Towards emotional interaction: using movies to automatically learn users’ emotional states

The HCI community is actively seeking novel methodologies to gain insight into the user's experience during interaction with both the application and the content. We propose an emotional recognition engine capable of automatically recognizing a set of human emotional states using psychophysiological measures of the autonomous nervous system, including galvanic skin response, respiration, and heart rate. A novel pattern recognition system, based on discriminant analysis and support vector machine classifiers is trained using movies' scenes selected to induce emotions ranging from the positive to the negative valence dimension, including happiness, anger, disgust, sadness, and fear. In this paper we introduce an emotion recognition system and evaluate its accuracy by presenting the results of an experiment conducted with three physiologic sensors.info:eu-repo/semantics/publishedVersio

Bradyzoite pseudokinase 1 is crucial for efficient oral infectivity of the Toxoplasma gondii tissue cyst.

The tissue cyst formed by the bradyzoite stage of Toxoplasma gondii is essential for persistent infection of the host and oral transmission. Bradyzoite pseudokinase 1 (BPK1) is a component of the cyst wall, but nothing has previously been known about its function. Here, we show that immunoprecipitation of BPK1 from in vitro bradyzoite cultures, 4 days postinfection, identifies at least four associating proteins: MAG1, MCP4, GRA8, and GRA9. To determine the role of BPK1, a strain of Toxoplasma was generated with the bpk1 locus deleted. This BPK1 knockout strain (Δbpk1) was investigated in vitro and in vivo. No defect was found in terms of in vitro cyst formation and no difference in pathogenesis or cyst burden 4 weeks postinfection (wpi) was detected after intraperitoneal (i.p.) infection with Δbpk1 tachyzoites, although the Δbpk1 cysts were significantly smaller than parental or BPK1-complemented strains at 8 wpi. Pepsin-acid treatment of 4 wpi in vivo cysts revealed that Δbpk1 parasites are significantly more sensitive to this treatment than the parental and complemented strains. Consistent with this, 4 wpi Δbpk1 cysts showed reduced ability to cause oral infection compared to the parental and complemented strains. Together, these data reveal that BPK1 plays a crucial role in the in vivo development and infectivity of Toxoplasma cysts

Anomalous versus slowed-down Brownian diffusion in the ligand-binding equilibrium

Measurements of protein motion in living cells and membranes consistently report transient anomalous diffusion (subdiffusion) which converges back to a Brownian motion with reduced diffusion coefficient at long times, after the anomalous diffusion regime. Therefore, slowed-down Brownian motion could be considered the macroscopic limit of transient anomalous diffusion. On the other hand, membranes are also heterogeneous media in which Brownian motion may be locally slowed-down due to variations in lipid composition. Here, we investigate whether both situations lead to a similar behavior for the reversible ligand-binding reaction in 2d. We compare the (long-time) equilibrium properties obtained with transient anomalous diffusion due to obstacle hindrance or power-law distributed residence times (continuous-time random walks) to those obtained with space-dependent slowed-down Brownian motion. Using theoretical arguments and Monte-Carlo simulations, we show that those three scenarios have distinctive effects on the apparent affinity of the reaction. While continuous-time random walks decrease the apparent affinity of the reaction, locally slowed-down Brownian motion and local hinderance by obstacles both improve it. However, only in the case of slowed-down Brownian motion, the affinity is maximal when the slowdown is restricted to a subregion of the available space. Hence, even at long times (equilibrium), these processes are different and exhibit irreconcilable behaviors when the area fraction of reduced mobility changes.Comment: Biophysical Journal (2013

Imaging of Viral Thymidine Kinase Gene Expression by Replicating Oncolytic Adenovirus and Prediction of Therapeutic Efficacy

PURPOSE: We have used a genetically attenuated adenoviral vector which expresses HSVtk to assess the possible additive role of suicidal gene therapy for enhanced oncolytic effect of the virus. Expression of TK was measured using a radiotracer-based molecular counting and imaging system. MATERIALS AND METHODS: Replication-competent recombinant adenoviral vector (Ad-DeltaE1B19/55) was used in this study, whereas replication-incompetent adenovirus (Ad-DeltaE1A) was generated as a control. Both Ad-DeltaE1B19/55-TK and Ad-DeltaE1A-TK comprise the HSVtk gene inserted into the E3 region of the viruses. YCC-2 cells were infected with the viruses and incubated with 2'-deoxy-2'-fluoro-beta-D-arabinofuranosyl-5-iodouracil (I-131 FIAU) to measure amount of radioactivity. The cytotoxicity of the viruses was determined, and gamma ray imaging of HSVtk gene was performed. MTT assay was also performed after GCV treatment. RESULTS: On gamma counter-analyses, counts/ minute (cpm)/microg of protein showed MOIs dependency with DeltaE1B19/55-TK infection. On MTT assay, Ad-DeltaE1B19/55-TK led to more efficient cell killing than Ad-DeltaE1A-TK. On plate imaging by gamma camera, both Ad-DeltaE1B19/55-TK and Ad-DeltaE1A-TK infected cells showed increased I-131 FIAU uptake in a MOI dependent pattern, and with GCV treatment, cell viability of DeltaE1B19/55-TK infection was remarkably reduced compared to that of Ad-DeltaE1A-TK infection. CONCLUSION: Replicating Ad-DeltaE1B19/55-TK showed more efficient TK expression even in the presence of higher-cancer cell killing effects compared to non-replicating Ad-DeltaE1A-TK. Therefore, GCV treatment still possessed an additive role to oncolytic effect of Ad-DeltaE1B19/55-TK. The expression of TK by oncolytic viruses could rapidly be screened using a radiotracer-based counting and imaging technique.ope

Assessment on Hydrologic Response by Climate Change in the Chao Phraya River Basin, Thailand

The Chao Phraya River in Thailand has been greatly affected by climate change and the occurrence of extreme flood events, hindering its economic development. This study assessed the hydrological responses of the Chao Phraya River basin under several climate sensitivity and greenhouse gas emission scenarios. The Soil and Water Assessment Tool (SWAT) model was applied to simulate the streamflow using meteorological and observed data over a nine-year period from 2003 to 2011. The SWAT model produced an acceptable performance for calibration and validation, yielding Nash-Sutcliffe efficiency (NSE) values greater than 0.5. Precipitation scenarios yielded streamflow variations that corresponded to the change of rainfall intensity and amount of rainfall, while scenarios with increased air temperatures predicted future water shortages. High CO2 concentration scenarios incorporated plant responses that led to a dramatic increase in streamflow. The greenhouse gas emission scenarios increased the streamflow variations to 6.8%, 41.9%, and 38.4% from the reference period (2003-2011). This study also provided a framework upon which the peak flow can be managed to control the nonpoint sources during wet season. We hope that the future climate scenarios presented in this study could provide predictive information for the river basin.close

Complete Chloroplast Genome Sequence of a Major Allogamous Forage Species, Perennial Ryegrass (Lolium perenne L.)

Lolium perenne L. (perennial ryegrass) is globally one of the most important forage and grassland crops. We sequenced the chloroplast (cp) genome of Lolium perenne cultivar Cashel. The L. perenne cp genome is 135 282 bp with a typical quadripartite structure. It contains genes for 76 unique proteins, 30 tRNAs and four rRNAs. As in other grasses, the genes accD, ycf1 and ycf2 are absent. The genome is of average size within its subfamily Pooideae and of medium size within the Poaceae. Genome size differences are mainly due to length variations in non-coding regions. However, considerable length differences of 1–27 codons in comparison of L. perenne to other Poaceae and 1–68 codons among all Poaceae were also detected. Within the cp genome of this outcrossing cultivar, 10 insertion/deletion polymorphisms and 40 single nucleotide polymorphisms were detected. Two of the polymorphisms involve tiny inversions within hairpin structures. By comparing the genome sequence with RT–PCR products of transcripts for 33 genes, 31 mRNA editing sites were identified, five of them unique to Lolium. The cp genome sequence of L. perenne is available under Accession number AM777385 at the European Molecular Biology Laboratory, National Center for Biotechnology Information and DNA DataBank of Japan

Trafficking of Siderophore Transporters in Saccharomyces cerevisiae and Intracellular Fate of Ferrioxamine B Conjugates

We have studied the intracellular trafficking of Sit1 [ferrioxamine B (FOB) transporter] and Enb1 (enterobactin transporter) in Saccharomyces cerevisiae using green fluorescent protein (GFP) fusion proteins. Enb1 was constitutively targeted to the plasma membrane. Sit1 was essentially targeted to the vacuolar degradation pathway when synthesized in the absence of substrate. Massive plasma membrane sorting of Sit1 was induced by various siderophore substrates of Sit1, and by coprogen, which is not a substrate of Sit1. Thus, different siderophore transporters use different regulated trafficking processes. We also studied the fate of Sit1-mediated internalized siderophores. Ferrioxamine B was recovered in isolated vacuolar fractions, where it could be detected spectrophotometrically. Ferrioxamine B coupled to an inhibitor of mitochondrial protoporphyrinogen oxidase (acifluorfen) could not reach its target unless the cells were disrupted, confirming the tight compartmentalization of siderophores within cells. Ferrioxamine B coupled to a fluorescent moiety, FOB-nitrobenz-2-oxa-1,3-diazole, used as a Sit1-dependent iron source, accumulated in the vacuolar lumen even in mutants displaying a steady-state accumulation of Sit1 at the plasma membrane or in endosomal compartments. Thus, the fates of siderophore transporters and siderophores diverge early in the trafficking process

Dyes That Bear Thiazolylazo Groups as Chromogenic Chemosensors for Metal Cations

A family of dyes (L 1-L 6) that contain a thiazolylazo group as signalling subunit and several macrocyclic cavities with different ring sizes and type and number of heteroatoms as binding sites has been synthesized and characterized. Solutions of L 1-L 6 in acetonitrile show broad and structureless absorption bands in the 554-577 nm range with typicalmolar absorption coefficients that range from 20000 to 32000 M -1 cm -1. A detailed protonation study was carried out with solutions of L 1, L 2 and L 5 in acetonitrile. Addition of one equivalent of protons to L 1 and L 2 resulted in the development of a new band at 425 and 370 nm, respectively, which was ascribed to protonation in the aniline nitrogen. In contrast, protonation of L 5 resulted in a bathochromic shift of 25 nm of the absorption band that was conceivable with protonation of one of the nitrogen atoms of the azo moiety. These results were in agreement with 1H NMR spectroscopic data. Theoretical studies on the model ligand L 1 and on different possible protonation species were also performed by using density functional theory (DFT) quantum mechanical calculations. Colour modulations in solutions of L 1-L 6 in acetonitrile in the presence of the metal cations Fe 3+, Ni 2+, Zn 2+, Cd 2+, Pb 2+ and Hg 2+ have been studied. A selective chromogenic response of L 4 in the presence of Pb 2+ and L 5 in the presence of Hg 2+ was observed. To get a better insight into the chromophoric nature in the presence of metal cations, the interaction of Hg 2+ with the model compound L 1 in two different coordination modes was studied theoretically by using density functional theory (DFT) quantum mechanical calculations.Financial support by the Spanish Ministerio de Ciencia e Innovacion (MICINN) through projects MAT2009-14564-C04-01, CTQ2010-15364, Molecular Nanoscience (Consolider Ingenio CSD2007-00010) and Generalitat Valenciana (PROMETEO/2009/016 and PROMETEO/2009/108) is gratefully acknowledged.Abalos Aguado, T.; Moragues Pons, ME.; Royo Calvo, S.; Jiménez, D.; Martínez Mañez, R.; Soto Camino, J.; Sancenón Galarza, F.... (2012). Dyes That Bear Thiazolylazo Groups as Chromogenic Chemosensors for Metal Cations. European Journal of Inorganic Chemistry. (1):76-84. doi:10.1002/ejic.201100834S76841Fabbrizzi, L., & Poggi, A. (1995). Sensors and switches from supramolecular chemistry. Chemical Society Reviews, 24(3), 197. doi:10.1039/cs9952400197Bissell, R. A., de Silva, A. P., Gunaratne, H. Q. N., Lynch, P. L. M., Maguire, G. E. M., & Sandanayake, K. R. A. S. (1992). Molecular fluorescent signalling with ‘fluor–spacer–receptor’ systems: approaches to sensing and switching devices via supramolecular photophysics. Chem. Soc. Rev., 21(3), 187-195. doi:10.1039/cs9922100187Dix, J. P., & Vögtle, F. (1978). Ionenselektive Kronenether-Farbstoffe. Angewandte Chemie, 90(11), 893-894. doi:10.1002/ange.19780901109Martínez-Máñez, R., & Sancenón, F. (2003). Fluorogenic and Chromogenic Chemosensors and Reagents for Anions. Chemical Reviews, 103(11), 4419-4476. doi:10.1021/cr010421eBeer, P. D., & Gale, P. A. (2001). Erkennung und Nachweis von Anionen: gegenwärtiger Stand und Perspektiven. Angewandte Chemie, 113(3), 502-532. doi:10.1002/1521-3757(20010202)113:33.0.co;2-aValeur, B. (2000). Design principles of fluorescent molecular sensors for cation recognition. Coordination Chemistry Reviews, 205(1), 3-40. doi:10.1016/s0010-8545(00)00246-0Czarnik, A. W. (1994). Chemical Communication in Water Using Fluorescent Chemosensors. Accounts of Chemical Research, 27(10), 302-308. doi:10.1021/ar00046a003Rurack, K., & Resch-Genger, U. (2002). Rigidization, preorientation and electronic decoupling—the ‘magic triangle’ for the design of highly efficient fluorescent sensors and switches. Chemical Society Reviews, 31(2), 116-127. doi:10.1039/b100604pDe Silva, A. P., Gunaratne, H. Q. N., Gunnlaugsson, T., Huxley, A. J. M., McCoy, C. P., Rademacher, J. T., & Rice, T. E. (1997). Signaling Recognition Events with Fluorescent Sensors and Switches. Chemical Reviews, 97(5), 1515-1566. doi:10.1021/cr960386pRurack, K. (2001). Flipping the light switch ‘ON’ – the design of sensor molecules that show cation-induced fluorescence enhancement with heavy and transition metal ions. Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 57(11), 2161-2195. doi:10.1016/s1386-1425(01)00492-9Loehr, H. G., & Voegtle, F. (1985). Chromo- and fluoroionophores. A new class of dye reagents. Accounts of Chemical Research, 18(3), 65-72. doi:10.1021/ar00111a001Takagi, M., & Ueno, K. (1984). Crown compounds as alkali and alkaline earth metal ion selective chromogenic reagents. Host Guest Complex Chemistry III, 39-65. doi:10.1007/3-540-12821-2_2Ros-Lis, J. V., Martínez-Máñez, R., Sancenón, F., Soto, J., Rurack, K., & Weißhoff, H. (2007). Signalling Mechanisms in Anion-Responsive Push-Pull Chromophores: The Hydrogen-Bonding, Deprotonation and Anion-Exchange Chemistry of Functionalized Azo Dyes. European Journal of Organic Chemistry, 2007(15), 2449-2458. doi:10.1002/ejoc.200601111Chen, Y.-J., & Chung, W.-S. (2009). Tetrazoles and para-Substituted Phenylazo-Coupled Calix[4]arenes as Highly Sensitive Chromogenic Sensors for Ca2+. European Journal of Organic Chemistry, 2009(28), 4770-4776. doi:10.1002/ejoc.200900603Lee, H. G., Lee, J.-E., & Choi, K. S. (2006). Chromoionophoric N2S2 macrocycles exhibiting mercury(II) selectivity. Inorganic Chemistry Communications, 9(6), 582-585. doi:10.1016/j.inoche.2006.03.005Mahato, P., Ghosh, A., Saha, S., Mishra, S., Mishra, S. K., & Das, A. (2010). Recognition of Hg2+Using Diametrically Disubstituted Cyclam Unit. Inorganic Chemistry, 49(24), 11485-11492. doi:10.1021/ic1014797Hovind, H. R. (1975). Thiazolylazo dyes and their applications in analytical chemistry. A review. The Analyst, 100(1196), 769. doi:10.1039/an9750000769Lemos, V. A., Santos, E. S., Santos, M. S., & Yamaki, R. T. (2007). Thiazolylazo dyes and their application in analytical methods. Microchimica Acta, 158(3-4), 189-204. doi:10.1007/s00604-006-0704-9Saeed, M. M., Bajwa, S. Z., Ansari, M. S., & Ahmed, R. (2005). Solid phase sorption of microamount of Hg(II) onto 1-(2-thiazolylazo)-2-naphthol (TAN) loaded polyurethane foam. Radiochimica Acta, 93(3). doi:10.1524/ract.93.3.177.61610Starvin, A. M., & Rao, T. P. (2004). Removal and recovery of mercury(II) from hazardous wastes using 1-(2-thiazolylazo)-2-naphthol functionalized activated carbon as solid phase extractant. Journal of Hazardous Materials, 113(1-3), 75-79. doi:10.1016/j.jhazmat.2004.04.021Wang, M., Lin, J.-M., Qu, F., Shan, X., & Chen, Z. (2004). On-capillary complexation of metal ions with 4-(2-thiazolylazo)resorcinol in capillary electrophoresis. Journal of Chromatography A, 1029(1-2), 249-254. doi:10.1016/j.chroma.2003.12.011Takase, I. (2003). The use of 2-2-thiazolylazo-p-cresol to minimize the interference of Ni and Cu for the bismuth determination in alloys by hydride generation atomic absorption spectrometry. Talanta, 61(5), 597-602. doi:10.1016/s0039-9140(03)00365-5Amin, A. S. (2001). SPECTROPHOTOMETRIC DETERMINATION OF CADMIUM USING THIAZOLYLAZO CHROMOGENIC REAGENTS IN THE PRESENCE OF TRITON X-100: APPLICATION IN ENVIRONMENTAL SAMPLES. Analytical Letters, 34(1), 163-176. doi:10.1081/al-100002714Moragues, M. E., Martínez-Máñez, R., & Sancenón, F. (2011). Chromogenic and fluorogenic chemosensors and reagents for anions. A comprehensive review of the year 2009. Chemical Society Reviews, 40(5), 2593. doi:10.1039/c0cs00015aMartínez-Máñez, R., Sancenón, F., Hecht, M., Biyikal, M., & Rurack, K. (2010). Nanoscopic optical sensors based on functional supramolecular hybrid materials. Analytical and Bioanalytical Chemistry, 399(1), 55-74. doi:10.1007/s00216-010-4198-2Richman, J. E., & Atkins, T. J. (1974). Nitrogen analogs of crown ethers. Journal of the American Chemical Society, 96(7), 2268-2270. doi:10.1021/ja00814a056MACROCYCLIC POLYAMINES: 1,4,7,10,13,16-HEXAÄZACYCLOÖCTADECANE. (1978). Organic Syntheses, 58, 86. doi:10.15227/orgsyn.058.0086Krakowiak, K. E., Bradshaw, J. S., & Zamecka-Krakowiak, D. J. (1989). Synthesis of aza-crown ethers. Chemical Reviews, 89(4), 929-972. doi:10.1021/cr00094a008Higashino, K., Nakaya, T., & Ishiguro, E. (1994). Photovoltaic properties of azo compounds containing the thiazole group. Journal of Photochemistry and Photobiology A: Chemistry, 79(1-2), 81-88. doi:10.1016/1010-6030(94)87017-9Mustroph, H., & Epperlein, J. (2010). Quantitative Beschreibung der Absorptionsmaxima von substituierten 2-Thiazol-azofarbstoffen. Zeitschrift für Chemie, 23(8), 298-299. doi:10.1002/zfch.19830230810Ros-Lis, J. V., Martínez-Máñez, R., Sancenón, F., Soto, J., Spieles, M., & Rurack, K. (2008). Squaraines as Reporter Units: Insights into their Photophysics, Protonation, and Metal-Ion Coordination Behaviour. Chemistry - A European Journal, 14(32), 10101-10114. doi:10.1002/chem.200800300Forlani, L., De Maria, P., & Fini, A. (1980). Electrical effects in substituted thiazoles. pK a Values of some 5-substituted 2-aminothiazoles and 5-substituted 2-NN-dimethylaminothiazoles. Journal of the Chemical Society, Perkin Transactions 2, (8), 1156. doi:10.1039/p29800001156Haake, P., & Bausher, L. P. (1968). Thiazolium ions and related heteroaromatic systems. II. The acidity constants of thiazolium, oxazolium, and imidazolium ions. The Journal of Physical Chemistry, 72(6), 2213-2217. doi:10.1021/j100852a057SAWICKI, E. (1957). Physical Properties of the Aminoazobenzene Dyes. IV. The Position of Proton Addition1. The Journal of Organic Chemistry, 22(4), 365-367. doi:10.1021/jo01355a004Siiman, O., & Lepp, A. (1984). Protonation of the methyl orange derivative of aspartate adsorbed on colloidal silver: a surface-enhanced resonance Raman scattering and fluorescence emission study. The Journal of Physical Chemistry, 88(12), 2641-2650. doi:10.1021/j150656a043WADA, H., NAKAZAWA, O., & NAKAGAWA, G. (1974). Evaluation of 1-(2-thiazolylazo)-2-hydroxy-3-naphthoic acid as a metallochromic indicator. Talanta, 21(1), 97-102. doi:10.1016/0039-9140(74)80068-8Critical Stability Cosntants R. M. Smith A. E. Martell New York Vol. 2 1974García-Acosta, B., Martínez-Máñez, R., Sancenón, F., Soto, J., Rurack, K., Spieles, M., … Gil, L. (2007). Ditopic N-Crowned 4-(p-Aminophenyl)-2,6-diphenylpyridines:  Implications of Macrocycle Topology on the Spectroscopic Properties, Cation Complexation, and Differential Anion Responses. Inorganic Chemistry, 46(8), 3123-3135. doi:10.1021/ic062069zHyperChem. 6.03 Molecular Modeling System 2000(s. f.). doi:10.1021/ol062351Kim, H. J., Kim, S. H., Kim, J. H., Anh, L. N., Lee, J. H., Lee, C.-H., & Kim, J. S. (2009). ICT-based Cu(II)-sensing 9,10-anthraquinonecalix[4]crown. Tetrahedron Letters, 50(23), 2782-2786. doi:10.1016/j.tetlet.2009.03.149Ábalos, T., Jiménez, D., Moragues, M., Royo, S., Martínez-Máñez, R., Sancenón, F., … Gil, S. (2010). Multi-channel receptors based on thiopyrylium functionalised with macrocyclic receptors for the recognition of transition metal cations and anions. Dalton Transactions, 39(14), 3449. doi:10.1039/b921486kSchmittel, M., & Lin, H.-W. (2007). Quadruple-Channel Sensing: A Molecular Sensor with a Single Type of Receptor Site for Selective and Quantitative Multi-Ion Analysis. Angewandte Chemie, 119(6), 911-914. doi:10.1002/ange.200603362Nolan, E. M., & Lippard, S. J. (2008). Tools and Tactics for the Optical Detection of Mercuric Ion. Chemical Reviews, 108(9), 3443-3480. doi:10.1021/cr068000qZhang, X., & Huang, J. (2010). Functional surface modification of natural cellulose substances for colorimetric detection and adsorption of Hg2+ in aqueous media. Chemical Communications, 46(33), 6042. doi:10.1039/c0cc01072cZhao, Q., Liu, S., Li, F., Yi, T., & Huang, C. (2008). Multisignaling detection of Hg2+ based on a phosphorescent iridium(iii) complex. Dalton Transactions, (29), 3836. doi:10.1039/b804858dTatay, S., Gaviña, P., Coronado, E., & Palomares, E. (2006). Optical Mercury Sensing Using a Benzothiazolium Hemicyanine Dye. Organic Letters, 8(17), 3857-3860. doi:10.1021/ol0615580Lee, H., & Lee, S. S. (2009). Thiaoxaaza-Macrocyclic Chromoionophores as Mercury(II) Sensors: Synthesis and Color Modulation. Organic Letters, 11(6), 1393-1396. doi:10.1021/ol900241pYoon, S., Miller, E. W., He, Q., Do, P. H., & Chang, C. J. (2007). A Bright and Specific Fluorescent Sensor for Mercury in Water, Cells, and Tissue. Angewandte Chemie, 119(35), 6778-6781. doi:10.1002/ange.200701785Rurack, K., Resch-Genger, U., Spieles, M., & Bricks, J. L. (2000). Cation-triggered ‘switching on’ of the red/near infra-red (NIR) fluorescence of rigid fluorophore–spacer–receptor ionophores. Chemical Communications, (21), 2103-2104. doi:10.1039/b006430kSu Lim, C., Won Kang, D., Shun Tian, Y., Hee Han, J., Lim Hwang, H., & Rae Cho, B. (2010). Detection of mercury in fish organs with a two-photon fluorescent probe. Chemical Communications, 46(14), 2388. doi:10.1039/b922305cRos-Lis, J. V., Martínez-Máñez, R., Rurack, K., Sancenón, F., Soto, J., & Spieles, M. (2004). Highly Selective Chromogenic Signaling of Hg2+in Aqueous Media at Nanomolar Levels Employing a Squaraine-Based Reporter. Inorganic Chemistry, 43(17), 5183-5185. doi:10.1021/ic049422qDescalzo, A. B., Martínez-Máñez, R., Radeglia, R., Rurack, K., & Soto, J. (2003). Coupling Selectivity with Sensitivity in an Integrated Chemosensor Framework:  Design of a Hg2+-Responsive Probe, Operating above 500 nm. Journal of the American Chemical Society, 125(12), 3418-3419. doi:10.1021/ja0290779Yuan, M., Li, Y., Li, J., Li, C., Liu, X., Lv, J., … Zhu, D. (2007). A Colorimetric and Fluorometric Dual-Modal Assay for Mercury Ion by a Molecule. Organic Letters, 9(12), 2313-2316. doi:10.1021/ol0706399Zhu, M., Yuan, M., Liu, X., Xu, J., Lv, J., Huang, C., … Zhu, D. (2008). Visible Near-Infrared Chemosensor for Mercury Ion. Organic Letters, 10(7), 1481-1484. doi:10.1021/ol800197tTian, M., & Ihmels, H. (2009). Selective ratiometric detection of mercury(ii) ions in water with an acridizinium-based fluorescent probe. Chemical Communications, (22), 3175. doi:10.1039/b821830gTian, M., Ihmels, H., & Benner, K. (2010). Selective detection of Hg2+ in the microenvironment of double-stranded DNA with an intercalator crown-ether conjugate. Chemical Communications, 46(31), 5719. doi:10.1039/c002727hWang, H.-H., Xue, L., Qian, Y.-Y., & Jiang, H. (2010). Novel Ratiometric Fluorescent Sensor for Silver Ions. Organic Letters, 12(2), 292-295. doi:10.1021/ol902624hAtilgan, S., Kutuk, I., & Ozdemir, T. (2010). A near IR di-styryl BODIPY-based ratiometric fluorescent chemosensor for Hg(II). Tetrahedron Letters, 51(6), 892-894. doi:10.1016/j.tetlet.2009.12.025Jiménez, D., Martínez-Máñez, R., Sancenón, F., Ros-Lis, J. V., Soto, J., Benito, Á., & García-Breijo, E. (2005). Multi-Channel Receptors and Their Relation to Guest Chemosensing and Reconfigurable Molecular Logic Gates. European Journal of Inorganic Chemistry, 2005(12), 2393-2403. doi:10.1002/ejic.200400844Becke, A. D. (1988). Density-functional exchange-energy approximation with correct asymptotic behavior. Physical Review A, 38(6), 3098-3100. doi:10.1103/physreva.38.3098Lee, C., Yang, W., & Parr, R. G. (1988). Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density. Physical Review B, 37(2), 785-789. doi:10.1103/physrevb.37.785Becke, A. D. (1993). Density‐functional thermochemistry. III. The role of exact exchange. The Journal of Chemical Physics, 98(7), 5648-5652. doi:10.1063/1.464913Schäfer, A., Horn, H., & Ahlrichs, R. (1992). Fully optimized contracted Gaussian basis sets for atoms Li to Kr. The Journal of Chemical Physics, 97(4), 2571-2577. doi:10.1063/1.463096Hay, P. J., & Wadt, W. R. (1985). Ab initio effective core potentials for molecular calculations. Potentials for the transition metal atoms Sc to Hg. The Journal of Chemical Physics, 82(1), 270-283. doi:10.1063/1.448799Gaussian 09 2009Casida, M. E., Jamorski, C., Casida, K. C., & Salahub, D. R. (1998). Molecular excitation energies to high-lying bound states from time-dependent density-functional response theory: Characterization and correction of the time-dependent local density approximation ionization threshold. The Journal of Chemical Physics, 108(11), 4439-4449. doi:10.1063/1.475855Tomasi, J., Mennucci, B., & Cammi, R. (2005). Quantum Mechanical Continuum Solvation Models. Chemical Reviews, 105(8), 2999-3094. doi:10.1021/cr990400

The U1, U2 and U5 snRNAs crosslink to the 5′ exon during yeast pre-mRNA splicing

Activation of pre-messenger RNA (pre-mRNA) splicing requires 5′ splice site recognition by U1 small nuclear RNA (snRNA), which is replaced by U5 and U6 snRNA. Here we use crosslinking to investigate snRNA interactions with the 5′ exon adjacent to the 5′ splice site, prior to the first step of splicing. U1 snRNA was found to interact with four different 5′ exon positions using one specific sequence adjacent to U1 snRNA helix 1. This novel interaction of U1 we propose occurs before U1-5′ splice site base pairing. In contrast, U5 snRNA interactions with the 5′ exon of the pre-mRNA progressively shift towards the 5′ end of U5 loop 1 as the crosslinking group is placed further from the 5′ splice site, with only interactions closest to the 5′ splice site persisting to the 5′ exon intermediate and the second step of splicing. A novel yeast U2 snRNA interaction with the 5′ exon was also identified, which is ATP dependent and requires U2-branchpoint interaction. This study provides insight into the nature and timing of snRNA interactions required for 5′ splice site recognition prior to the first step of pre-mRNA splicing

Hackable Instruments: Supporting Appropriation and Modification in Digital Musical Interaction

This paper investigates the appropriation of digital musical instruments, wherein the performer develops a personal working relationship with an instrument that may differ from the designer's intent. Two studies are presented which explore different facets of appropriation. First, a highly restrictive instrument was designed to assess the effects of constraint on unexpected creative use. Second, a digital instrument was created which initially shared several constraints and interaction modalities with the first instrument, but which could be rewired by the performer to discover sounds not directly anticipated by the designers. Each instrument was studied with 10 musicians working individually to prepare public performances on the instrument. The results suggest that constrained musical interactions can promote the discovery of unusual and idiosyncratic playing techniques, and that tighter constraints may paradoxically lead to a richer performer experience. The diversity of ways in which the rewirable instrument was modified and used indicates that its design is open to interpretation by the performer, who may discover interaction modalities that were not anticipated by the designers