Theory and data for area summation of contrast with and without uncertainty:evidence for a noisy energy model

Contrast sensitivity improves with the area of a sine-wave grating, but why? Here we assess this phenomenon against contemporary models involving spatial summation, probability summation, uncertainty, and stochastic noise. Using a two-interval forced-choice procedure we measured contrast sensitivity for circular patches of sine-wave gratings with various diameters that were blocked or interleaved across trials to produce low and high extrinsic uncertainty, respectively. Summation curves were steep initially, becoming shallower thereafter. For the smaller stimuli, sensitivity was slightly worse for the interleaved design than for the blocked design. Neither area nor blocking affected the slope of the psychometric function. We derived model predictions for noisy mechanisms and extrinsic uncertainty that was either low or high. The contrast transducer was either linear (c1.0) or nonlinear (c2.0), and pooling was either linear or a MAX operation. There was either no intrinsic uncertainty, or it was fixed or proportional to stimulus size. Of these 10 canonical models, only the nonlinear transducer with linear pooling (the noisy energy model) described the main forms of the data for both experimental designs. We also show how a cross-correlator can be modified to fit our results and provide a contemporary presentation of the relation between summation and the slope of the psychometric function.

Seventeen a-subunit isoforms of paramecium V-ATPase provide high specialization in localization and function

In the Paramecium tetraurelia genome, 17 genes encoding the 100-kDa-subunit (a-subunit) of the vacuolar-proton-ATPase were identified, representing by far the largest number of a-subunit genes encountered in any organism investigated so far. They group into nine clusters, eight pairs with >82% amino acid identity and one single gene. Green fluorescent protein-tagging of representatives of the nine clusters revealed highly specific targeting to at least seven different compartments, among them dense core secretory vesicles (trichocysts), the contractile vacuole complex, and phagosomes. RNA interference for two pairs confirmed their functional specialization in their target compartments: silencing of the trichocyst-specific form affected this secretory pathway, whereas silencing of the contractile vacuole complex-specific form altered organelle structure and functioning. The construction of chimeras between selected a-subunits surprisingly revealed the targeting signal to be located in the C terminus of the protein, in contrast with the N-terminal targeting signal of the a-subunit in yeast. Interestingly, some chimeras provoked deleterious effects, locally in their target compartment, or remotely, in the compartment whose specific a-subunit N terminus was used in the chimera.

High-pressure XPS of crotyl alcohol selective oxidation over metallic and oxidized Pd(111)

Here, we report on the first application of high-pressure XPS (HP-XPS) to the surface catalyzed selective oxidation of a hydrocarbon over palladium, wherein the reactivity of metal and oxide surfaces in directing the oxidative dehydrogenation of crotyl alcohol (CrOH) to crotonaldehyde (CrHCO) is evaluated. Crotonaldehyde formation is disfavored over Pd(111) under all reaction conditions, with only crotyl alcohol decomposition observed. In contrast, 2D Pd5O4 and 3D PdO overlayers are able to selectively oxidize crotyl alcohol (1 mTorr) to crotonaldehyde in the presence of co-fed oxygen (140 mTorr) at temperatures as low as 40 °C. However, 2D Pd5O4 ultrathin films are unstable toward reduction by the alcohol at ambient temperature, whereas the 3D PdO oxide is able to sustain catalytic crotonaldehyde production even up to 150 °C. Co-fed oxygen is essential to stabilize palladium surface oxides toward in situ reduction by crotyl alcohol, with stability increasing with oxide film dimensionality.

High-visibility photonic crystal fiber interferometer as multifunctional sensor

A photonic crystal fiber (PCF) interferometer that exhibits record fringe contrast (~40 dB) is demonstrated along with its sensing applications. The device operates in reflection mode and consists of a centimeter-long segment of properly selected PCF fusion spliced to single mode optical fibers. Two identical collapsed zones in the PCF combined with its modal properties allow high-visibility interference patterns. The interferometer is suitable for refractometric and liquid level sensing. The measuring refractive index range goes from 1.33 to 1.43 and the maximum resolution is ~1.6 × 10-5. © 2013 by the authors; licensee MDPI, Basel, Switzerland.

Superfocusing of high-M2 semiconductor laser beams:experimental demonstration

The focusing of multimode laser diode beams is probably the most significant problem that hinders the expansion of the high-power semiconductor lasers in many spatially-demanding applications. Generally, the 'quality' of laser beams is characterized by so-called 'beam propagation parameter' M2, which is defined as the ratio of the divergence of the laser beam to that of a diffraction-limited counterpart. Therefore, M2 determines the ratio of the beam focal-spot size to that of the 'ideal' Gaussian beam focused by the same optical system. Typically, M2 takes the value of 20-50 for high-power broad-stripe laser diodes thus making the focal-spot 1-2 orders of magnitude larger than the diffraction limit. The idea of 'superfocusing' for high-M2 beams relies on a technique developed for the generation of Bessel beams from laser diodes using a cone-shaped lens (axicon). With traditional focusing of multimode radiation, different curvatures of the wavefronts of the various constituent modes lead to a shift of their focal points along the optical axis that in turn implies larger focal-spot sizes with correspondingly increased values of M2. In contrast, the generation of a Bessel-type beam with an axicon relies on 'self-interference' of each mode thus eliminating the underlying reason for an increase in the focal-spot size. For an experimental demonstration of the proposed technique, we used a fiber-coupled laser diode with M2 below 20 and an emission wavelength in ~1μm range. Utilization of the axicons with apex angle of 140deg, made by direct laser writing on a fiber tip, enabled the demonstration of an order of magnitude decrease of the focal-spot size compared to that achievable using an 'ideal' lens of unity numerical aperture. © 2014 SPIE.

Fourth-root summation of contrast over area:no end in sight when spatially inhomogeneous sensitivity is compensated by a witch's hat

Measurements of area summation for luminance-modulated stimuli are typically confounded by variations in sensitivity across the retina. Recently we conducted a detailed analysis of sensitivity across the visual field (Baldwin et al, 2012) and found it to be well-described by a bilinear “witch’s hat” function: sensitivity declines rapidly over the first 8 cycles or so, more gently thereafter. Here we multiplied luminance-modulated stimuli (4 c/deg gratings and “Swiss cheeses”) by the inverse of the witch’s hat function to compensate for the inhomogeneity. This revealed summation functions that were straight lines (on double log axes) with a slope of -1/4 extending to ≥33 cycles, demonstrating fourth-root summation of contrast over a wider area than has previously been reported for the central retina. Fourth-root summation is typically attributed to probability summation, but recent studies have rejected that interpretation in favour of a noisy energy model that performs local square-law transduction of the signal, adds noise at each location of the target and then sums over signal area. Modelling shows our results to be consistent with a wide field application of such a contrast integrator. We reject a probability summation model, a quadratic model and a matched template model of our results under the assumptions of signal detection theory. We also reject the high threshold theory of contrast detection under the assumption of probability summation over area.

Stabilization of catalyst particles against sintering on oxide supports with high oxygen ion lability exemplified by Ir-catalyzed decomposition of N2O

Iridium nanoparticles deposited on a variety of surfaces exhibited thermal sintering characteristics that were very strongly correlated with the lability of lattice oxygen in the supporting oxide materials. Specifically, the higher the lability of oxygen ions in the support, the greater the resistance of the nanoparticles to sintering in an oxidative environment. Thus with γ-Al2O3 as the support, rapid and extensive sintering occurred. In striking contrast, when supported on gadolinia-ceria and alumina-ceria-zirconia composite, the Ir nanoparticles underwent negligible sintering. In keeping with this trend, the behavior found with yttria-stabilized zirconia was an intermediate between the two extremes. This resistance, or lack of resistance, to sintering is considered in terms of oxygen spillover from support to nanoparticles and discussed with respect to the alternative mechanisms of Ostwald ripening versus nanoparticle diffusion. Activity towards the decomposition of N2O, a reaction that displays pronounced sensitivity to catalyst particle size (large particles more active than small particles), was used to confirm that catalytic behavior was consistent with the independently measured sintering characteristics. It was found that the nanoparticle active phase was Ir oxide, which is metallic, possibly present as a capping layer. Moreover, observed turnover frequencies indicated that catalyst-support interactions were important in the cases of the sinter-resistant systems, an effect that may itself be linked to the phenomena that gave rise to materials with a strong resistance to nanoparticle sintering.

A high-resolution sedimentology and age determination of core PS2185 from the central Arctic Ocean

A high-resolution multiparameter stratigraphy allows the identification of late Quaternary glacial and interglacial cycles in a central Arctic Ocean sediment core. Distinct sandy layers in the upper part of the otherwise fine-grained sediment core from the Lomonosov Ridge (lat 87.5°N) correlate to four major glacials since ca. 0.7 Ma. The composition of these ice-rafted terrigenous sediments points to a glaciated northern Siberia as the main source. In contrast, lithic carbonates derived from North America are also present in older sediments and indicate a northern North American glaciation since at least 2.8 Ma. We conclude that large-scale northern Siberian glaciation began much later than other Northern Hemisphere ice sheets.

High resolution study of narrow tailed radio galaxies in clusters

Clusters of galaxies are the most massive and large gravitationally bounded systems in the whole Universe. Their study is of fundamental importance to constrain cosmological parameters and to obtain informations regarding various kind of emission in different wavebands. In particular, in the radio domain, beside the diffuse emission, the study is focused on the radio galaxies emission. Radio galaxies in clusters can have peculiar morphology, since they interact with the intracluster medium (ICM) in which they are embedded. Particularly, in this thesis we focused our attention on the so-called Narrow-Angle Tailed radio galaxies (NAT), which present radio jets that are bent at extreme angle, up to 90 degrees, from their original orientation. Some NAT show a narrow extended structure and the two radio tails are not resolved even with high resolution radio observations. An example is provided by the source IC310, in the Perseus Cluster, whose structure has been recently interpreted as due to Doppler boosting effects of a relativistic jet oriented at a small angle with respect to the line of sight. If the structure is due to relativistic effects, this implies that the jets are relativistic at about 400 kpc from the core, but this is in contrast with unified models, which predict that for low-power radio source (NAT are classified as FRI radio galaxies) the jets decelerate to sub-relativistic speed within a few kpc from the core. To investigate this scientific topic, in this thesis we have analyzed the innermost structure of a sample of eleven radio galaxies showing a very narrow NAT structure. We can conclude that the structure of these radio galaxies is different from that of IC310. These radio galaxies are indeed strongly influenced by environmental effects and are similar to classical NAT sources.

Enzymatic Polymerization of High Molecular Weight DNA

The use of DNA as a polymeric building material transcends its function in biology and is exciting in bionanotechnology for applications ranging from biosensing, to diagnostics, and to targeted drug delivery. These applications are enabled by DNA’s unique structural and chemical properties, embodied as a directional polyanion that exhibits molecular recognition capabilities. Hence, the efficient and precise synthesis of high molecular weight DNA materials has become key to advance DNA bionanotechnology. Current synthesis methods largely rely on either solid phase chemical synthesis or template-dependent polymerase amplification. The inherent step-by-step fashion of solid phase synthesis limits the length of the resulting DNA to typically less than 150 nucleotides. In contrast, polymerase based enzymatic synthesis methods (e.g., polymerase chain reaction) are not limited by product length, but require a DNA template to guide the synthesis. Furthermore, advanced DNA bionanotechnology requires tailorable structural and self-assembly properties. Current synthesis methods, however, often involve multiple conjugating reactions and extensive purification steps.

The research described in this dissertation aims to develop a facile method to synthesize high molecular weight, single stranded DNA (or polynucleotide) with versatile functionalities. We exploit the ability of a template-independent DNA polymerase−terminal deoxynucleotidyl transferase (TdT) to catalyze the polymerization of 2’-deoxyribonucleoside 5’-triphosphates (dNTP, monomer) from the 3’-hydroxyl group of an oligodeoxyribonucleotide (initiator). We termed this enzymatic synthesis method: TdT catalyzed enzymatic polymerization, or TcEP.

Specifically, this dissertation is structured to address three specific research aims. With the objective to generate high molecular weight polynucleotides, Specific Aim 1 studies the reaction kinetics of TcEP by investigating the polymerization of 2’-deoxythymidine 5’-triphosphates (monomer) from the 3’-hydroxyl group of oligodeoxyribothymidine (initiator) using in situ 1H NMR and fluorescent gel electrophoresis. We found that TcEP kinetics follows the “living” chain-growth polycondensation mechanism, and like in “living” polymerizations, the molecular weight of the final product is determined by the starting molar ratio of monomer to initiator. The distribution of the molecular weight is crucially influenced by the molar ratio of initiator to TdT. We developed a reaction kinetics model that allows us to quantitatively describe the reaction and predict the molecular weight of the reaction products.

Specific Aim 2 further explores TcEP’s ability to transcend homo-polynucleotide synthesis by varying the choices of initiators and monomers. We investigated the effects of initiator length and sequence on TcEP, and found that the minimum length of an effective initiator should be 10 nucleotides and that the formation of secondary structures close to the 3’-hydroxyl group can impede the polymerization reaction. We also demonstrated TcEP’s capacity to incorporate a wide range of unnatural dNTPs into the growing chain, such as, hydrophobic fluorescent dNTP and fluoro modified dNTP. By harnessing the encoded nucleotide sequence of an initiator and the chemical diversity of monomers, TcEP enables us to introduce molecular recognition capabilities and chemical functionalities on the 5’-terminus and 3’-terminus, respectively.

Building on TcEP’s synthesis capacities, in Specific Aim 3 we invented a two-step strategy to synthesize diblock amphiphilic polynucleotides, in which the first, hydrophilic block serves as a macro-initiator for the growth of the second block, comprised of natural and/or unnatural nucleotides. By tuning the hydrophilic length, we synthesized the amphiphilic diblock polynucleotides that can self-assemble into micellar structures ranging from star-like to crew-cut morphologies. The observed self-assembly behaviors agree with predictions from dissipative particle dynamics simulations as well as scaling law for polyelectrolyte block copolymers.

In summary, we developed an enzymatic synthesis method (i.e., TcEP) that enables the facile synthesis of high molecular weight polynucleotides with low polydispersity. Although we can control the nucleotide sequence only to a limited extent, TcEP offers a method to integrate an oligodeoxyribonucleotide with specific sequence at the 5’-terminus and to incorporate functional groups along the growing chains simultaneously. Additionally, we used TcEP to synthesize amphiphilic polynucleotides that display self-assemble ability. We anticipate that our facile synthesis method will not only advance molecular biology, but also invigorate materials science and bionanotechnology.

High-resolution pore-water and solid-phase analyses of sediment cores GeoB6520-3 (Hydrate Hole) and GeoB6521-2 (Worm Hole) of the northern Congo Fan

The geochemical cycling of barium was investigated in sediments of pockmarks of the northern Congo Fan, characterized by surface and subsurface gas hydrates, chemosynthetic fauna, and authigenic carbonates. Two gravity cores retrieved from the so-called Hydrate Hole and Worm Hole pockmarks were examined using high-resolution pore-water and solid-phase analyses. The results indicate that, although gas hydrates in the study area are stable with respect to pressure and temperature, they are and have been subject to dissolution due to methane-undersaturated pore waters. The process significantly driving dissolution is the anaerobic oxidation of methane (AOM) above the shallowest hydrate-bearing sediment layer. It is suggested that episodic seep events temporarily increase the upward flux of methane, and induce hydrate formation close to the sediment surface. AOM establishes at a sediment depth where the upward flux of methane from the uppermost hydrate layer counterbalances the downward flux of seawater sulfate. After seepage ceases, AOM continues to consume methane at the sulfate/methane transition (SMT) above the hydrates, thereby driving the progressive dissolution of the hydrates "from above". As a result the SMT migrates downward, leaving behind enrichments of authigenic barite and carbonates that typically precipitate at this biogeochemical reaction front. Calculation of the time needed to produce the observed solid-phase barium enrichments above the present-day depths of the SMT served to track the net downward migration of the SMT and to estimate the total time of hydrate dissolution in the recovered sediments. Methane fluxes were higher, and the SMT was located closer to the sediment surface in the past at both sites. Active seepage and hydrate formation are inferred to have occurred only a few thousands of years ago at the Hydrate Hole site. By contrast, AOM-driven hydrate dissolution as a consequence of an overall net decrease in upward methane flux seems to have persisted for a considerably longer time at the Worm Hole site, amounting to a few tens of thousands of years.

Dimethyl Acetals, an Indirect Marker of the Endogenous Antioxidant Plasmalogen Level, are Reduced in Blood Lipids of Sudanese Pre-eclamptic Subjects whose Background Diet is High in Carbohydrate

In Sudanese women with (n = 60) and without (n = 65) pre-eclampsia, circulating lipids, plasma and red cell saturated and monounsaturated fatty (MUFA) acids and dimethyl acetals (DMAs) were investigated. DMAs are an indirect marker of levels of plasmalogens, endogenous antioxidants, which play a critical role in oxidative protection, and cholesterol homeostasis. The pre-eclamptics had higher C18:1n-9 (p < 0.001) and ΣMUFA (p < 0.01) in plasma free fatty acids, C16:1n-7, C18:1n-9, ΣMUFA; 16:0/16:1n-7 (p < 0.01) in erythrocyte choline phosphoglycerides (ePC) and 16:1n-7, 18:1n-7 and 16:0/16:1n-7 (p < 0.01) in erythrocyte ethanolamine phosphoglycerides (ePE). In contrast, the DMAs 18:0, 18:1 and ΣDMAs in ePE, and 16:0, 18:0 and ΣDMAs in ePC were reduced (p < 0.001) in the pre-eclamptic women. This study of pregnant women with high carbohydrate and low fat background diet suggests pre-eclampsia is associated with oxidative stress and enhanced activity of the microsomal enzyme stearyl-CoA desaturase (delta 9 desaturase), as assessed by palmitic/palmitoleic (C16:0/C16:n-1) and stearic/oleic (C18/C18:1n-9) ratios.

U-Pb SHRIMP zircon dating of high-grade rocks from the Upper Allochthonous Terrane of Bragança and Morais Massifs (NE Portugal); geodynamic consequences

Bragança and Morais Massifs are part of the mega-klippen ensemble of NW Iberia, comprising a tectonic pile of four allochthonous units stacked above the Central-Iberian Zone autochthon. On top of this pile, the Upper Allochthonous Terrane (UAT) includes different high-grade metamorphic series whose age and geodynamic meaning are controversial. Mafic granulites provided U–Pb zircon ages at 399±7 Ma, dating the Variscan emplacement of UAT. In contrast,U–Pb zircon ages of ky- and hb-eclogites, felsic/intermediate HP/HT-granulites and orthogneisses (ca. 500–480 Ma) are identical to those of gabbros (488 ± 10 Ma) and Grt-pyroxenites (495 ± 8 Ma) belonging to a mafic/ultramafic igneous suite that records upper mantle melting and mafic magma crustal underplating at these times. Gabbros intrude the high-grade units of UAT and did not underwent the HP metamorphic event experienced by eclogites and granulites. These features and the zircon dates resemblance among different lithologies, suggest that extensive age resetting of older events may have been correlative with the igneous suite emplacement/crystallisation. Accordingly, reconciliation of structural, petrological and geochronological evidence implies that the development and early deformation of UAT high-grade rocks should be ascribed to an orogenic cycle prior to ≈500 Ma. Undisputable dating of this cycle is impossible, but the sporadic vestiges of Cadomian ages cannot be disregarded. The ca. 500–480 Ma time-window harmonises well with the Lower Palaeozoic continental rifting that trace the VariscanWilson Cycle onset and the Rheic Ocean opening. Subsequent preservation of the high heat-flowregime, possibly related to the Palaeotethys back-arc basin development (ca. 450–420 Ma), would explain the 461 ± 10 Ma age yielded by some zircon domains in felsic granulites, conceivably reflecting zircon dissolution/ recrystallisation till Ordovician times, long before the Variscan paroxysm (ca. 400–390 Ma). This geodynamic scenario suggests also that UAT should have been part of Armorica before its emplacement on top of Iberia after Palaeotethys closure.

A New Formulation of the Spectral Energy Budget of the Atmosphere, with Application to Two High-Resolution General Circulation Models

International audience

Accelerating retreat and high-elevation thinning of glaciers in central Spitsbergen

Svalbard is a heavily glacier-covered archipelago in the Arctic. Dickson Land (DL), in the central part of the largest island, Spitsbergen, is relatively arid, and as a result, glaciers there are relatively small and restricted mostly to valleys and cirques. This study presents a comprehensive analysis of glacier changes in DL based on inventories compiled from topographic maps and digital elevation models for the Little Ice Age maximum (LIA), the 1960s, 1990 and 2009/11. Total glacier area decreased by ~38 % since the LIA maximum, and front retreat has increased over the study period. Recently, most of the local glaciers have been consistently thinning in all elevation bands, in contrast to larger Svalbard ice masses which remain closer to balance. The mean 1990–2009/11 geodetic mass balance of glaciers in DL is among the most negative from the Svalbard regional means known from the literature.