Journal articles on the topic 'Spike density'
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Diggelmann, Roland, Michele Fiscella, Andreas Hierlemann, and Felix Franke. "Automatic spike sorting for high-density microelectrode arrays." Journal of Neurophysiology 120, no. 6 (December 1, 2018): 3155–71. http://dx.doi.org/10.1152/jn.00803.2017.
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High-density microelectrode arrays can be used to record extracellular action potentials from hundreds to thousands of neurons simultaneously. Efficient spike sorters must be developed to cope with such large data volumes. Most existing spike sorting methods for single electrodes or small multielectrodes, however, suffer from the “curse of dimensionality” and cannot be directly applied to recordings with hundreds of electrodes. This holds particularly true for the standard reference spike sorting algorithm, principal component analysis-based feature extraction, followed by k-means or expectation maximization clustering, against which most spike sorters are evaluated. We present a spike sorting algorithm that circumvents the dimensionality problem by sorting local groups of electrodes independently with classical spike sorting approaches. It is scalable to any number of recording electrodes and well suited for parallel computing. The combination of data prewhitening before the principal component analysis-based extraction and a parameter-free clustering algorithm obviated the need for parameter adjustments. We evaluated its performance using surrogate data in which we systematically varied spike amplitudes and spike rates and that were generated by inserting template spikes into the voltage traces of real recordings. In a direct comparison, our algorithm could compete with existing state-of-the-art spike sorters in terms of sensitivity and precision, while parameter adjustment or manual cluster curation was not required. NEW & NOTEWORTHY We present an automatic spike sorting algorithm that combines three strategies to scale classical spike sorting techniques for high-density microelectrode arrays: 1) splitting the recording electrodes into small groups and sorting them independently; 2) clustering a subset of spikes and classifying the rest to limit computation time; and 3) prewhitening the spike waveforms to enable the use of parameter-free clustering. Finally, we combined these strategies into an automatic spike sorter that is competitive with state-of-the-art spike sorters.
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Nwry, Rezhin Ghareb, Shang Haseeb Abdulqader, and Shwana Ahmad Hussain. "Effect of plant population and cultivars on growth, yield and its component of bread wheat (Triticum aestivum L.) under the rain-fed condition in Kurdistan- Iraq." Tikrit journal for agricultural sciences 21, no. 3 (September 30, 2021): 41–51. http://dx.doi.org/10.25130/tjas.21.3.5.
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This experiment was conducted at the research field of College of Agricultural Engineering Sciences-University of Sulaimani at Bakrajo, Sulaimani, Iraq during the growing season of 2016-2017 to assess the effect of three-row spaces (10, 15 and 20) cm and three plant densities (160, 200 and 240) kg/ha with their interaction on grain yield and yield components of two bread wheat cultivars (Adana-99 and Aras). For each trait, ranges of statistical analysis were performed, including a Factorial Experiment in a Completely Randomized Block Design (CRBD) with three replications. At a 5% significance level, mean comparisons were done using the least significant difference (L.S.D). Plant height, number of spikes/m2, spike length, spike weight, number of spikelets/spike, number of grain/spike, the weight of grain/spike, 1000-grain weight, harvest index, biological yield, and grain yield were all calculated as part of grain yield. The results show that row spaces have a significant impact on the studied characters, with 10 cm producing the highest values for all characteristics except the number of spikes/m2, spike length, and harvest index, which were provided by 15 cm. With the exception of the number of spikes/m2, spike length, and biological yields, the impact of varieties on agronomic traits was significant; the Adana-99 variety provided maximum values for all of the studied characters. With the exception of spike length, where 200kg/ha density had the ultimate value, plant density had a major impact on the studied characters, with 160kg/ha density producing maximum values for almost all of the characters, and 240kg/ha density producing maximum values for the number of spikes/m2 and biological yield. Based on our findings, the Adana-99 cultivar should be sown at a seed rate of 160 kg/ha with a 10 cm inter-row spacing in Bakrajo, Sulaimani Region under guaranteed rained conditions.
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Paunovic, Aleksandar, Desimir Knezevic, and Milomirka Madic. "Genotype variations in grain yield of spring barley depending on sowing density." Genetika 38, no. 2 (2006): 107–14. http://dx.doi.org/10.2298/gensr0602107k.
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A three-year study was carried out for grain yield in five cultivars of the spring brewer's barley at the Small Grains Research Center of in Kragujevac from 1996 to 1998. The effect of three sowing densities on the number of spikes, grain number per spike and grain yield was studied for each cultivars. Research results have shown that the cultivars displayed a highly significant effect on the grain number per spike and grain yield. It has also been noticed that, in the course of every research year, sowing density induced increases in spike number and grain yield. In contrast, the higher sowing density brought about a decrease in the grain number per spike.
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Uramoto, Takumi, and Hiroyuki Torikai. "A Calcium-Based Simple Model of Multiple Spike Interactions in Spike-Timing-Dependent Plasticity." Neural Computation 25, no. 7 (July 2013): 1853–69. http://dx.doi.org/10.1162/neco_a_00462.
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Spike-timing-dependent plasticity (STDP) is a form of synaptic modification that depends on the relative timings of presynaptic and postsynaptic spikes. In this letter, we proposed a calcium-based simple STDP model, described by an ordinary differential equation having only three state variables: one represents the density of intracellular calcium, one represents a fraction of open state NMDARs, and one represents the synaptic weight. We shown that in spite of its simplicity, the model can reproduce the properties of the plasticity that have been experimentally measured in various brain areas (e.g., layer 2/3 and 5 visual cortical slices, hippocampal cultures, and layer 2/3 somatosensory cortical slices) with respect to various patterns of presynaptic and postsynaptic spikes. In addition, comparisons with other STDP models are made, and the significance and advantages of the proposed model are discussed.
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Smith, M. A. H., and R. J. Lamb. "Factors influencing oviposition by Sitodiplosis mosellana (Diptera: Cecidomyiidae) on wheat spikes (Gramineae)." Canadian Entomologist 133, no. 4 (August 2001): 533–48. http://dx.doi.org/10.4039/ent133533-4.
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AbstractFactors that might contribute to variability in the densities of wheat midge eggs, Sitodiplosis mosellana (Géhin), on common and durum wheats, Triticum aestivum L. and Triticum durum Desf., were investigated to improve the quantification of oviposition preferences in relation to crop resistance. Egg densities on wheat spikes were highly variable, with a similar contagious distribution in the laboratory and field, although variance was highest in the laboratory. Females laid eggs in small groups, usually of one to six eggs; most infested spikes had more than one egg group. Females showed no preference for ovipositing on different parts of a spike, although spikelets on one side and at the base often received fewer eggs because these spikelets were covered by the flag leaf and inaccessible for longer than others. Oviposition rates varied from night to night, probably related to the weather. Females showed no preference for spikes at different growth stages, from the time spikes began to emerge until at least flowering. Spike size did not affect egg density, and spike height was a factor only for spikes deep within or protruding above the canopy. Sources of environmental variation such as effects of weather on oviposition rates in the field or spatial phenomena in cages were measurable but of secondary importance. In the field, comparisons among spikes which emerged on the same day could reduce variation in egg density. In the laboratory, variation in egg density could be reduced by using arrays of excised spikes arranged at the same height, leaving the central portion of the array empty. The primary cause of high variability in egg density among spikes was variation in egg-group size and the presence of multiple egg groups on a single spike, factors which cannot be experimentally controlled because they are the result of oviposition behaviour rather than environmental heterogeneity.
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Daghigh, Ramin G., and Gabor Kunstatter. "Spacetime Metrics and Ringdown Waveforms for Galactic Black Holes Surrounded by a Dark Matter Spike." Astrophysical Journal 940, no. 1 (November 1, 2022): 33. http://dx.doi.org/10.3847/1538-4357/ac940b.
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Abstract Theoretical models suggest the existence of a dark matter spike surrounding the supermassive black holes at the core of galaxies. The spike density is thought to obey a power law that starts at a few times the black hole horizon radius and extends to a distance, R sp, of the order of a kiloparsec. We use the Tolman–Oppenheimer–Volkoff equations to construct the spacetime metric representing a black hole surrounded by such a dark matter spike. We consider the dark matter to be a perfect fluid, but make no other assumption about its nature. The assumed power-law density provides in principle three parameters with which to work: the power-law exponent γ sp, the external radius R sp, and the spike density ρ DM sp at R sp. These in turn determine the total mass of the spike. We focus on Sagittarius A* and M87 for which some theoretical and observational bounds exist on the spike parameters. Using these bounds in conjunction with the metric obtained from the Tolman–Oppenheimer–Volkoff equations, we investigate the possibility of detecting the dark matter spikes surrounding these black holes via the gravitational waves emitted at the ringdown phase of black hole perturbations. Our results suggest that if the spike to black hole mass ratio is roughly constant, greater mass black holes require relatively smaller spike densities to yield potentially observable signals. We find that is unlikely for the spike in M87 to be detected via the ringdown waveform with currently available techniques unless its mass is roughly an order of magnitude larger than existing observational estimates. However, given that the signal increases with black hole mass, dark matter spikes might be observable for more massive galactic black holes in the not too distant future.
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Galimidi, Rachel, Joshua Klein, Maria Politzer, Shiyu Bai, Michael Seaman, Michel Nussenzweig, Anthony West, and Pamela Bjorkman. "Intra-spike crosslinking overcomes antibody evasion by HIV-1 (VIR1P.1131)." Journal of Immunology 194, no. 1_Supplement (May 1, 2015): 74.8. http://dx.doi.org/10.4049/jimmunol.194.supp.74.8.
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Abstract Antibodies developed during HIV-1 infection lose efficacy as the viral spike mutates. We postulated that anti-HIV-1 antibodies primarily bind monovalently because HIV’s low spike density impedes bivalent binding through inter-spike crosslinking, and the spike structure prohibits bivalent binding through intra-spike crosslinking. Monovalent binding reduces avidity and potency, thus expanding the range of mutations permitting antibody evasion. To test this idea, we engineered antibody-based molecules capable of bivalent binding through intra-spike crosslinking. We used DNA as a “molecular ruler” to measure intra-epitope distances on virion-bound spikes and construct intra-spike crosslinking molecules. Optimal bivalent reagents exhibited up to 2.5 orders-of-magnitude increased potency (>100-fold average increases across virus panels) and identified conformational states of virion-bound spikes. The demonstration that intra-spike crosslinking lowers the concentration of antibodies required for neutralization supports the hypothesis that low spike densities facilitate antibody evasion and the use of molecules capable of intra-spike crosslinking for therapy or passive protection.
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Alvarez, J., J. Gómez, A. Martín, and L. Martín. "Gene effects for spike length, spikelets per spike and spike density inHordeum chilense." Cereal Research Communications 38, no. 2 (June 2010): 266–71. http://dx.doi.org/10.1556/crc.38.2010.2.13.
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VAN DIJCK, GERT, KARSTEN SEIDL, OLIVER PAUL, PATRICK RUTHER, MARC M. VAN HULLE, and REINOUD MAEX. "ENHANCING THE YIELD OF HIGH-DENSITY ELECTRODE ARRAYS THROUGH AUTOMATED ELECTRODE SELECTION." International Journal of Neural Systems 22, no. 01 (February 2012): 1–19. http://dx.doi.org/10.1142/s0129065712003055.
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Recently developed CMOS-based microprobes contain hundreds of electrodes on a single shaft with inter-electrode distances as small as 30 μm. So far, neuroscientists needed to select electrodes manually from hundreds of electrodes. Here we present an electronic depth control algorithm that allows to select electrodes automatically, hereby allowing to reduce the amount of data and locating those electrodes that are close to neurons. The electrodes are selected according to a new penalized signal-to-noise ratio (PSNR) criterion that demotes electrodes from becoming selected if their signals are redundant with previously selected electrodes. It is shown that, using the PSNR, interneurons generating smaller spikes are also selected. We developed a model that aims to evaluate algorithms for electronic depth control, but also generates benchmark data for testing spike sorting and spike detection algorithms. The model comprises a realistic tufted pyramidal cell, non-tufted pyramidal cells and inhibitory interneurons. All neurons are synaptically activated by hundreds of fibers. This arrangement allows the algorithms to be tested in more realistic conditions, including backgrounds of synaptic potentials, varying spike rates with bursting and spike amplitude attenuation.
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De Zeeuw, C. I., S. K. E. Koekkoek, D. R. W. Wylie, and J. I. Simpson. "Association Between Dendritic Lamellar Bodies and Complex Spike Synchrony in the Olivocerebellar System." Journal of Neurophysiology 77, no. 4 (April 1, 1997): 1747–58. http://dx.doi.org/10.1152/jn.1997.77.4.1747.
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De Zeeuw, C. I., S.K.E. Koekkoek, D.R.W. Wylie, and J. I. Simpson. Association between dendritic lamellar bodies and complex spike synchrony in the olivocerebellar system. J. Neurophysiol. 77: 1747–1758, 1997. Dendritic lamellar bodies have been reported to be associated with dendrodendritic gap junctions. In the present study we investigated this association at both the morphological and electrophysiological level in the olivocerebellar system. Because cerebellar GABAergic terminals are apposed to olivary dendrites coupled by gap junctions, and because lesions of cerebellar nuclei influence the coupling between neurons in the inferior olive, we postulated that if lamellar bodies and gap junctions are related, then the densities of both structures will change together when the cerebellar input is removed. Lesions of the cerebellar nuclei in rats and rabbits resulted in a reduction of the density of lamellar bodies, the number of lamellae per lamellar body, and the density of gap junctions in the inferior olive, whereas the number of olivary neurons was not significantly reduced. The association between lamellar bodies and electrotonic coupling was evaluated electrophysiologically in alert rabbits by comparing the occurrence of complex spike synchrony in different Purkinje cell zones of the flocculus that receive their climbing fibers from olivary subnuclei with different densities of lamellar bodies. The complex spike synchrony of Purkinje cell pairs, that receive their climbing fibers from an olivary subnucleus with a high density of lamellar bodies, was significantly higher than that of Purkinje cells, that receive their climbing fibers from a subnucleus with a low density of lamellar bodies. To investigate whether the complex spike synchrony is related to a possible synchrony between simple spikes, we recorded simultaneously the complex spike and simple spike responses of Purkinje cell pairs during natural visual stimulation. Synchronous simple spike responses did occur, and this synchrony tended to increase as the synchrony between the complex spikes increased. This relation raises the possibility that synchronously activated climbing fibers evoke their effects in part via the simple spike response of Purkinje cells. The present results indicate that dendritic lamellar bodies and dendrodendritic gap junctions can be downregulated concomitantly, and that the density of lamellar bodies in different olivary subdivisions is correlated with the degree of synchrony of their climbing fiber activity. Therefore these data support the hypothesis that dendritic lamellar bodies can be associated with dendrodendritic gap junctions. Considering that the density of dedritic lamellar bodies in the inferior olive is higher than in any other area of the brain, this conclusion implies that electrotonic coupling is important for the function of the olivocerebellar system.
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Alvim, Karen Rodrigues de Toledo, Césio Humberto de Brito, Afonso Maria Brandão, Luiz Savelli Gomes, and Maria Teresa Gomes Lopes. "The effect of leaf area reduction on corn plants during the reproduction phase." Revista Ceres 58, no. 4 (August 2011): 413–18. http://dx.doi.org/10.1590/s0034-737x2011000400002.
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Reduction in leaf area in corn plants during reproduction changes physiological metabolism and consequently the accumulation of dry matter in grains. The aim of this work was to study changes in agronomic characteristics caused by defoliation in corn during the reproduction phase. The experiment was carried out in Uberlândia, Minas Gerais state, in the agricultural year 2007/2008. The experiment was arranged in a randomized block design, consisting of seven treatments: control without defoliation, removal of two apical leaves, removal of four apical leaves, removal of all leaves above spike, removal of four intermediate leaves, removal of all leaves below spike, and removal of all plant leaves, with five repetitions. The genotype used for the evaluations was hybrid NB 7376. Defoliation was carried out when plants were at the growth stage R2. The variables assessed were: yield, density of spikes and corncobs, root resistance and stem integrity. When all leaves above the spike were removed, grain yield was reduced by 20%. Corncob density, stem integrity and root resistance to uprooting were also affected. Spike density was only affected when all plant leaves were removed. The leaf area remaining physiologically active above the spike was found to be most efficient in terms of grain yield.
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Pouzat, Christophe, Matthieu Delescluse, Pascal Viot, and Jean Diebolt. "Improved Spike-Sorting By Modeling Firing Statistics and Burst-Dependent Spike Amplitude Attenuation: A Markov Chain Monte Carlo Approach." Journal of Neurophysiology 91, no. 6 (June 2004): 2910–28. http://dx.doi.org/10.1152/jn.00227.2003.
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Spike-sorting techniques attempt to classify a series of noisy electrical waveforms according to the identity of the neurons that generated them. Existing techniques perform this classification ignoring several properties of actual neurons that can ultimately improve classification performance. In this study, we propose a more realistic spike train generation model. It incorporates both a description of “nontrivial” (i.e., non-Poisson) neuronal discharge statistics and a description of spike waveform dynamics (e.g., the events amplitude decays for short interspike intervals). We show that this spike train generation model is analogous to a one-dimensional Potts spin-glass model. We can therefore tailor to our particular case the computational methods that have been developed in fields where Potts models are extensively used, including statistical physics and image restoration. These methods are based on the construction of a Markov chain in the space of model parameters and spike train configurations, where a configuration is defined by specifying a neuron of origin for each spike. This Markov chain is built such that its unique stationary density is the posterior density of model parameters and configurations given the observed data. A Monte Carlo simulation of the Markov chain is then used to estimate the posterior density. We illustrate the way to build the transition matrix of the Markov chain with a simple, but realistic, model for data generation. We use simulated data to illustrate the performance of the method and to show that this approach can easily cope with neurons firing doublets of spikes and/or generating spikes with highly dynamic waveforms. The method cannot automatically find the “correct” number of neurons in the data. User input is required for this important problem and we illustrate how this can be done. We finally discuss further developments of the method.
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Hart, T. K., A. M. Klinkner, J. Ventre, and P. J. Bugelski. "Morphometric analysis of envelope glycoprotein gp120 distribution on HIV-1 virions." Journal of Histochemistry & Cytochemistry 41, no. 2 (February 1993): 265–71. http://dx.doi.org/10.1177/41.2.7678271.
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The surface of HIV-1, like that of other retroviruses, is studied with virally encoded glycoproteins which appear ultrastructurally as electron-dense spikes or knobs. The glycoprotein that forms the spike structure, gp120, is non-covalently bound to the transmembrane glycoprotein gp41. Mature HIV-1 virions do not have as many spikes as the genetically related retroviruses HIV-2 and SIV. gp120 is lost from HIV-1 during viral morphogenesis and after incubation of the virus with the soluble form of cellular receptor CD4. In this study we used ultrastructural cytochemistry and morphometry to quantitate the distribution of envelope glycoprotein spikes on budding and mature HIV-1 virions and to look for alternatives to the laborious and somewhat subjective spike-counting technique for envelope spike analysis on HIV-1. HIV-1, strain HTLV-IIIB, was examined after staining of envelope glycoproteins with either tannic acid, immunogold staining for gp120 (gp120-immunogold), or lectin-gold staining with concanavalin A for mannose residues (ConA-HRP-gold) and frequency distributions of spikes or gold particles per micron HIV-1 membrane generated. Envelope spikes were normally distributed on membranes of budding and mature HIV-1. However, the density of spikes per micron viral membrane on mature HIV-1 virions was approximately 50% of that observed on budding virions. ConA-HRP-gold and gp120-immunogold did not efficiently label budding virions. The shape of the frequency distribution for ConA-HRP-gold particles on mature virions was similar to that for envelope spikes and could be used to quantitate envelope glycoproteins on HIV-1. In addition, ConA-HRP-gold staining was able to detect the loss of envelope proteins after treatment of virus with soluble CD4. gp120-immunogold labeling was patchy and many virions were unlabeled. ConA-HRP-gold staining proved to be a rapid, reliable, and easily quantifiable method for estimation of envelope glycoprotein density on mature HIV-1. However, the loss of spike structures throughout the life cycle of HIV-1 can effectively be determined only by direct spike counting.
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Zhao, Yanan, Yufang Huang, Shuai Li, Xu Chu, and Youliang Ye. "Improving the growth, lodging and yield of different density-resistance maize by optimising planting density and nitrogen fertilisation." Plant, Soil and Environment 66, No. 9 (September 14, 2020): 453–60. http://dx.doi.org/10.17221/178/2020-pse.
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Matching the planting density, fertilisation, and genotype is crucial to improve the maize yield. Here, two-year field trials, including 4 densities and 3 nitrogen (N) rates for 2 maize cultivars, were conducted to study the effects of planting density and N rate on maize growth, lodging, spike characters, and yield. Compared with 360 kg/ha, N application of 180 kg/ha decreased the plant, ear height, and stem circumference of WeiKe 702 (WK702), while increased the plant height and stem circumference, but decreased ear height of ZhongDan 909 (ZD909). Meanwhile, the N application of 180 kg/ha greatly reduced the lodging rates of maize under the high density. The maize yield increased and reached the maximum yield at 7.5 × 10<sup>4</sup> plant/ha, and then decreased with increasing density. The N application of 180 kg/ha increased yield by 0.49, 0.73, 5.38, 7.81% from low to high planting densities, and reduced the bald tip length by 18.86%. WK702 was more sensitive to the planting density and N application, with greater variation of yield and spike traits than ZD909 under the densification. Therefore, the N application of 180 kg/ha and a density of 7.5 × 10<sup>4</sup> plant/ha could improve maize growth and lodging, and therefore increase maize yield.
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Graham, Bruce P., Ausra Saudargiene, and Stuart Cobb. "Spine Head Calcium as a Measure of Summed Postsynaptic Activity for Driving Synaptic Plasticity." Neural Computation 26, no. 10 (October 2014): 2194–222. http://dx.doi.org/10.1162/neco_a_00640.
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We use a computational model of a hippocampal CA1 pyramidal cell to demonstrate that spine head calcium provides an instantaneous readout at each synapse of the postsynaptic weighted sum of all presynaptic activity impinging on the cell. The form of the readout is equivalent to the functions of weighted, summed inputs used in neural network learning rules. Within a dendritic layer, peak spine head calcium levels are either a linear or sigmoidal function of the number of coactive synapses, with nonlinearity depending on the ability of voltage spread in the dendrites to reach calcium spike threshold. This is strongly controlled by the potassium A-type current, with calcium spikes and the consequent sigmoidal increase in peak spine head calcium present only when the A-channel density is low. Other membrane characteristics influence the gain of the relationship between peak calcium and the number of active synapses. In particular, increasing spine neck resistance increases the gain due to increased voltage responses to synaptic input in spine heads. Colocation of stimulated synapses on a single dendritic branch also increases the gain of the response. Input pathways cooperate: CA3 inputs to the proximal apical dendrites can strongly amplify peak calcium levels due to weak EC input to the distal dendrites, but not so strongly vice versa. CA3 inputs to the basal dendrites can boost calcium levels in the proximal apical dendrites, but the relative electrical compactness of the basal dendrites results in the reverse effect being less significant. These results give pointers as to how to better describe the contributions of pre- and postsynaptic activity in the learning “rules” that apply in these cells. The calcium signal is closer in form to the activity measures used in traditional neural network learning rules than to the spike times used in spike-timing-dependent plasticity.
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Matkovic-Stojsin, Mirela, Veselinka Zecevic, Sofija Petrovic, Miodrag Dimitrijevic, Danica Micanovic, Borislav Banjac, and Desimir Knezevic. "Variability, correlation, path analysis and stepwise regression for yield components of different wheat genotypes." Genetika 50, no. 3 (2018): 817–28. http://dx.doi.org/10.2298/gensr1803817m.
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In order to evaluate the variability and relationship between different wheat yield components, a randomized complete block design experiment with ten genotypes of wheat had been carried out during three growing seasons (2010-2012). The number of spikelet per spike and grain weight per spike had low genotypic and phenotypic variability, while plant height had the highest one. High heritability was observed for plant height (h2=93.1%), spike length (h2=92.3%) and spike density (h2=92.9%). The low heritability was found for grain weight per spike (h2=35.6%). Grain weight per spike was in significant positive genotypic and phenotypic correlation with all the traits (plant height, spike height, number of spikelet per spike, number of grain per spike and spike weight) except spike density. The spike weight had the highest phenotypic (rp=0.988), while number of spikelet per spike had the highest genotypic correlation with grain weight per spike (rg=0.981). Path coefficient analysis revealed that all the traits had highly significant direct effect on grain weight per spike, except spike length. The stepwise regression revealed that 87.1% of the grain weight per spike variation was explained by model which excludes spike length. Spike weight and plant height had the highest shared and unique contribution to grain weight per spike.
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Fernandez, Fernando R., W. Hamish Mehaffey, and Ray W. Turner. "Dendritic Na+ Current Inactivation Can Increase Cell Excitability By Delaying a Somatic Depolarizing Afterpotential." Journal of Neurophysiology 94, no. 6 (December 2005): 3836–48. http://dx.doi.org/10.1152/jn.00653.2005.
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Many central neurons support active dendritic spike backpropagation mediated by voltage-gated currents. Active spikes in dendrites have been shown capable of providing feedback to the soma to influence somatic excitability and firing dynamics through a depolarizing afterpotential (DAP). In pyramidal cells of the electrosensory lobe of weakly electric fish, Na+ spikes in dendrites undergo a frequency-dependent broadening that enhances the DAP to increase somatic firing frequency. We use a combination of dynamical analysis and electrophysiological recordings to demonstrate that spike broadening in dendrites is primarily caused by a cumulative inactivation of dendritic Na+ current. We further show that a reduction in dendritic Na+ current increases excitability by decreasing the interspike interval and promoting burst firing. This process arises when inactivation of dendritic Na+ current shifts the latency of the dendritic spike to delay the arrival of the DAP sufficiently to increase its impact on somatic membrane potential despite a reduction in dendritic excitability. Furthermore, the relationship between dendritic Na+ current density and somatic excitability is nonmonotonic, as intermediate levels of dendritic Na+ current exert the greatest excitatory influence. These results reveal that temporal shifts in dendritic spike firing provide a novel means for backpropagating spikes to influence the final output of a cell.
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Frantová, Nicole, Michal Rábek, Petr Elzner, Tomáš Středa, Ivana Jovanović, Ludmila Holková, Petr Martinek, Pavlína Smutná, and Ilja Prášil. "Different Drought Tolerance Strategy of Wheat Varieties in Spike Architecture." Agronomy 12, no. 10 (September 27, 2022): 2328. http://dx.doi.org/10.3390/agronomy12102328.
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Spike characteristics include spike length, total spikelet number per spike, number of fertile flowers, spike density, spike fertility, grain number, thousand kernel weight, the number of spikes per square meter, harvest index and the grain yield during the flowering and ripening stage. The six winter and one facultative variety differed in earliness, derived in part from the allele of the Ppd-D1 gene and phenological observation. The two sites significantly differed in the soil moisture, which varied during continual microclimate monitoring. The spike architecture of winter wheat was affected by drought. The plant samples from the site FIELD 2 (more drought stressed) showed a higher reduction in spike characteristics such as a lower spike length, total spikelet number, number of fertile flowers and spike fertility, leading to a lower yield than the site FIELD 1. Both early and late varieties possess compensatory abilities to create the grain yield during drought stress; however, the timing and duration of exposure to drought determine the application and success of the compensatory ability. In our experiment, the late varieties (photoperiod sensitive) performed better in yield than the early varieties during both growing seasons. That is at odds with the generally recommended “drought escape strategy” (early varieties) and suggests a possible direction for variety selection and breeding in arid areas in Central Europe.
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Börner, Andreas, Marina Schäfer, Andrea Schmidt, Michael Grau, and Jörn Vorwald. "Associations between geographical origin and morphological characters in bread wheat (Triticum aestivum L.)." Plant Genetic Resources 3, no. 3 (December 2005): 360–72. http://dx.doi.org/10.1079/pgr200589.
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We report the morphological typing of 13,337 accessions of bread wheat. The individual characters assessed were: awnedness, awn colour, glume colour, presence/absence of glume hairs, spike type, spike density, spike branching, grain colour, stem type (hollow/solid) and presence/absence of ligules. We have associated these morphological data with accession provenance, to analyse global patterns of the traits. Whereas some of the traits (awnedness, awn colour, glume colour, presence/absence of hairs on glumes, stem type) are concentrated in distinct geographical regions, others (spike type, spike density, grain colour, presence/absence of ligules) appear to be randomly distributed. Spike branching was not observed. Possible reasons for the geographical distributions of the characters, in the light of their inheritance, are discussed.
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Jäckel, David, Urs Frey, Michele Fiscella, Felix Franke, and Andreas Hierlemann. "Applicability of independent component analysis on high-density microelectrode array recordings." Journal of Neurophysiology 108, no. 1 (July 1, 2012): 334–48. http://dx.doi.org/10.1152/jn.01106.2011.
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Emerging complementary metal oxide semiconductor (CMOS)-based, high-density microelectrode array (HD-MEA) devices provide high spatial resolution at subcellular level and a large number of readout channels. These devices allow for simultaneous recording of extracellular activity of a large number of neurons with every neuron being detected by multiple electrodes. To analyze the recorded signals, spiking events have to be assigned to individual neurons, a process referred to as “spike sorting.” For a set of observed signals, which constitute a linear mixture of a set of source signals, independent component (IC) analysis (ICA) can be used to demix blindly the data and extract the individual source signals. This technique offers great potential to alleviate the problem of spike sorting in HD-MEA recordings, as it represents an unsupervised method to separate the neuronal sources. The separated sources or ICs then constitute estimates of single-neuron signals, and threshold detection on the ICs yields the sorted spike times. However, it is unknown to what extent extracellular neuronal recordings meet the requirements of ICA. In this paper, we evaluate the applicability of ICA to spike sorting of HD-MEA recordings. The analysis of extracellular neuronal signals, recorded at high spatiotemporal resolution, reveals that the recorded data cannot be modeled as a purely linear mixture. As a consequence, ICA fails to separate completely the neuronal signals and cannot be used as a stand-alone method for spike sorting in HD-MEA recordings. We assessed the demixing performance of ICA using simulated data sets and found that the performance strongly depends on neuronal density and spike amplitude. Furthermore, we show how postprocessing techniques can be used to overcome the most severe limitations of ICA. In combination with these postprocessing techniques, ICA represents a viable method to facilitate rapid spike sorting of multidimensional neuronal recordings.
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Libbrecht, Kenneth G., and Kevin Lui. "An investigation of laboratory-grown ice spikes." Journal of Glaciology 50, no. 170 (2004): 371–74. http://dx.doi.org/10.3189/172756504781830015.
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AbstractWe have investigated the formation of 10-50 mm long ice spikes that sometimes appear on the free surface of water when it solidifies. By freezing water under different conditions, we measured the probability of ice-spike formation as a function of: (1) the air temperature in the freezing chamber, (2) air motion in the freezing chamber (which promotes evaporative cooling), (3) the quantity of dissolved salts in the water, and (4) the size, shape and composing material of the freezing vessel. We found that the probability of ice-spike formation is greatest when the air temperature is near -7°C, the water is pure and the air in the freezing chamber is moving. Even small quantities of dissolved solids greatly reduce the probability of ice-spike formation. Under optimal conditions, approximately half the ice cubes in an ordinary ice-cube tray will form ice spikes. Guided by these observations, we have examined the Bally-Dorsey model for the formation of ice spikes. In this model, the density change during solidification forces super cooled water up through a hollow ice tube, where it freezes around the rim to lengthen the tube. We propose that any dissolved solids in the water will tend to concentrate at the tip of a growing ice spike and inhibit its growth. This can qualitatively explain the observation that ice spikes do not readily form using water containing even small quantities of dissolved solids.
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Kloosterman, Fabian, Pascal Peloquin, and L. Stan Leung. "Apical and Basal Orthodromic Population Spikes in Hippocampal CA1 In Vivo Show Different Origins and Patterns of Propagation." Journal of Neurophysiology 86, no. 5 (November 1, 2001): 2435–44. http://dx.doi.org/10.1152/jn.2001.86.5.2435.
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There is controversy concerning whether orthodromic action potentials originate from the apical or basal dendrites of CA1 pyramidal cells in vivo. The participation of the dendrites in the initialization and propagation of population spikes in CA1 of urethan-anesthetized rats in vivo was studied using simultaneously recorded field potentials and current source density (CSD) analysis. CSD analysis revealed that the antidromic population spike, evoked by stimulation of the alveus, invaded in succession, the axon initial segment (stratum oriens), cell body and ∼200 μm of the proximal apical dendrites. Excitation of the basal dendrites of CA1, following stimulation of CA3 stratum oriens, evoked an orthodromic spike that started near the cell body or initial segment and then propagated ∼200 μm into the proximal apical dendrites. In contrast, the population spike that followed excitation of the apical dendrites of CA1 initiated at the proximal apical dendrites, 50–100 μm distal to the cell body layer, and then propagated centripetally to the cell body and the proximal basal dendrites. A late apical dendritic spike may arise in the mid-apical dendrites (250–300 μm from the cell layer) and propagated distally. The origin or the pattern of propagation of each population spike type was similar for near-threshold to supramaximal stimulus intensities. In summary, population spikes following apical dendritic and basal dendritic excitation in vivo appeared to originate from different locations. Apical dendritic excitation evoked a population spike that initiated in the proximal apical dendrites while basal dendritic excitation evoked a spike that started near the initial segment or cell body. An original finding of this study is the propagation of the population spike from basal to apical dendrites in vivo or vice versa. This backpropagation from one dendritic tree to the other may play an important role in the synaptic plasticity among a network of CA3 to CA1 neurons.
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Amitai, Assaf. "Viral surface geometry shapes influenza and coronavirus spike evolution through antibody pressure." PLOS Computational Biology 17, no. 12 (December 13, 2021): e1009664. http://dx.doi.org/10.1371/journal.pcbi.1009664.
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The evolution of circulating viruses is shaped by their need to evade antibody response, which mainly targets the viral spike. Because of the high density of spikes on the viral surface, not all antigenic sites are targeted equally by antibodies. We offer here a geometry-based approach to predict and rank the probability of surface residues of SARS spike (S protein) and influenza H1N1 spike (hemagglutinin) to acquire antibody-escaping mutations utilizing in-silico models of viral structure. We used coarse-grained MD simulations to estimate the on-rate (targeting) of an antibody model to surface residues of the spike protein. Analyzing publicly available sequences, we found that spike surface sequence diversity of the pre-pandemic seasonal influenza H1N1 and the sarbecovirus subgenus highly correlates with our model prediction of antibody targeting. In particular, we identified an antibody-targeting gradient, which matches a mutability gradient along the main axis of the spike. This identifies the role of viral surface geometry in shaping the evolution of circulating viruses. For the 2009 H1N1 and SARS-CoV-2 pandemics, a mutability gradient along the main axis of the spike was not observed. Our model further allowed us to identify key residues of the SARS-CoV-2 spike at which antibody escape mutations have now occurred. Therefore, it can inform of the likely functional role of observed mutations and predict at which residues antibody-escaping mutation might arise.
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Kong, Deting, Yuan Wang, Xinyan Wu, Xiyu Liu, Jianhua Qu, and Jie Xue. "A Grid-Density Based Algorithm by Weighted Spiking Neural P Systems with Anti-Spikes and Astrocytes in Spatial Cluster Analysis." Processes 8, no. 9 (September 11, 2020): 1132. http://dx.doi.org/10.3390/pr8091132.
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In this paper, we propose a novel clustering approach based on P systems and grid- density strategy. We present grid-density based approach for clustering high dimensional data, which first projects the data patterns on a two-dimensional space to overcome the curse of dimensionality problem. Then, through meshing the plane with grid lines and deleting sparse grids, clusters are found out. In particular, we present weighted spiking neural P systems with anti-spikes and astrocyte (WSNPA2 in short) to implement grid-density based approach in parallel. Each neuron in weighted SN P system contains a spike, which can be expressed by a computable real number. Spikes and anti-spikes are inspired by neurons communicating through excitatory and inhibitory impulses. Astrocytes have excitatory and inhibitory influence on synapses. Experimental results on multiple real-world datasets demonstrate the effectiveness and efficiency of our approach.
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Boehler, Michael D., Bruce C. Wheeler, and Gregory J. Brewer. "Added astroglia promote greater synapse density and higher activity in neuronal networks." Neuron Glia Biology 3, no. 2 (April 20, 2007): 127–40. http://dx.doi.org/10.1017/s1740925x07000440.
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AbstractAstroglia are known to potentiate individual synapses, but their contribution to networks is unclear. Here we examined the effect of adding either astroglia or media conditioned by astroglia on entire networks of rat hippocampal neurons cultured on microelectrode arrays. Added astroglia increased spontaneous spike rates nearly two-fold and glutamate-stimulated spiking by six-fold, with desensitization eliminated for bath addition of 25 μM glutamate. Astrocyte-conditioned medium partly mimicked the effects of added astroglia. Bursting behavior was largely unaffected by added astroglia except with added glutamate. Addition of the GABAA receptor antagonist bicuculline also increased spike rates but with more subtle differences between networks without or with added astroglia. This indicates that networks without added astroglia were inhibited greatly. In all conditions, the log–log distribution of spike rates fit well to linear distributions over three orders of magnitude. Networks with added astroglia shifted consistently toward higher spike rates. Immunostaining for GFAP revealed a linear increase with added astroglia, which also increased neuronal survival. The increased spike rates with added astroglia correlated with a 1.7-fold increase in immunoreactive synaptophysin puncta, and increases of six-fold for GABAAβ, two-fold for NMDA-R1 and two-fold for Glu-R1 puncta, with receptor clustering that indicated synaptic scaling. Together, these results indicate that added astroglia increase the density of synapses and receptors, and facilitate higher spike rates for many elements in the network. These effects are reproduced by glia-conditioned media, with the exception of glutamate-mediated transmission.
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Richardson, T. L., R. W. Turner, and J. J. Miller. "Action-potential discharge in hippocampal CA1 pyramidal neurons: current source-density analysis." Journal of Neurophysiology 58, no. 5 (November 1, 1987): 981–96. http://dx.doi.org/10.1152/jn.1987.58.5.981.
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1. The site of origin of evoked action-potential discharge in hippocampal CA1 pyramidal neurons was investigated using the in vitro rat hippocampal slice preparation. 2. Action-potential discharge in pyramidal cells was evoked by stimulation of efferent pyramidal cell fibers in the alveus (antidromic) or afferent synaptic inputs in stratum oriens (SO) or stratum radiatum (SR). Laminar profiles of evoked extracellular field potentials were recorded at 25-micron intervals along the entire dendrosomatic axis of the pyramidal cell and a one-dimensional current source-density analysis was applied. 3. Suprathreshold stimulation of the alveus evoked an antidromic population spike response and current sink with the shortest peak latency in stratum pyramidale or proximal stratum oriens. A biphasic positive/negative potential associated with a current source/sink was recorded in dendritic regions, with both components increasing in peak latency with distance from the border of stratum pyramidale. 4. Suprathreshold stimulation of SO or SR evoked a population spike response superimposed upon the underlying synaptic depolarization at all levels of the dendrosomatic axis. The shortest latency population spike and current sink were recorded in stratum pyramidale or proximal stratum oriens. In dendritic regions, a biphasic positive/negative potential and current source/sink conducted with increasing latency from the border of stratum pyramidale. 5. A direct comparison of alvear- and SR-evoked responses revealed a basic similarity in population spike potentials and associated sink/source relationships at both the somatic and dendritic level and a similar shift in peak latency of spike components along the pyramidal cell axis. 6. It is concluded that the initial site for generation of a spike along the dendrosomatic axis of the pyramidal cell following antidromic or orthodromic stimulation is in the region of the cell body layer (soma or axon hillock). Action-potential discharge in dendritic regions then occurs as the result of a subsequent retrograde spike invasion of basal and apical dendritic arborizations.
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Chen, Mei, Yong-He Zhu, Ming-Jian Ren, Long Jiang, Jin He, and Rui Dong. "Does Belt Uniform Sowing Improve Winter Wheat Yield under High Sowing Density?" Agronomy 12, no. 12 (November 23, 2022): 2936. http://dx.doi.org/10.3390/agronomy12122936.
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The belt uniform (BU) sowing pattern can improve the yield of winter wheat, but whether and how the BU sowing pattern can increase yield under different sowing densities is unknown. The field study was conducted in Guiyang (Guizhou province) during the growing season in 2017–2018, 2018–2019, and 2019–2020. Four winter wheat cultivars were used in field experiments to investigate the changes of the dry matter accumulation and partition, yield and yield components at maturity under five sowing densities (75, 150, 225, 300, and 375 plants per m2), and three sowing patterns: line and dense (LD) sowing with 33.3 cm row spacing (LDS); the belt uniform (BU) sowing with 15 cm (BUN), and 20 cm (BUW) row spacing. The BU sowing pattern significantly increases shoot dry matter and grain yield in all four winter wheat cultivars under all five sowing densities and in each growing season, particularly under the high sowing density of 300 and 375 plants m−2. Harvest index was unaffected by the different sowing densities and sowing patterns. While spike number increased, grain weight per spike decreased with the increase in sowing density. The 1000-grain weight and grain number per spike were unaffected by the sowing patterns. The variation in the shoot dry weight can explain 94% variation in grain yield and 66% variation in spike number. Allometric analysis showed that more dry matter was partitioned to the spike than to the stem and leaf. We conclude that the BU sowing pattern can increase grain yield under high sowing densities associated with a high shoot dry matter accumulation and its partition to the spike.
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Loginova. "ON FUNCTIONAL PURPOSE OF THE TALE SPIKE AND DORSAL SPINE IN PROTOSTRONGYLIDAE LARVAE." THEORY AND PRACTICE OF PARASITIC DISEASE CONTROL, no. 22 (May 19, 2021): 301–5. http://dx.doi.org/10.31016/978-5-6046256-1-3.2021.22.301-305.
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This article presents an attempt to analyze the functional purpose of the tail spike and dorsal spine of protostrongylid species. The actual material was obtained from the feces of reindeer (Rangifer tarandus) (the species Elaphostrongylus rangiferi was verified genetically), red deer (Cervus elaphus) and dapple deer (C. nippon) by the Vajda method and has been studied from 2018 to the present day by means of lightfield and dark-field light microscopy, and phase-contrast and scanning electron microscopy. It was found that the tail spike and dorsal spine 1) do not surpass the rest of the cuticle in their density (they are squashed by pressure of the cover slide, shriveled in preparation for scanning electron microscopy, and look uniform in relation to the body of the larva in polarized light); 2) have no openings in the apical areas. On this basis, the versions about the role of spines in episodes of intra- or interspecific competition and defensive function were rejected. The assumptions about the deposition (of substances or ultramicroscopic objects) and about fixation (linking) remain possible. The reliable purpose of the tail spike and dorsal spine of protostrongylid species larvae remains unknown. The further study of a connection between these larvae and their intermediate hosts, gastropods, seems promising.
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Paul, P. A., P. E. Lipps, E. De Wolf, G. Shaner, G. Buechley, T. Adhikari, S. Ali, J. Stein, L. Osborne, and L. V. Madden. "A Distributed Lag Analysis of the Relationship Between Gibberella zeae Inoculum Density on Wheat Spikes and Weather Variables." Phytopathology® 97, no. 12 (December 2007): 1608–24. http://dx.doi.org/10.1094/phyto-97-12-1608.
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In an effort to characterize the association between weather variables and inoculum of Gibberella zeae in wheat canopies, spikes were sampled and assayed for pathogen propagules from plots established in Indiana, North Dakota, Ohio, Pennsylvania, South Dakota, and Manitoba between 1999 and 2005. Inoculum abundance was quantified as the daily number of colony forming units per spike (CFU/spike). A total of 49 individual weather variables for 24-h periods were generated from measurements of ambient weather data. Polynomial distributed lag regression analysis, followed by linear mixed model analysis, was used to (i) identify weather variables significantly related to log-transformed CFU/spike (the response variable; Y), (ii) determine the time window (i.e., lag length) over which each weather variable affected Y, (iii) determine the form of the relationship between each weather variable and Y (defined in terms of the polynomial degree for the relationship between the parameter weights for the weather variables and the time lag involved), and (iv) account for location-specific effects and random effects of years within locations on the response variable. Both location and year within location affected the magnitude of Y, but there was no consistent trend in Y over time. Y on each day was significantly and simultaneously related to weather variables on the day of sampling and on the 8 days prior to sampling (giving a 9-day time window). The structural relationship corresponded to polynomial degrees of 0, 1, or 2, generally showing a smooth change in the parameter weights and time lag. Moisture- (e.g., relative humidity-) related variables had the strongest relationship with Y, but air temperature- and rainfall-related variables also significantly affected Y. The overall marginal effect of each weather variable on Y was positive. Thus, local weather conditions can be utilized to improve estimates of spore density on wheat spikes around the time of flowering.
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Yang, Weibing, Zheng Wang, Liping Ren, Zhijie Ye, Xinhuan Gao, Jiangang Gao, Hongyao Lou, Bing Du, Zhaobo Chen, and Shengquan Zhang. "Effects of Population Regulation on the Source–Sink System of Hybrid Wheat Jingmai 6." Agronomy 12, no. 10 (October 17, 2022): 2530. http://dx.doi.org/10.3390/agronomy12102530.
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Hybrid wheat is considered to be one of the main ways to greatly improve the wheat yield in the future, and population construction is an important factor affecting their yield heterosis formation. In order to clarify the effect of population regulation of hybrid wheat on source–sink systems, the two-line hybrid wheat variety Jingmai 6 was used to carry out relevant research in this experiment. The leaf area index (LAI) of Jingmai 6 showed an increasing trend, while the tiller-spike rate exhibited a downward trend with the increase of planting density. The total accumulation of dry matter at maturity increased with the increase of planting density, among which the relative proportion of dry matter pre-anthesis gradually increased, while that after anthesis gradually decreased. The sink capacity and spikes number of hybrid wheat were positively correlated with the grain yield. There was higher sink capacity, spike to leaf ratio and grain to leaf ratio under A2 and A3 conditions. With the increase of planting density, the hybrid wheat yield showed a unimodal curve, and A3 had the highest grain yield. Combined with the change trend of dry matter accumulation before and after anthesis, it was proved that suitable planting density was the key to obtaining high yield of hybrid wheat.
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Aoki, Takahiro, and Tadashi Tsubone. "Bifurcation of Chaos and Density Spectrum of Inter-Spike-Intervals from Piecewise-Constant Spike Oscillator." IEICE Proceeding Series 1 (March 17, 2014): 840–43. http://dx.doi.org/10.15248/proc.1.840.
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Galimidi, Rachel, Anthony West, and Pamela Bjorkman. "Thwarting HIV evasion of antibody avidity with novel antibody architectures (P4489)." Journal of Immunology 190, no. 1_Supplement (May 1, 2013): 179.7. http://dx.doi.org/10.4049/jimmunol.190.supp.179.7.
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Abstract Despite decades of effort, no current vaccine elicits neutralizing antibodies at concentrations blocking HIV infection. In addition to structural features of HIV's envelope spike that facilitate antibody evasion, a hypothesis for the ineffective immune response lies in the low density and limited mobility of HIV envelope spikes, which impedes bivalent binding by antibodies, reducing avidity, minimizing the potential for high affinity binding and virus neutralization. We intend to engineer anti-HIV reagents that bind with high avidity to single spikes, overcoming potential problems with the low density of HIV spikes. Here, we demonstrate a strategy to use dsDNA as a rigid molecular ruler to map epitopes on the HIV envelope protein to gain insight into the relatively unknown spatial environment of the spike trimer. Upon determining the optimal separation distance between epitopes, the dsDNA linker will be replaced with a structured protein linker. This technique should allow for the development of a novel multivalent antibody reagent improving binding and increasing avidity. Optimal HIV binding proteins will be trimerized by attaching a trimerization motif, reducing the concentration required for sterilizing immunity. To date, we have several bispecific DNA reagents that have the ability to neutralize various strains of HIV with greater potency than its individual components. These results demonstrate the promise for discovery of optimal anti-HIV reagents using this technology.
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Huiskonen, Juha T., Jussi Hepojoki, Pasi Laurinmäki, Antti Vaheri, Hilkka Lankinen, Sarah J. Butcher, and Kay Grünewald. "Electron Cryotomography of Tula Hantavirus Suggests a Unique Assembly Paradigm for Enveloped Viruses." Journal of Virology 84, no. 10 (March 10, 2010): 4889–97. http://dx.doi.org/10.1128/jvi.00057-10.
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ABSTRACT Hantaviruses (family Bunyaviridae) are rodent-borne emerging viruses that cause a serious, worldwide threat to human health. Hantavirus diseases include hemorrhagic fever with renal syndrome and hantavirus cardiopulmonary syndrome. Virions are enveloped and contain a tripartite single-stranded negative-sense RNA genome. Two types of glycoproteins, GN and GC, are embedded in the viral membrane and form protrusions, or “spikes.” The membrane encloses a ribonucleoprotein core, which consists of the RNA segments, the nucleocapsid protein, and the RNA-dependent RNA polymerase. Detailed information on hantavirus virion structure and glycoprotein spike composition is scarce. Here, we have studied the structures of Tula hantavirus virions using electron cryomicroscopy and tomography. Three-dimensional density maps show how the hantavirus surface glycoproteins, membrane, and ribonucleoprotein are organized. The structure of the GN-GC spike complex was solved to 3.6-nm resolution by averaging tomographic subvolumes. Each spike complex is a square-shaped assembly with 4-fold symmetry. Spike complexes formed ordered patches on the viral membrane by means of specific lateral interactions. These interactions may be sufficient for creating membrane curvature during virus budding. In conclusion, the structure and assembly principles of Tula hantavirus exemplify a unique assembly paradigm for enveloped viruses.
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Wang, Can, Lingbo Zhou, Guobing Zhang, Yan Xu, Xu Gao, Ne Jiang, Liyi Zhang, and Mingbo Shao. "Effects of Sowing Time and Growing Density on Agronomic Traits, Grain Yield, and Grain Quality of Waxy Sorghum Cultivar Hongliangfeng 1." Journal of Agricultural Science 11, no. 6 (May 15, 2019): 12. http://dx.doi.org/10.5539/jas.v11n6p12.
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The aim of this study was to determine the effects of sowing time and growing density on the yield and quality of grain in waxy sorghum (Sorghum bicolor L. Moench). The main plots were two sowing time: early sowing (5 April) and late sowing (20 April), and the subplots were three growing densities: 0.8 × 105, 1.1 × 105, and 1.4 × 105 plants/ha. Results showed that sowing time and growing density had significant effects on grain yield and grain quality of waxy sorghum cultivar Hongliangfeng 1. Grain yield, plant height, spike length, culm diameter, grain number per spike, grain weight per plant, 1000-grain weight, protein content, starch content, and amylopectin content were reduced by a delay of sowing time, while the tannin content and amylose content were increased by a delay of sowing time. Grain yield, plant height, spike length, culm diameter, grain number per spike, grain weight per plant, 1000-grain weight, protein content, starch content, and amylopectin content increased and then decreased with the increase of growing density, while the tannin content and amylose content decreased and then increased with the increase of growing density. These results hinted that appropriate sowing time and growing density are key cultivation measures to ensure high yield and good quality in waxy sorghum production.
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Lv, Guohua, Wei Han, Hanbo Wang, Wenbo Bai, and Jiqing Song. "Effect of subsoiling on tillers, root density and nitrogen use efficiency of winter wheat in loessal soil." Plant, Soil and Environment 65, No. 9 (October 9, 2019): 456–62. http://dx.doi.org/10.17221/311/2019-pse.
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A 2-year field experiment was carried out in loessal soil in a semi-humid climate to research winter wheat (Triticum aestivum L.) growth and nitrogen use efficiency. The result showed that subsoiling increased root penetration and promoted deep soil water absorption, which resulted in high resilience to the adverse dry climate. Soil NO<sub>3</sub><sup>–</sup>-N residue throughout the profile was decreased but increased in rotary tillage. Grain yield was significantly increased by 21.9% and 11.3% in 2016 and 2017, respectively, mainly due to the significantly larger spikes per hectare and grains per spike. Nitrogen use efficiency was significantly improved by 26.7% in 2016 and 13.8% in 2017. For loessal soil in semi-humid climate, breaking the plough pan was necessary, and it was useful for the increase of grain yield and nitrogen use efficiency.
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Ahmad, Iftikhar, Waqas Hassain Naeem, and Bilal Abdullah. "Optimal planting density for cut Lilium and tuberose production." Ornamental Horticulture 25, no. 2 (June 14, 2019): 144–48. http://dx.doi.org/10.14295/oh.v25i2.1736.
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Lilium and tuberose are promising geophytic flowers, which have high market demand in global floral markets. A study was conducted to optimize planting densities for cut lilium and tuberose production. Bulbs of Asiatic lily ‘Brunello’ and tuberose ‘Single’ were planted on 7.5 cm, 15.0 cm and 22.5 cm between bulbs while ridge were spaced at 60 cm apart. Lilium bulbs planted at 22.5 cm took 185 d, while tuberose took 101 d to produce flowers as compared to 7.5 cm spacing (173 d and 93 d, respectively). Bulbs of lilium and tuberose planted at 22.5 cm resulted in tallest plants with highest leaf area for both tested species, 69.1 cm and 11.4 cm2 for lilium and 110.6 cm and 30.2 cm2 for tuberose, respectively. Both species had highest number of florets with longer stem/ spike length and stem/spike diameter when planted 22.5 cm apart, while close planting further decrease number of buds/florets and stem/spike length. Similar results were recorded for fresh weight of a stem, while vase life and dry weight of a stem were relatively less affected by plant spacing. However, lilium and tuberose bulbs when planted at 22.5 cm plant spacing produced higher number of best quality stems for market as compared to other planting densities.
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Chiarion, Giovanni, and Luca Mesin. "Resolution of Spike Overlapping by Biogeography-Based Optimization." Electronics 10, no. 12 (June 18, 2021): 1469. http://dx.doi.org/10.3390/electronics10121469.
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There are many cases in which the separation of different sources from single channel recordings is important, for example, in fluorescence spectral overlap compensation, electrical impedance signaling, intramuscular electromyogram decomposition or in the case of spike sorting of neuron potentials from microelectrode arrays (MEA). Focusing on the latter, the problem can be faced by identifying spikes emerging from the background and clustering into different groups, indicating the activity of different neurons. Problems are found when more spikes are superimposed in overlapped waveforms. We discuss the application of Biogeography-Based Optimization (BBO) to resolve this specific problem. Our algorithm is compared with three spike-sorting methods (SpyKING Circus, Common Basis Pursuit and Klusta), showing statistically better performance (in terms of F1 score, True Positive Rate—TPR and Positive Predictive Value—PPV) in resolving overlaps in realistic, simulated data. Specifically, BBO showed median F1, TPR and PPV of 100%, 100% and about 75%, respectively, considering a simulated noise with the same spectral density as the experimental one and a similar power with highly statistically significant improvements of at least two performance indexes over each of the other three tested algorithms.
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Omi, Takahiro, and Shigeru Shinomoto. "Optimizing Time Histograms for Non-Poissonian Spike Trains." Neural Computation 23, no. 12 (December 2011): 3125–44. http://dx.doi.org/10.1162/neco_a_00213.
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The time histogram is a fundamental tool for representing the inhomogeneous density of event occurrences such as neuronal firings. The shape of a histogram critically depends on the size of the bins that partition the time axis. In most neurophysiological studies, however, researchers have arbitrarily selected the bin size when analyzing fluctuations in neuronal activity. A rigorous method for selecting the appropriate bin size was recently derived so that the mean integrated squared error between the time histogram and the unknown underlying rate is minimized (Shimazaki & Shinomoto, 2007 ). This derivation assumes that spikes are independently drawn from a given rate. However, in practice, biological neurons express non-Poissonian features in their firing patterns, such that the spike occurrence depends on the preceding spikes, which inevitably deteriorate the optimization. In this letter, we revise the method for selecting the bin size by considering the possible non-Poissonian features. Improvement in the goodness of fit of the time histogram is assessed and confirmed by numerically simulated non-Poissonian spike trains derived from the given fluctuating rate. For some experimental data, the revised algorithm transforms the shape of the time histogram from the Poissonian optimization method.
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Tahon, Koen, Mike Wijnants, Erik De Schutter, and Reinoud Maex. "Current source density correlates of cerebellar Golgi and Purkinje cell responses to tactile input." Journal of Neurophysiology 105, no. 3 (March 2011): 1327–41. http://dx.doi.org/10.1152/jn.00317.2010.
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The overall circuitry of the cerebellar cortex has been known for over a century, but the function of many synaptic connections remains poorly characterized in vivo. We used a one-dimensional multielectrode probe to estimate the current source density (CSD) of Crus IIa in response to perioral tactile stimuli in anesthetized rats and to correlate current sinks and sources to changes in the spike rate of corecorded Golgi and Purkinje cells. The punctate stimuli evoked two distinct early waves of excitation (at <10 and ∼20 ms) associated with current sinks in the granular layer. The second wave was putatively of corticopontine origin, and its associated sink was located higher in the granular layer than the first trigeminal sink. The distinctive patterns of granular-layer sinks correlated with the spike responses of corecorded Golgi cells. In general, Golgi cell spike responses could be linearly reconstructed from the CSD profile. A dip in simple-spike activity of coregistered Purkinje cells correlated with a current source deep in the molecular layer, probably generated by basket cell synapses, interspersed between sparse early sinks presumably generated by synapses from granule cells. The late (>30 ms) enhancement of simple-spike activity in Purkinje cells was characterized by the absence of simultaneous sinks in the granular layer and by the suppression of corecorded Golgi cell activity, pointing at inhibition of Golgi cells by Purkinje axon collaterals as a likely mechanism of late Purkinje cell excitation.
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Sanger, Terence David. "Probability Density Methods for Smooth Function Approximation and Learning in Populations of Tuned Spiking Neurons." Neural Computation 10, no. 6 (August 1, 1998): 1567–86. http://dx.doi.org/10.1162/089976698300017313.
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This article proposes a new method for interpreting computations performed by populations of spiking neurons. Neural firing is modeled as a rate-modulated random process for which the behavior of a neuron in response to external input can be completely described by its tuning function. I show that under certain conditions, cells with any desired tuning functions can be approximated using only spike coincidence detectors and linear operations on the spike output of existing cells. I show examples of adaptive algorithms based on only spike data that cause the underlying cell-tuning curves to converge according to standard supervised and unsupervised learning algorithms. Unsupervised learning based on principal components analysis leads to independent cell spike trains. These results suggest a duality relationship between the random discrete behavior of spiking cells and the deterministic smooth behavior of their tuning functions. Classical neural network approximation methods and learning algorithms based on continuous variables can thus be implemented within networks of spiking neurons without the need to make numerical estimates of the intermediate cell firing rates.
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LIU, GUODONG, PAN REN, DAYONG ZHANG, WEIPING WANG, and JIANFENG LI. "INVESTIGATION OF NEAR-SURFACE DEFECTS INDUCED BY SPIKE RAPID THERMAL ANNEALING IN c-SILICON SOLAR CELLS." Surface Review and Letters 23, no. 02 (February 29, 2016): 1550107. http://dx.doi.org/10.1142/s0218625x15501073.
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The defects induced by a spike rapid thermal annealing (RTA) process in crystalline silicon (c-Si) solar cells were investigated by the photoluminescence (PL) technique and the transmission electron microscopy (TEM), respectively. Dislocation defects were found to form in the near-surface junction region of the monocrystalline Si solar cell after a spike RTA process was performed at 1100[Formula: see text]C. Photo J–V characteristics were measured on the Si solar cell before and after the spike RTA treatments to reveal the effects of defects on the Si cell performances. In addition, the Silvaco device simulation program was used to study the effects of defects density on the cell performances by fitting the experimental data of RTA-treated cells. The results demonstrate that there was an obvious degradation in the Si solar cell performances when the defect density after the spike RTA treatment was above [Formula: see text][Formula: see text]cm[Formula: see text].
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Yilmaz, Ilyas. "Large eddy simulation of high atwood number rayleigh-taylor mixing." E3S Web of Conferences 128 (2019): 08001. http://dx.doi.org/10.1051/e3sconf/201912808001.
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Large eddy simulation of Rayleigh-Taylor instability at high Atwood numbers is performed using recently developed, kinetic energy-conserving, non-dissipative, fully-implicit, finite volume algorithm. The algorithm does not rely on the Boussinesq assumption. It also allows density and viscosity to vary. No interface capturing mechanism is requried. Because of its advanced features, unlike the pure incompressible ones, it does not suffer from the loss of physical accuracy at high Atwood numbers. Many diagnostics including local mole fractions, bubble and spike growth rates, mixing efficiencies, Taylor micro-scales, Reynolds stresses and their anisotropies are computed to analyze the high Atwood number effects. The density ratio dependence for the ratio of spike to bubble heights is also studied. Results show that higher Atwood numbers are characterized by increasing ratio of spike to bubble growth rates, higher speeds of bubble and especially spike fronts, faster development in instability, similarity in late time mixing values, and mixing asymmetry.
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Farooq, Muhammad Umer, Abdus Salam Khan, Iqra Ishaaq, Asim Ali Cheema, Muhammad Shahzad Afzal, Asif Ali, and Jianqing Zhu. "Growing Degree Days during the Late Reproductive Phase Determine Spike Density and Cognate Yield Traits." Agronomy 8, no. 10 (October 4, 2018): 217. http://dx.doi.org/10.3390/agronomy8100217.
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Drought has become more frequent in central Asia causing large losses in cereal yield. To surmount the existing problem, it is imperative to emphasize early maturing varietal development. However, the impact of heat units on spike morphology and its relationship with yield potential is still unclear. Thus, the current investigation was carried out to test wheat lines and varieties for variation in total heat unit’s accretion for anthesis and maturity and to understand the manipulating impact of sunlight on spike morphology, grain yield and its cognate traits. Furthermore, the gene action controlling major traits inheritance, combining ability effects, heritability, and association studies were also estimated. Following the Half Sib/Full Sib approach 27 hybrids along with 12 parents were tested. Results depicted broad variation in genetic stock. Correlation study demonstrated that earliness negatively affects the yield, while positively influencing spike density. Genetic variances were greater than variances due to environment, pointing to higher heritability (>50%) for all the characters except for grain’s weight spike−1. The degree of dominance revealed that the partial and over-dominant type of gene action conditioned inheritance of investigated traits. Thus, earliness can be used as an indirect selection criterion for yield advance.
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Allen, Brian D., Caroline Moore-Kochlacs, Jacob G. Bernstein, Justin P. Kinney, Jorg Scholvin, Luís F. Seoane, Chris Chronopoulos, et al. "Automated in vivo patch-clamp evaluation of extracellular multielectrode array spike recording capability." Journal of Neurophysiology 120, no. 5 (November 1, 2018): 2182–200. http://dx.doi.org/10.1152/jn.00650.2017.
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Much innovation is currently aimed at improving the number, density, and geometry of electrodes on extracellular multielectrode arrays for in vivo recording of neural activity in the mammalian brain. To choose a multielectrode array configuration for a given neuroscience purpose, or to reveal design principles of future multielectrode arrays, it would be useful to have a systematic way of evaluating the spike recording capability of such arrays. We describe an automated system that performs robotic patch-clamp recording of a neuron being simultaneously recorded via an extracellular multielectrode array. By recording a patch-clamp data set from a neuron while acquiring extracellular recordings from the same neuron, we can evaluate how well the extracellular multielectrode array captures the spiking information from that neuron. To demonstrate the utility of our system, we show that it can provide data from the mammalian cortex to evaluate how the spike sorting performance of a close-packed extracellular multielectrode array is affected by bursting, which alters the shape and amplitude of spikes in a train. We also introduce an algorithmic framework to help evaluate how the number of electrodes in a multielectrode array affects spike sorting, examining how adding more electrodes yields data that can be spike sorted more easily. Our automated methodology may thus help with the evaluation of new electrode designs and configurations, providing empirical guidance on the kinds of electrodes that will be optimal for different brain regions, cell types, and species, for improving the accuracy of spike sorting. NEW & NOTEWORTHY We present an automated strategy for evaluating the spike recording performance of an extracellular multielectrode array, by enabling simultaneous recording of a neuron with both such an array and with patch clamp. We use our robot and accompanying algorithms to evaluate the performance of multielectrode arrays on supporting spike sorting.
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Golparvar, Ahmad, Mohammad Gheisari, Davoud Naderi, Ali Mehrabi, Amin Hadipanah, and Saeed Salehi. "Determination of the best indirect selection criteria in Iranian durum wheat (Triticum aestivum L.) genotypes under irrigated and drought stress conditions." Genetika 47, no. 2 (2015): 549–58. http://dx.doi.org/10.2298/gensr1502549g.
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In order to evaluate and classify morphological and morpho-physiological traits of durum wheat genotypes in drought and irrigated conditions 200 durum wheat genotypes were sown in modify augmented design with four replications during 2013- 2014 farming season. Two replications were considered as drought condition and two as irrigated. Factor analysis based on principal component analysis method and varimax rotation indicated that four important factors accounted for about 87 and 92 percent of the total variation among traits in drought and irrigated conditions, respectively. In drought stress condition, the first factor assigned 37 percent of total variation between traits and was significantly related with spike yield and it?s components. Therefore, this factor was regarded as spike seed yield factor. Other factors in drought stress condition accounted for 22, 16 and 12 percent of variation between traits and were entitled as plant seed yield, spike density and assimilate transmission factors, respectively. In irrigated condition, the first factor assigned 36 percent of total variation between traits and was significantly related with traits plant and spike seed yield, plant and spike harvest index, No. seed/spike and plant height. This factor was regarded as plant seed yield factor. Other factors in irrigated condition accounted for 24, 18 and 14 percent of variation between traits and were entitled as production, assimilate transmission and spike density factors, respectively. Overall, results revealed effect of different environments on extracted factors, percent of variation accounted for by factors and traits related with each factor.
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Fang, Yan, Bingcheng Xu, Neil C. Turner, and Fengmin Li. "Does root pruning increase yield and water-use efficiency of winter wheat?" Crop and Pasture Science 61, no. 11 (2010): 899. http://dx.doi.org/10.1071/cp10125.
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A pot and a field experiment were conducted to assess whether seeding density in winter wheat affects grain yield and water-use efficiency when combined with root pruning. Both experiments compared four treatments, namely (i) low (normal) plant density with no root pruning; (ii) low plant density with root pruning; (iii) high plant density (25% higher than low density) with no root pruning; and (iv) high plant density with root pruning. Roots to a depth of 25 cm were cut back to keep their length to 13 cm and to limit their lateral spread to 13 cm from the plant. In the pot experiment, two water regimes were employed from stem elongation: (i) plants maintained at 85% field capacity, and (ii) plants maintained at 55% field capacity by regular watering. Low rainfall in spring at the terminal stage of plant growth served as natural water stress in the field experiment. In the field, the higher plant density induced higher root biomass at all sample depths at anthesis. Root pruning significantly decreased the root biomass in the upper soil layer (0–40 cm) and increased the root biomass in the deep soil layer (80–120 cm). When water was limited, increasing the seeding density by 25% reduced the grain yield, but with adequate water increasing the seeding density increased the grain yield. Root pruning increased the grain yield, but there was no interaction between seeding density and root pruning on grain yield in either the pots or field. Root pruning reduced water use between stem elongation and anthesis which led to more available soil water in the field between anthesis and maturity, and increased the rate of flag leaf photosynthesis at anthesis, whereas the reverse was true of increasing seeding density. Measurements of chlorophyll fluorescence suggested that initially root pruning induced a stress in the plants, but that the pruned plants rapidly recovered so that by anthesis and during grain filling the level of stress was reduced. Increasing the seeding density increased the number of spikes (fertile tillers), but decreased the grain yield per spike and had no effect on the thousand-kernel weight. In contrast, root pruning reduced the number of spikes in both the field and pots, but increased the grain yield per spike and thousand-kernel weight. Under our experimental conditions, restricting the root size by root pruning increased the yield and water-use efficiency of winter wheat in water-limited environments.
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GALLAGHER, SHAWN P., and DAVID P. M. NORTHMORE. "Responses of the teleostean nucleus isthmi to looming objects and other moving stimuli." Visual Neuroscience 23, no. 2 (March 2006): 209–19. http://dx.doi.org/10.1017/s0952523806232061.
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Visually evoked extracellular neural activity was recorded from the nucleus isthmi (NI) of goldfish and bluegill sunfish. When moving anywhere within the right eye's visual field, three-dimensional checkered balls or patterns on a computer screen evoked bursts of spikes in the left NI. Object motion parallel to the longitudinal body axis gave responses that habituated markedly upon repetition, but movement into recently unstimulated regions of the visual field gave vigorous responses. Thus, while NI's response is not visuotopic, its habituation is. An object approaching the animal's body generated a rising spike density, whereas object recession generated only a transient burst. During the approach of a checkered stimulus ball, average NI spike density rose linearly as the ball-to-eye distance decreased and at a rate proportional to the ball's speed (2.5–30 cm/s). Increasing ball size (2.2–9.2 cm) did not affect the rate of activity rise at a given speed, but did increase overall activity levels. NI also responded reliably to expanding textures of fixed overall size. The results suggest that NI signals changes in motion of objects relative to the fish, and estimates the proximity of approaching objects.
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Kolokolnikov, Theodore, and Shuangquan Xie. "Spike density distribution for the Gierer–Meinhardt model with precursor." Physica D: Nonlinear Phenomena 402 (January 2020): 132247. http://dx.doi.org/10.1016/j.physd.2019.132247.
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Oka, Makio, Katsuhiro Kobayashi, Tomoyuki Akiyama, Tatsuya Ogino, and Eiji Oka. "A study of spike-density on EEG in West syndrome." Brain and Development 26, no. 2 (March 2004): 105–12. http://dx.doi.org/10.1016/s0387-7604(03)00101-3.
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Swindale, Nicholas V., and Martin A. Spacek. "Spike detection methods for polytrodes and high density microelectrode arrays." Journal of Computational Neuroscience 38, no. 2 (November 20, 2014): 249–61. http://dx.doi.org/10.1007/s10827-014-0539-z.
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