Prediction of sequential antigenic regions in proteins

AbstractPrediction of antigenic regions in a protein will be helpful for a rational approach to the synthesis of peptides which may elicit antibodies reactive with the intact protein. Earlier methods are based on the assumption that antigenic regions are primarily hydrophilic regions at the surface of the protein molecule. The method presented here is based on the amino acid composition of known antigenic regions in 20 proteins which is compared with that of 314 proteins [(1978) Atlas of Protein Sequence and Structure, vol. 5, suppl. 3, 363-373]. Antigenicity values were derived from the differences between the two data sets. The method was applied to bovine ribonuclease, the B-subunit of cholera toxin and herpes simplex virus type 1 glycoprotein D. There was a good correlation between the predicted regions and previously determined antigenic regions

Can the salt-advection feedback be detected in internal variability of the atlantic meridional overturning circulation?

Evidence for the assumptions of the salt-advection feedback in box models is sought by studying the Atlantic meridional overturning circulation (AMOC) internal variability in the long preindustrial control runs of two Earth system models. The first assumption is that AMOC strength is proportional to the meridional density difference between the North Atlantic and the Southern Oceans. The model simulations support this assumption, with the caveat that nearly all the long time-scale variability occurs in the North Atlantic density. The second assumption is that the freshwater transport variability by the overturning at the Atlantic southern boundary is controlled by the strength of AMOC. Only one of the models shows some evidence that AMOC variability at 45°N leads variability in the overturning freshwater transport at the southern boundary by about 30 years, but the other model shows no such coherence. In contrast, in both models this freshwater transport variability is dominated by local salinity variations. The third assumption is that changes in the overturning freshwater transport at the Atlantic southern boundary perturb the north-south density difference, and thus feed back on AMOC strength in the north. No evidence for this assumption is found in either model at any time scale, although this does not rule out that the salt-advection feedback may be excited by a strong enough freshwater perturbation

Coupled Oscillators with Chemotaxis

A simple coupled oscillator system with chemotaxis is introduced to study morphogenesis of cellular slime molds. The model successfuly explains the migration of pseudoplasmodium which has been experimentally predicted to be lead by cells with higher intrinsic frequencies. Results obtained predict that its velocity attains its maximum value in the interface region between total locking and partial locking and also suggest possible roles played by partial synchrony during multicellular development.Comment: 4 pages, 5 figures, latex using jpsj.sty and epsf.sty, to appear in J. Phys. Soc. Jpn. 67 (1998

Fast anisotropic Gauss filtering

Abstract. We derive the decomposition of the anisotropic Gaussian in a one dimensional Gauss filter in the x-direction followed by a one dimensional filter in a non-orthogonal direction ϕ. So also the anisotropic Gaussian can be decomposed by dimension. This appears to be extremely efficient from a computing perspective. An implementation scheme for normal convolution and for recursive filtering is proposed. Also directed derivative filters are demonstrated. For the recursive implementation, filtering an 512 × 512 image is performed within 65 msec, independent of the standard deviations and orientation of the filter. Accuracy of the filters is still reasonable when compared to truncation error or recursive approximation error. The anisotropic Gaussian filtering method allows fast calculation of edge and ridge maps, with high spatial and angular accuracy. For tracking applications, the normal anisotropic convolution scheme is more advantageous, with applications in the detection of dashed lines in engineering drawings. The recursive implementation is more attractive in feature detection applications, for instance in affine invariant edge and ridge detection in computer vision. The proposed computational filtering method enables the practical applicability of orientation scale-space analysis

Learning multiple views with orthogonal denoising autoencoders

Multi-view learning techniques are necessary when data is described by multiple distinct feature sets because single-view learning algorithms tend to overt on these high-dimensional data. Prior successful approaches followed either consensus or complementary principles. Recent work has focused on learning both the shared and private latent spaces of views in order to take advantage of both principles. However, these methods can not ensure that the latent spaces are strictly independent through encouraging the orthogonality in their objective functions. Also little work has explored representation learning techniques for multiview learning. In this paper, we use the denoising autoencoder to learn shared and private latent spaces, with orthogonal constraints | disconnecting every private latent space from the remaining views. Instead of computationally expensive optimization, we adapt the backpropagation algorithm to train our model

Sensitivity of the Atlantic meridional overturning circulation to South Atlantic freshwater anomalies

The sensitivity of the Atlantic Meridional Overturning Circulation (AMOC) to changes in basin integrated net evaporation is highly dependent on the zonal salinity contrast at the southern border of the Atlantic. Biases in the freshwater budget strongly affect the stability of the AMOC in numerical models. The impact of these biases is investigated, by adding local anomaly patterns in the South Atlantic to the freshwater fluxes at the surface. These anomalies impact the freshwater and salt transport by the different components of the ocean circulation, in particular the basin-scale salt-advection feedback, completely changing the response of the AMOC to arbitrary perturbations. It is found that an appropriate dipole anomaly pattern at the southern border of the Atlantic Ocean can collapse the AMOC entirely even without a further hosing. The results suggest a new view on the stability of the AMOC, controlled by processes in the South Atlantic. <br/

Celio (\u2705), Orkand (\u2707) Named Up and Coming Leaders

BackgroundAlthough auditory verbal hallucinations (AVH) are a core symptom of schizophrenia, they also occur in non-psychotic individuals, in the absence of other psychotic, affective, cognitive and negative symptoms. AVH have been hypothesized to result from deviant integration of inferior frontal, parahippocampal and superior temporal brain areas. However, a direct link between dysfunctional connectivity and AVH has not yet been established. To determine whether hallucinations are indeed related to aberrant connectivity, AVH should be studied in isolation, for example in non-psychotic individuals with AVH.MethodResting-state connectivity was investigated in 25 non-psychotic subjects with AVH and 25 matched control subjects using seed regression analysis with the (1) left and (2) right inferior frontal, (3) left and (4) right superior temporal and (5) left parahippocampal areas as the seed regions. To correct for cardiorespiratory (CR) pulsatility rhythms in the functional magnetic resonance imaging (fMRI) data, heartbeat and respiration were monitored during scanning and the fMRI data were corrected for these rhythms using the image-based method for retrospective correction of physiological motion effects RETROICOR.ResultsIn comparison with the control group, non-psychotic individuals with AVH showed increased connectivity between the left and the right superior temporal regions and also between the left parahippocampal region and the left inferior frontal gyrus. Moreover, this group did not show a negative correlation between the left superior temporal region and the right inferior frontal region, as was observed in the healthy control group.ConclusionsAberrant connectivity of frontal, parahippocampal and superior temporal brain areas can be specifically related to the predisposition to hallucinate in the auditory domain.</jats:sec

Stability of the Atlantic Meridional Overturning Circulation: A Review and Synthesis

The notion that the Atlantic Meridional Overturning Circulation (AMOC) can have more than one stable equilibrium emerged in the 1980s as a powerful hypothesis to explain rapid climate variability during the Pleistocene. Ever since, the idea that a temporary perturbation of the AMOC—or a permanent change in its forcing—could trigger an irreversible collapse has remained a reason for concern. Here we review literature on the equilibrium stability of the AMOC and present a synthesis that puts our understanding of past and future AMOC behavior in a unifying framework. This framework is based on concepts from Dynamical Systems Theory, which has proven to be an important tool in interpreting a wide range of model behavior. We conclude that it cannot be ruled out that the AMOC in our current climate is in, or close to, a regime of multiple equilibria. But there is considerable uncertainty in the location of stability thresholds with respect to our current climate state, so we have no credible indications of where our present‐day AMOC is located with respect to thresholds. We conclude by identifying gaps in our knowledge and proposing possible ways forward to address these gaps

Oceanic hindcast simulations at high resolution suggest that the Atlantic MOC is bistable

All climate models predict a freshening of the North Atlantic at high latitude that may induce an abrupt change of the Atlantic Meridional Overturning Circulation (hereafter AMOC) if it resides in the bistable regime, where both a strong and a weak state coexist. The latter remains uncertain as there is no consensus among observations and ocean reanalyses, where the AMOC is bistable, versus most climate models that reproduce a mono-stable strong AMOC. A series of four hindcast simulations of the global ocean at 1/12° resolution, which is presently unique, are used to diagnose freshwater transport by the AMOC in the South Atlantic, an indicator of AMOC bistability. In all simulations, the AMOC resides in the bistable regime: it exports freshwater southward in the South Atlantic, implying a positive salt advection feedback that would act to amplify a decreasing trend in subarctic deep water formation as projected in climate scenarios

Mesoscale perturbations control inter-ocean exchange south of Africa

The quantification of inter-ocean leakage from the South Indian to the South Atlantic Ocean is an important measure for the role of the Agulhas system in the global thermohaline circulation. To explore the specific role of mesoscale variability (such as Agulhas rings and Mozambique eddies) in this process a high-resolution model (based on NEMO-ORCA) for the Agulhas region has been set up. It is nested into a global coarse-resolution model. The high-resolution nest captures all salient features of the greater Agulhas region, including the upstream perturbations of the Agulhas Current and Natal Pulses along the African coast. A comparison of the inter-ocean exchange in the high-resolution nest with its coarse resolution counterpart reveals that the latter significantly over-estimates the amount of water flowing into the Atlantic Ocean, demonstrating the need to explicitly simulate the mesoscale features. A sensitivity experiment that excludes the upstream perturbations revealed no difference in the amount of inter-ocean exchange. However, the realistic representation of Agulhas rings and their drift path into the South Atlantic depends on the simulation of those upstream perturbations