Optical potentials using resonance states in Supersymmetric Quantum Mechanics

Complex potentials are constructed as Darboux-deformations of short range, radial nonsingular potentials. They behave as optical devices which both refracts and absorbs light waves. The deformation preserves the initial spectrum of energies and it is implemented by means of a Gamow-Siegert function (resonance state). As straightforward example, the method is applied to the radial square well. Analytical derivations of the involved resonances show that they are `quantized' while the corresponding wave-functions are shown to behave as bounded states under the broken of parity symmetry of the related one-dimensional problem.Comment: 16 pages, 6 figures, 1 tabl

Pelagic calcium carbonate production and shallow dissolution in the North Pacific Ocean

Planktonic calcifying organisms play a key role in regulating ocean carbonate chemistry and atmospheric CO 2 . Surprisingly, references to the absolute and relative contribution of these organisms to calcium carbonate production are lacking. Here we report quantification of pelagic calcium carbonate produc- tion in the North Pacific, providing new insights on the contribution of the three main planktonic calcifying groups. Our results show that coccolitho- phores dominate the living calcium carbonate (CaCO 3 ) standing stock, with coccolithophore calcite comprising ~90% of total CaCO 3 production, and pteropods and foraminifera playing a secondary role. We show that pelagic CaCO 3 production is higher than the sinking flux of CaCO 3 at 150 and 200 m at ocean stations ALOHA and PAPA, implying that a large portion of pelagic calcium carbonate is remineralised within the photic zone; this extensive shallow dissolution explains the apparent discrepancy between previous estimates of CaCO 3 production derived from satellite observations/biogeo- chemical modeling versus estimates from shallow sediment traps. We suggest future changes in the CaCO 3 cycle and its impact on atmospheric CO 2 will largely depend on how the poorly-understood processes that determine whether CaCO 3 is remineralised in the photic zone or exported to depth respond to anthropogenic warming and acidification

Long-term postharvest aroma evolution of tomatoes with the alcobaça (alc) mutation

The postharvest evolution of Penjar tomatoes has been studied in four accessions representative of the variability of the varietal type. The long-term shelf life of these materials, which carry the alc allele, was confirmed with 31.2-59.1% of commercial fruits after 6 months of effective conservation at room temperature and a limited loss of weight (21.1-27.9%). Aroma in Penjar tomatoes is differentiated from other tomato varieties by a characteristic 'sharp-floral' aroma descriptor. The evolution of the 'sharp-floral' aroma during postharvest showed a peak of intensity at 2 months of postharvest, though in one accession a delay of 2 months in this response was detected. Out of 25 volatiles analysed, including main and background notes, a reverse iPLS variable selection revealed that the main candidates behind this aromatic behaviour are ¿-terpineol, trans-2-hexenal, 6-methyl-5-hepten-2-one, trans-2-octenal, ¿-pinene, ß-ionone, 2 + 3-methylbutanol and phenylacetaldehyde. Between harvest and 2 months postharvest, most compounds reduced considerably their concentration, while the intensity of the 'sharp-floral' descriptor increased, which means that probably there is a rearrangement of the relative concentrations among volatiles that may lead to masking/unmasking processes. © 2011 Springer-Verlag.This work was supported by grants from the Conselleria de Agricultura, Pesca y Alimentacio de la Comunidad Valenciana, the Fundacion de la Comunidad Valenciana para la Investigacion Agroalimentaria (AGROALIMED) and from the Departament d'Agricultura, Alimentacio i Accio Rural (DAR) de la Generalitat de Catalunya.Casals Missio, J.; Cebolla Cornejo, J.; Rosello Ripolles, S.; Beltran Arandes, J.; Casanas, F.; Nuez Viñals, F. (2011). Long-term postharvest aroma evolution of tomatoes with the alcobaça (alc) mutation. European Food Research and Technology. 233(2):331-342. doi:10.1007/s00217-011-1517-6S3313422332Petro-Turza M (1987) Flavor of tomato and tomato products. Food Rev Int 2:309–351Butterry RG (1993) Quantitative and sensory aspects of flavor of tomato and other vegetables and fruits. In: Acree TE, Teranishi R (eds) Flavor science: sensible principles and techniques. American Chemical Society, WashingtonGoff SA, Klee HJ (2006) Plant volatile compounds: sensory cues for health and nutritional value? Science 311:815–819Tieman DM, Zeigler M, Schmelz EA, Taylor MG, Bliss P, Kirst M, Klee MJ (2006) Identification of loci affecting flavour volatile emissions in tomato fruits. J Exp Bot 57:887–896Zanor MI, Rambla JL, Chaïb J, Steppa A, Medina A, Granell A, Fernie AR, Causse M (2009) Metabolic characterization of loci affecting sensory attributes allows an assessment of the influence of the levels of primary metabolites and volatile organic contents. J Exp Bot 60:2139–2154Ortiz-Serrano P, Gil JV (2010) Quantitative comparison of free and bound volatiles of two commercial tomato cultivars (Solanum lycopersicum L.) during ripening. J Agric Food Chem 58:1106–1114Boukobza F, Taylor AJ (2002) Effect of postharvest treatment on flavour volatiles of tomatoes. Postharvest Biol Technol 25:321–331Vrebalov J, Ruezinsky D, Padmanabhan V, White R, Medrano D, Drake R, Schuch W, Giovannoni J (2002) A MADS-box gene necessary for fruit ripening at the tomato ripening-inhibitor (rin) locus. Science 296:343–346Giovannoni JJ, Tanksley SD, Vrebalov J, Noensie E (2004) NOR gene for use in manipulation of fruit quality and ethylene response. US Patent No 5,234,834 issued 13 July 2004McGlasson WB, Last JH, Shaw KJ, Meldrum SK (1987) Influence of the non-ripening mutants rin and nor on the aroma of tomato fruit. HortScience 22:632–634Baldwin EA, Scott JW, Shewmaker CK, Schuch W (2000) Flavor trivia and tomato aroma: biochemistry and possible mechanisms for control of important aroma components. HortScience 35:1013–1022Kovács K, Rupert CF, Tikunov Y, Graham N, Bradley G, Seymour GB, Bovy AG, Grierson D (2009) Effect of pleiotropic ripening mutations on flavour volatile biosynthesis. Phytochemistry 70:1003–1008Gao HY, Zhu BZ, Zhu HL, Zhang YL, Xie YH, Li YC, Luo YB (2007) Effect of suppression of ethylene biosynthesis on flavour products in tomato fruits. Russ J Plant Physiol 54:80–88Lewinsohn E, Sitrit Y, Bar E, Azulay Y, Meir A, Zamir D, Tadmor Y (2005) Carotenoid pigmentation affects the volatile composition of tomato and watermelon fruits, as revealed by comparative genetic analyses. J Agric Food Chem 53:3142–3148Kopeliovitch E, Mizrahi Y, Rabinowitch D, Kedar N (1980) Physiology of the mutant alcobaca. Physiol Plant 48:307–311Casals J, Pacual L, Cañizares J, Cebolla-Cornejo J, Casañas F, Nuez F (2011) Genetic basis of long shelf life and variability into Penjar tomato. Genet Resour Crop Evol. doi: 10.1007/s10722-011-9677-6Kuzyomenskii AV (2007) Effect of cumulative polymery of tomato keeping life genes. Cytol Genet 41:268–275Paran I, van der Knaap E (2007) Genetic and molecular regulation of fruit and plant domestication traits in tomato and pepper. J Exp Bot 58:3841–3852Moretti CL, Baldwin EA, Sargent SA, Huber DJ (2002) Internal bruising alters aroma volatile profiles in tomato fruit tisúes. HortScience 37:378–382Buttery RG, Teranishi R, Ling LC (1987) Fresh tomato aroma volatiles: a qualitative study. J Agric Food Chem 35:540–544Romero del Castillo R, Valero J, Casañas F, Costell E (2008) Training validation and maintenance of a panel to evaluate the texture of dry beans (Phaseolus vulgaris L.). J Sens Stud 23:303–319Beltran J, Serrano E, López FJ, Peruga A, Valcárcel M, Roselló S (2006) Comparison of two quantitative GC-MS methods for analysis of tomato aroma based on purge-and-trap and on solid-phase microextraction. Anal Bioanal Chem 385:1255–1264Martens H, Naes T (1989) Multivariate Calibration. Wiley, New YorkWise BM, Gallagher NB, Bro R, Shaver JM, Windig W, Koch RS (2006) Chemometrics tutorial for PLS_Toolbox and Solo. Eigenvector Research, WenatcheeHongsoongnern P, Chambers E (2008) A lexicon for texture and flavor characteristics of fresh and processed tomatoes. J Sens Stud 23:583–599Norgaard L, Saudland A, Wagner J, Nielsen JP, Munck L, Engelsen SB (2000) Interval partial least-squares regression (iPLS): A comparative chemometric study with an example from near-infrared spectroscopy. Appl Spectrosc 54:413–419Javanmardi J, Kubota C (2006) Variation of lycopene, antioxidant activity, total soluble solids and weight loss of tomato during postharvest storage. Postharvest Biol Technol 41:151–155Kader AA (1986) Effects of postharvest handling procedures on tomato quality. Acta Hort 190:209–222Maul F, Sargent SA, Sims CA, Baldwin EA, Balaban MO, Huber DJ (2000) Tomato flavor and aroma quality as affected by storage temperature. J Food Sci 65:1228–1237Krumbein A, Auerswald H (1998) Characterization of aroma volatiles in tomatoes by sensory analyses. Nahrung 6:S395–S399Tandon KS, Baldwin EA, Shewfelt RL (2000) Aroma perception of individual volatile compounds in fresh tomatoes (Lycopersicon esculentum Mill.) as affected by the medium of evaluation. Postharvest Biol Technol 20:261–268Cebolla-Cornejo J, Roselló S, Valcárcel M, Serrano E, Beltran J, Nuez F (2011) Evaluation of genotype and environment effects on taste and aroma flavour components of Spanish fresh tomato varieties. J Agric Food Chem 59:2440–2450Carbonell-Barrachina AA, Agustí A, Ruiz JJ (2006) Analysis of flavor volatile compounds by dynamic headspace in traditional and hybrid cultivars of Spanish tomatoes. Eur Food Res Technol 222:536–542Alonso A, Vázquez-Araújo L, García-Martínez S, Ruiz JJ, Carbonell Barrachina AA (2009) Volatile compounds of traditional and virus-resistant breeding lines of Muchamiel tomatoes. Eur Food Res Technol 230:315–323Liggett E, Drake MA, Delwiche JF (2008) Impact of flavor attributes on consumer liking of Swiss cheese. J Dairy Sci 91:466–476Ortiz-Serrano P, Gil JV (2007) Quantitation of free and glycosidically bound volatiles in and effect of glycosidase addition on three tomato varieties (Solanum lycopersicum L.). J Agric Food Chem 55:9170–9176Xu Y, Barringer S (2010) Comparison of tomatillo and tomato volatile compounds in the headspace by selected ion flow tube mass spectrometry (SIFT-MS). J Food Sci 75:C268–C273Berna AZ, Lammertyn J, Saevels S, Di Natale C, Nicolai BM (2004) Electronic nose systems to study shelf life and cultivar effect on tomato aroma profile. Sens Actuators B Chem 97:324–333Baldwin EA, Scott JW, Einstein MA, Malundo TMM, Carr BT, Shewfelt RL, Tandon KS (1998) Relationship between sensory and instrumental analysis for tomato flavor. J Am Soc Hortic Sci 12:906–915Krumbein A, Peters P, Brückner B (2004) Flavour compounds and a quantitative descriptive analysis of tomatoes (Lycopersicon esculentum Mill.) of different cultivars in short-term storage. Postharvest Biol Technol 32:15–2

Osteoprotegerin in Exosome-Like Vesicles from Human Cultured Tubular Cells and Urine

Urinary exosomes have been proposed as potential diagnostic tools. TNF superfamily cytokines and receptors may be present in exosomes and are expressed by proximal tubular cells. We have now studied the expression of selected TNF superfamily proteins in exosome-like vesicles from cultured human proximal tubular cells and human urine and have identified additional proteins in these vesicles by LC-MS/MS proteomics. Human proximal tubular cells constitutively released exosome-like vesicles that did not contain the TNF superfamily cytokines TRAIL or TWEAK. However, exosome-like vesicles contained osteoprotegerin (OPG), a TNF receptor superfamily protein, as assessed by Western blot, ELISA or selected reaction monitoring by nLC-(QQQ)MS/MS. Twenty-one additional proteins were identified in tubular cell exosomelike vesicles, including one (vitamin D binding protein) that had not been previously reported in exosome-like vesicles. Twelve were extracellular matrix proteins, including the basement membrane proteins type IV collagen, nidogen-1, agrin and fibulin-1. Urine from chronic kidney disease patients contained a higher amount of exosomal protein and exosomal OPG than urine from healthy volunteers. Specifically OPG was increased in autosomal dominant polycystic kidney disease urinary exosome-like vesicles and expressed by cystic epithelium in vivo. In conclusion, OPG is present in exosome-like vesicles secreted by proximal tubular epithelial cells and isolated from Chronic Kidney Disease urine.This work was supported by grants from the Instituto de Salud Carlos III (ISCIIIRETIC REDINREN RD06/0016, RD12/0021, PI11/01854, PI10/00072 PI09/ 00641 and PS09/00447); Comunidad de Madrid (Fibroteam S2010/BMD-2321, S2010/BMD-2378); Sociedad Española de NefrologÍa; European Network (HEALTH F2-2008-200647); DIALOK European project LSHB-CT-2007-036644; Fundacion Lilly and IRSIN/FRIAT to JE; Programa Intensificación Actividad Investigadora (ISCIII/ Agencia Laín-Entralgo/CM) to AO; Instituto de Salud Carlos III (FIS PI11/01401, CP09/00229); and Fundación Conchita Rábago de Jiménez DÍaz to GAL. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscrip

Cross-Over between Discrete and Continuous Protein Structure Space: Insights into Automatic Classification and Networks of Protein Structures

Structural classifications of proteins assume the existence of the fold, which is an intrinsic equivalence class of protein domains. Here, we test in which conditions such an equivalence class is compatible with objective similarity measures. We base our analysis on the transitive property of the equivalence relationship, requiring that similarity of A with B and B with C implies that A and C are also similar. Divergent gene evolution leads us to expect that the transitive property should approximately hold. However, if protein domains are a combination of recurrent short polypeptide fragments, as proposed by several authors, then similarity of partial fragments may violate the transitive property, favouring the continuous view of the protein structure space. We propose a measure to quantify the violations of the transitive property when a clustering algorithm joins elements into clusters, and we find out that such violations present a well defined and detectable cross-over point, from an approximately transitive regime at high structure similarity to a regime with large transitivity violations and large differences in length at low similarity. We argue that protein structure space is discrete and hierarchic classification is justified up to this cross-over point, whereas at lower similarities the structure space is continuous and it should be represented as a network. We have tested the qualitative behaviour of this measure, varying all the choices involved in the automatic classification procedure, i.e., domain decomposition, alignment algorithm, similarity score, and clustering algorithm, and we have found out that this behaviour is quite robust. The final classification depends on the chosen algorithms. We used the values of the clustering coefficient and the transitivity violations to select the optimal choices among those that we tested. Interestingly, this criterion also favours the agreement between automatic and expert classifications. As a domain set, we have selected a consensus set of 2,890 domains decomposed very similarly in SCOP and CATH. As an alignment algorithm, we used a global version of MAMMOTH developed in our group, which is both rapid and accurate. As a similarity measure, we used the size-normalized contact overlap, and as a clustering algorithm, we used average linkage. The resulting automatic classification at the cross-over point was more consistent than expert ones with respect to the structure similarity measure, with 86% of the clusters corresponding to subsets of either SCOP or CATH superfamilies and fewer than 5% containing domains in distinct folds according to both SCOP and CATH. Almost 15% of SCOP superfamilies and 10% of CATH superfamilies were split, consistent with the notion of fold change in protein evolution. These results were qualitatively robust for all choices that we tested, although we did not try to use alignment algorithms developed by other groups. Folds defined in SCOP and CATH would be completely joined in the regime of large transitivity violations where clustering is more arbitrary. Consistently, the agreement between SCOP and CATH at fold level was lower than their agreement with the automatic classification obtained using as a clustering algorithm, respectively, average linkage (for SCOP) or single linkage (for CATH). The networks representing significant evolutionary and structural relationships between clusters beyond the cross-over point may allow us to perform evolutionary, structural, or functional analyses beyond the limits of classification schemes. These networks and the underlying clusters are available at http://ub.cbm.uam.es/research/ProtNet.ph

Mapping Brain Response to Pain in Fibromyalgia Patients Using Temporal Analysis of fMRI

Background: Nociceptive stimuli may evoke brain responses longer than the stimulus duration often partially detected by conventional neuroimaging. Fibromyalgia patients typically complain of severe pain from gentle stimuli. We aimed to characterize brain response to painful pressure in fibromyalgia patients by generating activation maps adjusted for the duration of brain responses. Methodology/Principal Findings: Twenty-seven women (mean age: 47.8 years) were assessed with fMRI. The sample included nine fibromyalgia patients and nine healthy subjects who received 4 kg/cm2 of pressure on the thumb. Nine additional control subjects received 6.8 kg/cm2 to match the patients for the severity of perceived pain. Independent Component Analysis characterized the temporal dynamics of the actual brain response to pressure. Statistical parametric maps were estimated using the obtained time courses. Brain response to pressure (18 seconds) consistently exceeded the stimulus application (9 seconds) in somatosensory regions in all groups. fMRI maps following such temporal dynamics showed a complete pain network response (sensory-motor cortices, operculo-insula, cingulate cortex, and basal ganglia) to 4 kg/cm2 of pressure in fibromyalgia patients. In healthy subjects, response to this low intensity pressure involved mainly somatosensory cortices. When matched for perceived pain (6.8 kg/cm2), control subjects showed also comprehensive activation of pain-related regions, but fibromyalgia patients showed significantly larger activation in the anterior insula-basal ganglia complex and the cingulate cortex. Conclusions/Significance: The results suggest that data-driven fMRI assessments may complement conventional neuroimaging for characterizing pain responses and that enhancement of brain activation in fibromyalgia patients may be particularly relevant in emotion-related regions

Suppression of charged particle production at large transverse momentum in central Pb-Pb collisions at sNN=2.76\sqrt{s_{\rm NN}} = 2.76 TeV

Inclusive transverse momentum spectra of primary charged particles in Pb-Pb collisions at $\sqrt{s_{_{\rm NN}}}$ = 2.76 TeV have been measured by the ALICE Collaboration at the LHC. The data are presented for central and peripheral collisions, corresponding to 0-5% and 70-80% of the hadronic Pb-Pb cross section. The measured charged particle spectra in $|\eta|<0.8$ and $0.3 < p_T < 20$ GeV/$c$ are compared to the expectation in pp collisions at the same $\sqrt{s_{\rm NN}}$, scaled by the number of underlying nucleon-nucleon collisions. The comparison is expressed in terms of the nuclear modification factor $R_{\rm AA}$. The result indicates only weak medium effects ($R_{\rm AA} \approx$ 0.7) in peripheral collisions. In central collisions, $R_{\rm AA}$ reaches a minimum of about 0.14 at $p_{\rm T}=6$-7GeV/$c$ and increases significantly at larger $p_{\rm T}$. The measured suppression of high-$p_{\rm T}$ particles is stronger than that observed at lower collision energies, indicating that a very dense medium is formed in central Pb-Pb collisions at the LHC.Comment: 15 pages, 5 captioned figures, 3 tables, authors from page 10, published version, figures at http://aliceinfo.cern.ch/ArtSubmission/node/98

Two-pion Bose-Einstein correlations in central Pb-Pb collisions at sNN\sqrt{s_{\rm NN}} = 2.76 TeV

The first measurement of two-pion Bose-Einstein correlations in central Pb-Pb collisions at $\sqrt{s_{\rm NN}} = 2.76$ TeV at the Large Hadron Collider is presented. We observe a growing trend with energy now not only for the longitudinal and the outward but also for the sideward pion source radius. The pion homogeneity volume and the decoupling time are significantly larger than those measured at RHIC.Comment: 17 pages, 5 captioned figures, 1 table, authors from page 12, published version, figures at http://aliceinfo.cern.ch/ArtSubmission/node/388