Pessanha, V, Dias RJ, Lourenço JM, Farchi E, Sousa D.
2011.
Practical verification of high-level dataraces in transactional memory programs, July. Proceedings of 9th the Workshop on Parallel and Distributed Systems: Testing, Analysis, and Debugging. :26–34., New York, NY, USA: ACM
AbstractIn this paper we present MoTh, a tool that uses static analysis to enable the automatic verification of concurrency anomalies in Transactional Memory Java programs. Currently MoTh detects high-level dataraces and stale-value errors, but it is extendable by plugging-in sensors, each sensor implementing an anomaly detecting algorithm. We validate and benchmark MoTh by applying it to a set of well known concurrent buggy programs and by close comparison of the results with other similar tools. The results achieved so far are very promising, yielding good accuracy while triggering only a very limited number of false warnings.
Silva, {LB}, Veigas B, c}alo Doria G{\c, Costa P, Inácio J, Martins R, Fortunato E, Baptista {PV}.
2011.
Portable optoelectronic biosensing platform for identification of mycobacteria from the Mycobacterium tuberculosis complex, jan. Biosensors & Bioelectronics. 26:2012–2017., Number 5: Elsevier
AbstractIn this paper we report on the fabrication and performance of a portable and low cost optoelectronic platform integrating a double color tuned light emitting diode as light source, an amorphous/nanocrystalline silicon photodetector with a flat spectral response in the wavelength range from 520. nm to 630. nm and integrated electronic for signal acquisition and conditioning constituted by current to voltage converter, a filter and an amplification stage, followed by an analog to digital converter, with appropriate software for full automation to minimize human error. Incorporation of the double color tuned light emitting diode provides for a simple yet innovative solution to signal acquisition independently from the light intensity and/or solution concentration, while considerably decreasing production costs. Detection based on Au-nanoprobes constitutes the biorecognition step and allowed identification of specific sequences of Mycobacterium tuberculosis complex, namely Mycobacterium bovis and M. tuberculosis in biological samples.
Barbosa, DJ, Capela JP, Oliveira JMA, Ferreira L, Branco P, Fernandes E, Bastos ML, Carvalho F.
2011.
Pro-oxidant effects of ``ecstasy{''} and its metabolites in mouse brain synaptosomes, AUG 28. TOXICOLOGY LETTERS. 205:S113., Number 1: European Soc Toxicol
Abstractn/a
Avo, J, Parola AJ, Lima JC, Pina F, Cunha-Silva L.
2011.
Phase transition thermochromism based on C-H acidity of 4-alkylflavylium compounds in Pluronic F-127, 2011. Journal of Materials Chemistry. 21:16628-16637.
AbstractIn moderately acidic water/ethanol solutions, 7-(naphthalen-2-ylmethyl)-5,6-dihydrobenzo[c]xanthen12-ium perchlorate shows C-H proton acidity giving rise to an ethylenic base species, instead of the hydration products of the typical flavylium network of chemical reactions, hemiketal, cis-chalcone and trans-chalcone. The kinetics of this acid-base process is much slower, k(obs)(s(-1)) = 3.5 x 10(-3) + 0.16[H(+)], than those commonly observed for O-H deprotonation. In the presence of the triblock copolymer Pluronic F-127, the ethylenic base is dramatically stabilized shifting the pK(a) from 1.35 (in ethanol : water (1 : 1) to -0.35. Taking profit from the well-described temperature dependence of this polymer, a phase transition thermochromic system was achieved. The system was cycled between 5 and 35 degrees C with negligible changes in absorbance after 20 cycles.
Leydet, Y, Gavara R, Cunha-Silva L, Parola AJ, Pina F.
2011.
Phase-Dependent Photochromism of a Lactone-Stabilized Chromene from a Flavylium Reaction Network, 2011. Chemistry-a European Journal. 17:3663-3671.
AbstractNew trans-2-hydroxychalcones bearing a carboxylate group at position 2' (Ct(-)) were synthesized (compounds 2 and 3). These compounds lead to a network of chemical reactions depending on pH value, light, and solvent. In water, when the pH value is lowered, the ionized trans-chalcone is protonated and the flavylium cation AH(+) is formed at very acidic pH values through hemiketal B and cis-chalcone Cc, with global acidity constants of pK'(a) <= -1 and approximate to 0.1, respectively, for 2 and 3. The electron-acceptor character of the carboxylic substituent not only increases the observed acidity of the flavylium cation, but also decreases the rate of the ring-opening/closing from a subsecond timescale to hours relative to model compound 1 (without carboxylate). The photochemistry of the network was studied in detail by means of continuous irradiation, monitored by UV/Vis absorption and H-1 and C-13 NMR spectroscopic analysis. Although compound 3 is only slightly photoactive, compound 2 (Ct(-)) reacts in aqueous solutions (lambda(irr) = 313 nm) to form B- and Cc(-), with a global quantum yield of 0.15, and fully reverts back to Ct(-) with a rate constant of k = 6.7 x 10(-5) s(-1). The flavylium cation is no longer formed in methanol, and irradiation of Ct(-) leads to the formation of B- and the new lactone-trapped chromene species La. The formation of La takes place through a sequence of three photochemical steps: photoisomerization of Ct(-), photo-ring-closing reaction of Cc , and photolactonization of B-. Only the cis/trans isomerization and ring-closing reactions are thermally reversible on a timescale of seconds and hours, respectively. A photochromic system was achieved in rigid matrices of methanol (at 77 K) and 1-dodecanol (5 degrees C) by irradiating lactone La to give a red ortho-quinone allide through a photo-ring-opening reaction; the color disappears with a rate constant of k = 1.25 x 10(-2) s(-1) in 1-dodecanol at 5 degrees C.
Merino, EG, Rodrigues C, Viciosa TM, Melo C, Sotomayor J, Dionísio M, Correia NT.
2011.
Phase Transformations Undergone by Triton X-100 Probed by Differential Scanning Calorimetry and Dielectric Relaxation Spectroscopy. Physical Chemistry B. 12336(1):12336–12347.
AbstractThe phase transformations of the surfactant Triton X-100 were investigated by differential scanning calorimetry (DSC), polarized optical microscopy (POM), and dielectric relaxation spectroscopy (DRS). In particular, crystallization was induced at different cooling rates comprised between 13 and 0.5 K min–1. Vitrification was detected by both DSC and DRS techniques with a glass transition temperature of 212 K (measured on heating by DSC) allowing classifying Triton X-100 as a glass former. A fully amorphous material was obtained by cooling at a rate ≥10 K min–1, while crystallization was observed for lower cooling rates. The temperature of the onset of melt-crystallization was found to be dependent on the cooling scan rate, being higher the lower was the scan rate. In subsequent heating scans, the material undergoes cold-crystallization except if cooled previously at a rate ≤1 K min–1. None of the different thermal histories led to a 100% crystalline material because always the jump typical of the glass transformation in both heat flux (DSC) and real permittivity (DRS) is observed. It was also observed that the extent/morphology of the crystalline phase depends on the degree of undercooling, with higher spherulites developing for lower undercooling degree (24 K ≤ Tm – Tcr ≤ 44 K) in melt-crystallization and a grain-like morphology emerging for Tm – Tcr ≈ 57 K either in melt- or cold-crystallization. The isothermal cold- and melt-crystallizations were monitored near above the calorimetric glass transition temperature by POM (221 K) and real-time DRS (Tcr = 219, 220, and 221 K) to evaluate the phase transformation from an amorphous to a semicrystalline material. By DRS, the α-relaxation associated with the dynamic glass transition was followed, with the observation that it depletes upon both type of crystallizations with no significant changes either in shape or in location. Kinetic parameters were obtained from the time evolution of the normalized permittivity according to a modified Avrami model taking in account the induction time. The reason the isothermal crystallization occurs to a great extent in the vicinity of the glass transition was rationalized as the simultaneous effect of (i) a high dynamic fragile behavior and (ii) the occurrence of catastrophic nucleation/crystal growth probably enabled by a preordering tendency of the surfactant molecules. This is compatible with the estimated low Avrami exponent (1.12 ≤ n ≤ 1.6), suggesting that relative short length scale motions govern the crystal growth in Triton X-100 coherent with the observation of a grainy crystallization by POM.
Borlido, L, Azevedo AM, Roque ACA, Aires-Barros MR.
2011.
Potential of boronic acid functionalized magnetic particles in the adsorption of human antibodies under mammalian cell culture conditions. Journal of Chromatography A. 1218(43):7821-7827.
AbstractIn this work, we systematically evaluated the potential of using boronic acid functionalized magnetic particles in the capturing of human immunoglobulin G under typical mammalian cell culture conditions. For comparison, Protein A coated magnetic particles were also used. The binding pH was found to significantly influence the adsorption isotherms of boronic acid particles with the higher capacities (0.216 g IgG/g support) being observed at pH 7.4. Comparatively, this value was 0.109 g IgG/g support, for Protein A particles under the same conditions. Both particles revealed very fast adsorption kinetics with more than 70% of the maximum binding capacity being achieved in a few seconds. The effect of glucose and lactate, which are known to interact with boronic acid, was evaluated. For glucose, the binding capacity was significantly influenced by the pH and decreased as pH increased. At pH 9.5, a 70% lower binding capacity was observed for glucose concentrations as low as 0.5 g/l. The effect of lactate was less pronounced and almost pH independent reaching at most 20% decrease in binding capacity. Nevertheless, the effect of both molecules was always lower at pH 7.4. The optimization of the elution conditions enabled complete recovery of bound IgG from boronic acid particles using 50mM Tris-HCl, 200 mM sorbitol, 200 mM NaCl at pH 8.5.
Pessanha, V.
2011.
Practical Verification of Anomalies in Transactional Memory Programs. FCT - Universidade Nova de Lisboa. (
João M. Lourenço, Ed.).: Universidade Nova de Lisboa
AbstractTransactional Memory (TM) is an approach to concurrency control in general pur- pose programming languages that inherits the concept of transaction from the database setting. Unlike other language constructs such as locks, TM has an optimistic approach to concurrency control by allowing more than one thread to access simultaneously the same critical section. A transaction always executes as if it is alone in the system, and in the end its effects are undone (rolled back) if it conflicts with another concurrent transac- tions. In spite of the potential for increasing scalability and performance, TM is a recent and developing programming model and still has a very limited impact in real-world applications.
Designing and developing concurrent software is difficult and error prone. Concur- rent programs exhibit concurrency anomalies that originate faults and failures. Despite some claims that TM programs are less error prone, they still exhibit concurrency anoma- lies such as high-level dataraces, i.e., wrong delimitations of transactions’ scope, and stale-value errors, that occur when the value of a shared variable jumps from an atomic block to another.
Programs with this kind of anomalies can exhibit unpredictable and wrong behaviour, not fulfilling the goals for which they were conceived.
This work aims the detection of anomalies through static analysis of transactional Java ByteCode programs that execute in strong atomicity. A extensible and flexible framework is proposed, which can be extended with plugins that detect specific types of anomalies. With this framework we expect to prove that high-level dataraces and stale-value errors can be detected with reasonable precision through static analysis.
Keywords: Atomicity Violation, High-Level Datarace, Static Analysis, Concurrency, Software Transactional Memory