Training enhances the ability of listeners to exploit visual information for auditory scene analysis

The ability to use temporal relationships between cross-modal cues facilitates perception and behavior. Previously we observed that temporally correlated changes in the size of a visual stimulus and the intensity in an auditory stimulus influenced the ability of listeners to perform an auditory selective attention task (Maddox et al., 2015). In this task participants detected timbral changes in a target sound while ignoring those in a simultaneously presented masker. When the visual stimulus was temporally coherent with the target sound, performance was significantly better than when it was temporally coherent with the masker sound, despite the visual stimulus conveying no task-relevant information. Here, we trained observers to detect audiovisual temporal coherence and asked whether this improved their ability to benefit from visual cues during the auditory selective attention task. We observed these listeners improved performance in the auditory selective attention task and changed the way in which they benefited from a visual stimulus: after training performance was better when the visual stimulus was temporally coherent with either the target or the masker stream, relative to the condition in which the visual stimulus was coherent with neither auditory stream. A second group which trained to discriminate modulation rate differences between temporally coherent audiovisual streams improved task performance, but did not change the way in which they used visual information. A control group did not change their performance between pretest and post-test. These results provide insights into how crossmodal experience may optimize multisensory integration

Training enhances the ability of listeners to exploit visual information for auditory scene analysis

The ability to use temporal relationships between cross-modal cues facilitates perception and behavior. Previously we observed that temporally correlated changes in the size of a visual stimulus and the intensity in an auditory stimulus influenced the ability of listeners to perform an auditory selective attention task (Maddox, Atilgan, Bizley, & Lee, 2015). Participants detected timbral changes in a target sound while ignoring those in a simultaneously presented masker. When the visual stimulus was temporally coherent with the target sound, performance was significantly better than when the visual stimulus was temporally coherent with the masker, despite the visual stimulus conveying no task-relevant information. Here, we trained observers to detect audiovisual temporal coherence and asked whether this changed the way in which they were able to exploit visual information in the auditory selective attention task. We observed that after training, participants were able to benefit from temporal coherence between the visual stimulus and both the target and masker streams, relative to the condition in which the visual stimulus was coherent with neither sound. However, we did not observe such changes in a second group that were trained to discriminate modulation rate differences between temporally coherent audiovisual streams, although they did show an improvement in their overall performance. A control group did not change their performance between pretest and post-test and did not change how they exploited visual information. These results provide insights into how crossmodal experience may optimize multisensory integration

Subtle pH differences trigger single residue motions for moderating conformations of calmodulin

This study reveals the essence of ligand recognition mechanisms by which calmodulin (CaM) controls a variety of Ca2+ signaling processes. We study eight forms of calcium-loaded CaM each with distinct conformational states. Reducing the structure to two degrees of freedom conveniently describes main features of the conformational changes of CaM via simultaneous twist-bend motions of the two lobes. We utilize perturbation-response scanning (PRS) technique, coupled with molecular dynamics simulations. PRS is based on linear response theory, comprising sequential application of directed forces on selected residues followed by recording the resulting protein coordinates. We analyze directional preferences of the perturbations and resulting conformational changes. Manipulation of a single residue reproduces the structural change more effectively than that of single/pairs/triplets of collective modes of motion. Our findings also give information on how the flexible linker acts as a transducer of binding information to distant parts of the protein. Furthermore, by perturbing residue E31 located in one of the EF hand motifs in a specific direction, it is possible to induce conformational change relevant to five target structures. Independently, using four different pKa calculation strategies, we find this particular residue to be the charged residue (out of a total of 52), whose ionization state is most sensitive to subtle pH variations in the physiological range. It is plausible that at relatively low pH, CaM structure is less flexible. By gaining charged states at specific sites at a pH value around 7, such as E31 found in the present study, local conformational changes in the protein will lead to shifts in the energy landscape, paving the way to other conformational states. These findings are in accordance with Fluorescence Resonance Energy Transfer (FRET) measured shifts in conformational distributions towards more compact forms with decreased pH. They also corroborate mutational studies and proteolysis results which point to the significant role of E31 in CaM dynamics

Modeling of composite beams and plates for static and dynamic analysis

A rigorous theory and corresponding computational algorithms was developed for a variety of problems regarding the analysis of composite beams and plates. The modeling approach is intended to be applicable to both static and dynamic analysis of generally anisotropic, nonhomogeneous beams and plates. Development of a theory for analysis of the local deformation of plates was the major focus. Some work was performed on global deformation of beams. Because of the strong parallel between beams and plates, the two were treated together as thin bodies, especially in cases where it will clarify the meaning of certain terminology and the motivation behind certain mathematical operations

Anharmonicity and self-similarity of the free energy landscape of protein G

The near-native free energy landscape of protein G is investigated through 0.4 microseconds-long atomistic molecular dynamics simulations in explicit solvent. A theoretical and computational framework is used to assess the time-dependence of salient thermodynamical features. While the quasi-harmonic character of the free energy is found to degrade in a few ns, the slow modes display a very mild dependence on the trajectory duration. This property originates from a striking self-similarity of the free energy landscape embodied by the consistency of the principal directions of the local minima, where the system dwells for several ns, and of the virtual jumps connecting them.Comment: revtex, 6 pages, 5 figure

Functional modes of proteins are among the most robust ones

It is shown that a small subset of modes which are likely to be involved in protein functional motions of large amplitude can be determined by retaining the most robust normal modes obtained using different protein models. This result should prove helpful in the context of several applications proposed recently, like for solving difficult molecular replacement problems or for fitting atomic structures into low-resolution electron density maps. Moreover, it may also pave the way for the development of methods allowing to predict such motions accurately.Comment: 4 pages, 5 figure

The effects of different irrigation methods on root distribution, intensity and effective root depth of young dwarf apple trees

The aim of this study is to determine the effects of different irrigation methods (drip, subsurface drip, surface and under-tree micro sprinkler) on the root distribution, intensity and effective root depth of “Williams Pride” and “Jersey Mac” apple cultivars budded on M9, rapidly grown in Isparta Region. The rootstocks were shallow root system and their root distribution was placed near trunk center and accumulated in diameter of 0.5 m and depth of 0.4 m of soil volume as bowl shape. The root intensity was reduced gradually away from surface and trunk; the root distribution was uniform in all irrigation methods used in the study. In other words, the effect of irrigation methods on root distribution was similar. Generally, the amount of “Williams Pride” root was higher than that of “Jersey Mac” variety. Therefore, these varieties have partial effect on root of the rootstock. Also, effective root depth was increased during the experimental years. Over the years, effective root depths obtained were 28.4 - 36.6 cm in 2006; 32.3 - 42.5 cm in 2007 and 37.1 - 45.2 cm in 2008, respectively. As a result, effective root depths for irrigation of the varieties can be taken as 40 - 45 cm until 3 years old

Effects of different irrigation programs on yield and quality parameters of eggplant (Solanum melongena L.) under greenhouse conditions

This study was carried out to determine the effects of different irrigation programs on yield and quality parameters of eggplant under greenhouse conditions, using Class A pan evaporation calculations and different plant-pan coefficients. Irrigation water was applied through drip irrigation method twice a week during the growing period. Irrigation treatments consisted of five plant-pan coefficients (S1: kcp = nonirrigation, S2: kcp = 0.50, S3: kcp = 0.75, S4: kcp = 1.00 and S5: kcp = 1.25). The amount of irrigation water ranged between 95.2 and 238.7 mm among the treatments. Evapotranspiration (ET) values varied from 93.1 to 466.3 mm for the treatments. The highest yield was obtained from the S3 and S4 treatments. A significant polynomial correlation was obtained between the yield and irrigation water, and between the yield and ET (P < 0.01). This indicated that when irrigation water and ET increased, yield also increased to a certain point. However, when the amount of irrigation water exceeded the plant water requirement, eggplant yield decreased. Yield response factor (Ky) was determined as 0.81. Since Ky < 1, eggplants were not sensitive to water deficiency. In addition, the highest water use efficiency (WUE) and irrigation water use efficiency (IWUE) values were calculated in the S3 (12.9 kgm-3) and S2 (44.2 kgm-3) treatments, while the lowest WUE and IWUE values were calculated in the S5 (7.9 and 15.5 kgm-3) treatment to which the highest irrigation water was applied. This finding indicated that WUE and IWUE values decreased with the increasing irrigation water and ET. These results suggested that S3 (kcp = 0.75) treatment can be the most appropriate irrigation program for eggplant with higher yield and WUE under greenhouse conditions.Key words: Eggplant, yield response factor, water use efficiency, Class A pan, evapotranspiration

Subtle pH differences trigger single residue motions for moderating conformations of calmodulin

This study reveals the essence of ligand recognition mechanisms by which calmodulin (CaM) controls a variety of Ca2+ signaling processes. We study eight forms of calcium-loaded CaM each with distinct conformational states. Reducing the structure to two degrees of freedom conveniently describes main features of conformational changes of CaM via simultaneous twist-bend motions of the two lobes. We utilize perturbation-response scanning (PRS) technique, coupled with molecular dynamics simulations to analyze conformational preferences of calcium-loaded CaM, initially in extended form. PRS is comprised of sequential application of directed forces on residues followed by recording the resulting coordinates. We show that manipulation of a single residue, E31 located in one of the EF hand motifs, reproduces structural changes to compact forms, and the flexible linker acts as a transducer of binding information to distant parts of the protein. Independently, using four different pKa calculation strategies, we find E31 to be the charged residue (out of 52), whose ionization state is most sensitive to subtle pH variations in the physiological range. It is proposed that at relatively low pH, CaM structure is less flexible. By gaining charged states at specific sites at a pH value around 7, local conformational changes in the protein will lead to shifts in the energy landscape, paving the way to other conformational states. These findings are in accordance with FRET measured shifts in conformational distributions towards more compact forms with decreased pH. They also corroborate mutational studies and proteolysis results which point to the significant role of E31 in CaM dynamics.Comment: 47 pages, 4 figure

Driving calmodulin protein towards conformational shift by changing ionization states of select residues

Proteins are complex systems made up of many conformational sub-states which are mainly determined by the folded structure. External factors such as solvent type, temperature, pH and ionic strength play a very important role in the conformations sampled by proteins. Here we study the conformational multiplicity of calmodulin (CaM) which is a protein that plays an important role in calcium signaling pathways in the eukaryotic cells. CaM can bind to a variety of other proteins or small organic compounds, and mediates different physiological processes by activating various enzymes. Binding of calcium ions and proteins or small organic molecules to CaM induces large conformational changes that are distinct to each interacting partner. In particular, we discuss the effect of pH variation on the conformations of CaM. By using the pKa values of the charged residues as a basis to assign protonation states, the conformational changes induced in CaM by reducing the pH are studied by molecular dynamics simulations. Our current view suggests that at high pH, barrier crossing to the compact form is prevented by repulsive electrostatic interactions between the two lobes. At reduced pH, not only is barrier crossing facilitated by protonation of residues, but also conformations which are on average more compact are attained. The latter are in accordance with the fluorescence resonance energy transfer experiment results of other workers. The key events leading to the conformational change from the open to the compact conformation are (i) formation of a salt bridge between the N-lobe and the linker, stabilizing their relative motions, (ii) bending of the C-lobe towards the N-lobe, leading to a lowering of the interaction energy between the two-lobes, (iii) formation of a hydrophobic patch between the two lobes, further stabilizing the bent conformation by reducing the entropic cost of the compact form, (iv) sharing of a Ca+2 ion between the two lobes