To design an efficient auction framework, we first study the supply and demand pressures and the competitive equilibrium of the secondary spectrum market, considering the spectrum reusability. In well-designed auctions, competition among participants should lead to the competitive equilibrium according to the traditional economic point of view. Then, a discriminatory price spectrum double auction framework is proposed for this market. In this framework, rational participants compete with each other by using bidding prices, and their profits are guaranteed to be non-negative. A near-optimal heuristic algorithm is also proposed to solve the auction clearing problem of the proposed framework efficiently. Experimental results verify the efficiency of the proposed auction clearing algorithm and demonstrate that competition among secondary users and primary users can lead to the competitive equilibrium during auction iterations using the proposed auction framework. Copyright © 2011 John Wiley & Sons, Ltd.

18-Fluorodeoxyglucose positron emission tomography/computed tomography in the management of aggressive non-Hodgkin's B-cell lymphoma

18-Fluorodeoxyglucose (FDG-PET/CT) is an established imaging modality that has been proven to be of benefit in the management of aggressive B-cell non-Hodgkin's lymphoma, such as diffuse large B-cell lymphoma and advanced stage follicular lymphoma. The combination of anatomic and functional imaging afforded by FDG-PET/CT has led to superior sensitivity and specificity in the primary staging, restaging, and assessment of response to treatment of hematological malignancies when compared to FDG-PET and CT alone. The use of FDG-PET/CT for post treatment surveillance imaging remains controversial, and further study is needed to ascertain whether this modality is cost effective and appropriate for use in this setting.

Postoperative analgesic effect, of preoperatively administered dexamethasone, after operative fixation of fractured neck of femur: randomised, double blinded controlled study.

Background: Fractured neck of femur is a common cause of hospital admission in the elderly and usually requires operative fixation. In a variety of clinical settings, preoperative glucocorticoid administration has improved analgesia and decreased opioid consumption. Our objective was to define the postoperative analgesic efficacy of single dose of dexamethasone administered preoperatively in patients undergoing operative fixation of fractured neck of femur. Methods: Institutional ethical approval was granted and written informed consent was obtained from each patient. Patients awaiting for surgery at Cork University Hospital were recruited between July 2009 and August 2012. Participating patients, scheduled for surgery were randomly allocated to one of two groups (Dexamethasone or Placebo). Patients in the dexamethasone group received a single dose of intravenous dexamethasone 0.1 mg kg -1 immediately preoperatively. Patients in the placebo group received the same volume of normal saline. Patients underwent operative fixation of fractured neck of femur using standardised spinal anaesthesia and surgical techniques. The primary outcome was pain scores at rest 6 h after the surgery. Results: Thirty seven patients were recruited and data from thirty patients were analysed. The groups were similar in terms of patient characteristics. Pain scores at rest 6 h after the surgery (the principal outcome) were lesser in the dexamethasone group compared with the placebo group [0.8(1.3) vs. 3.9(2.9), mean(SD) p = 0.0004]. Cumulative morphine consumption 24 h after the surgery was also lesser in the dexamethasone group [7.7(8.3) vs. 15.1(9.4), mean(SD) mg, p = 0.04]. Conclusions: A single dose of intravenous dexamethasone 0.1 mg kg -1 administered before operative fixation of fractured neck of femur improve significantly the early postoperative analgesia. Trial registration: ClinicalTrials.gov identifier: NCT01550146, date of registration: 07/03/2012

SN 2011A: A low-luminosity interacting transient with a double plateau and strong sodium absorpton

We present optical photometry and spectroscopy of the optical transient SN 2011A. Our data span 140 days after discovery including BVRI u′g′r′i′z′ photometry and 11 epochs of optical spectroscopy. Originally classified as a type IIn supernova (SN IIn) due to the presence of narrow Hα emission, this object shows exceptional characteristics. First, the light curve shows a double plateau, a property only observed before in the impostor SN 1997bs. Second, SN 2011A has a very low luminosity (M_V=-15.72), placing it between normal luminous SNe IIn and SN impostors. Third, SN 2011A shows low velocity and high equivalent width absorption close to the sodium doublet, which increases with time and is most likely of circumstellar origin. This evolution is also accompanied by a change in line profile; when the absorption becomes stronger, a P Cygni profile appears. We discuss SN 2011A in the context of interacting SNe IIn and SN impostors, which appears to confirm the uniqueness of this transient. While we favor an impostor origin for SN 2011A, we highlight the difficulty in differentiating between terminal and non-terminal interacting transients.

Uncertainty and Speculators in an Auction for Emissions Permits

Auctions have become popular as means of allocating emissions permits in the emissions trading schemes developed around the world. Mostly, only a subset of the regulated polluters participate in these auctions along with speculators, creating a market with relatively few participants and, thus, incentive for strategic bidding. I characterize the bidding behavior of the polluters and the speculators, examining the effect of the latter on the profits of the former and on the auction outcome. It turns out that in addition to bidding for compliance, polluters also bid for speculation in the aftermarket. While the presence of the speculators forces the polluters to bid closer to their true valuations, it also creates a trade-off between increasing the revenue accrued to the regulator and reducing the profits of the auction-participating polluters. Nevertheless, the profits of the latter increase in the speculators' risk aversion.

Incentive based policies on climate change: taxes and tradable emssions permits

The reduction of Greenhouse Gases (GHG) plays a central role in the environmental policies considered by countries for implementation not only at its own level but also at supranational levels. This thesis is dedicated to investigate some aspects of two of the most relevant climate change policies. The first part is dedicated to emission permit markets and the second part to optimal carbon taxes. On emission permit markets we explore the strategic behavior of oligopolistic firms operating in polluting industrial sectors that are regulated by cap and trade systems. Our aim is to identify how market power influences the main results obtained under perfect competition assumptions and to understand how actions taken in one market affects the outcome of the other related market. A partial equilibrium model is developed for this purpose with specific abatement cost functions. In Chapter 2 we use the model to explain some of the most relevant literature results. In Chapter 3 the model is used to analyze different oligopolistic structures in the product market under the assumption of competitive permits market. There are two significant findings. Firstly, under the assumption of a Stackelberg oligopoly, firms have no incentives for lobbying in order to manipulate permit prices up, as they have under Cournot competition...

Double-trouble for respiratory control in Pompe disease

A commentary on ‘Hypoglossal neuropathology and respiratory activity in Pompe mice’, by Lee, K.-Z., Qiu, K., Sandhu, M. S., Elmullah, M. K., Falk, D. J., Lane, M. A., Reier, P. J., Byrne, B. J., and Fuller, D. D. (2011). Front. Physiol. 2:31. doi: 10.3389/fphys.2011.00031.

Thermal Treatments of Fe—Mn Alkoxide of Glycerol: Infrared absorption and emission

Synthetic Fe—Mn alkoxide of glycerol samples are submitted to controlled heating conditions and examined by IR absorption spectroscopy. On the other hand, the same sample is studied by infrared emission spectroscopy (IRES), upon heating in situ from 100 to 600°C. The spectral techniques employed in this contribution, especially IRES, show that as a result of the thermal treatments ferromagnetic oxides (manganese ferrite) are formed between 350 and 400°C. Some further spectral changes are seen at higher temperatures.

Vibrational spectroscopy of phthalocyanine and naphthalocyanine in sandwich-type (na)phthalocyaninato and porphyrinato rare earth complexes: Part 14. The infrared and Raman characteristics of phthalocyanine in “pinwheel-like” homoleptic bis[1,8,15,22-tetrakis(3-pentyloxy)phthalocyaninato] rare earth(III) double-decker complexes

The infrared (IR) spectroscopic data and Raman spectroscopic properties for a series of 13 “pinwheel-like” homoleptic bis(phthalocyaninato) rare earth complexes M[Pc(α-OC5H11)4]2 [M = Y and Pr–Lu except Pm; H2Pc(α-OC5H11)4 = 1,8,15,22-tetrakis(3-pentyloxy)phthalocyanine] have been collected and comparatively studied. Both the IR and Raman spectra for M[Pc(α-OC5H11)4]2 are more complicated than those of homoleptic bis(phthalocyaninato) rare earth analogues, namely M(Pc)2 and M[Pc(OC8H17)8]2, but resemble (for IR) or are a bit more complicated (for Raman) than those of heteroleptic counterparts M(Pc)[Pc(α-OC5H11)4], revealing the decreased molecular symmetry of these double-decker compounds, namely S8. Except for the obvious splitting of the isoindole breathing band at 1110–1123 cm−1, the IR spectra of M[Pc(α-OC5H11)4]2 are quite similar to those of corresponding M(Pc)[Pc(α-OC5H11)4] and therefore are similarly assigned. With laser excitation at 633 nm, Raman bands derived from isoindole ring and aza stretchings in the range of 1300–1600 cm−1 are selectively intensified. The IR spectra reveal that the frequencies of pyrrole stretching and pyrrole stretching coupled with the symmetrical CH bending of –CH3 groups are sensitive to the rare earth ionic size, while the Raman technique shows that the bands due to the isoindole stretchings and the coupled pyrrole and aza stretchings are similarly affected. Nevertheless, the phthalocyanine monoanion radical Pc′− IR marker band of bis(phthalocyaninato) complexes involving the same rare earth ion is found to shift to lower energy in the order M(Pc)2 > M(Pc)[Pc(α-OC5H11)4] > M[Pc(α-OC5H11)4]2, revealing the weakened π–π interaction between the two phthalocyanine rings in the same order.

Tuning the valence of the cerium center in (Na)phthalocyaninato and porphyrinato cerium double-deckers by changing the nature of the tetrapyrrole ligands

A series of 7 cerium double-decker complexes with various tetrapyrrole ligands including porphyrinates, phthalocyaninates, and 2,3-naphthalocyaninates have been prepared by previously described methodologies and characterized with elemental analysis and a range of spectroscopic methods. The molecular structures of two heteroleptic \[(na)phthalocyaninato](porphyrinato) complexes have also been determined by X-ray diffraction analysis which exhibit a slightly distorted square antiprismatic geometry with two domed ligands. Having a range of tetrapyrrole ligands with very different electronic properties, these compounds have been systematically investigated for the effects of ligands on the valence of the cerium center. On the basis of the spectroscopic (UV−vis, near-IR, IR, and Raman), electrochemical, and structural data of these compounds and compared with those of the other rare earth(III) counterparts reported earlier, it has been found that the cerium center adopts an intermediate valence in these complexes. It assumes a virtually trivalent state in cerium bis(tetra-tert-butylnaphthalocyaninate) as a result of the two electron rich naphthalocyaninato ligands, which facilitate the delocalization of electron from the ligands to the metal center. For the rest of the cerium double-deckers, the cerium center is predominantly tetravalent. The valences (3.59−3.68) have been quantified according to their LIII-edge X-ray absorption near-edge structure (XANES) profiles.

Raman spectroscopic characteristics of phthalocyanine and naphthalocyanine in sandwich-type phthalocyaninato and porphyrinato rare earth complexes Part 5. – Raman spectroscopic characteristics of naphthalocyanine in mixed [tetrakis(4-tert-butylphenyl)porphyrinato]-(naphthalocyaninato) rare earth double-deckers

Raman spectra were recorded in the range 400–1800 cm−1 for a series of 15 mixed \[tetrakis(4-tert-butylphenyl)porphyrinato](2,3-naphthalocyaninato) rare earth double-deckers M(TBPP)(Nc) (M = Y; La–Lu except Pm) using laser excitation at 632.8 and 785 nm. Comparisons with bis(naphthalocyaninato) rare earth counterparts reveal that the vibrations of the metallonaphthalocyanine M(Nc) fragment dominate the Raman features of M(TBPP)(Nc). When excited with radiation of 632.8 nm, the most intense vibration appears at about 1595 cm−1, due to the naphthalene stretching. These complexes exhibit the marker Raman band for Nc•− as a medium-intense band in the range 1496–1507 cm−1, attributed to the coupling of pyrrole and aza stretching, while the marker Raman band of Nc2− in intermediate-valence Ce(TBPP)(Nc) appears as a strong band at 1493 cm−1 and is due to the isoindole stretchings. By contrast, when excited with radiation of 785 nm that is in close resonance with the main Q absorption band of the naphthalocyanine ligand, the ring radial vibrations at ca 680 and 735 cm−1 for MIII(TBPP)(Nc) are selectively intensified and are the most intense bands. For the cerium double-decker, the most intense vibration also acting as the marker Raman band of Nc2− appears at 1497 cm−1 with contributions from both pyrrole CC and aza CN stretches. The same vibrational modes show weak to medium intensity scattering at 1506–1509 cm−1 for MIII(TBPP)(Nc) and this is the marker Raman band of Nc•− when thus excited. The scatterings due to the Nc breathings, ring radial vibration, aza group stretchings, naphthalene stretchings, benzoisoindole stretchings and the coupling of pyrrole CC and aza CN stretchings in MIII(TBPP)(Nc) are all slightly blue shifted along with the decrease in rare earth ionic radius, confirming the effects of increased ring–ring interactions on the Raman characteristics of naphthalocyanine in the mixed ring double-deckers.

Thermal treatment of weddellite—a Raman and infrared emission spectroscopic study

Thermal transformations of natural calcium oxalate dihydrate known in mineralogy as weddellite have been undertaken using a combination of Raman microscopy and infrared emission spectroscopy. The vibrational spectroscopic data was complimented with high resolution thermogravimetric analysis combined with evolved gas mass spectrometry. TG–MS identified three mass loss steps at 114, 422 and 592 °C. In the first mass loss step water is evolved only, in the second and third steps carbon dioxide is evolved. The combination of Raman microscopy and a thermal stage clearly identifies the changes in the molecular structure with thermal treatment. Weddellite is the phase in the temperature range up to the pre-dehydration temperature of 97 °C. At this temperature, the phase formed is whewellite (calcium oxalate monohydrate) and above 114 °C the phase is the anhydrous calcium oxalate. Above 422 °C, calcium carbonate is formed. Infrared emission spectroscopy shows that this mineral decomposes at around 650 °C. Changes in the position and intensity of the C=O and C---C stretching vibrations in the Raman spectra indicate the temperature range at which these phase changes occur.