7 research outputs found
Generalized Sparse Convolutional Neural Networks for Semantic Segmentation of Point Clouds Derived from Tri-Stereo Satellite Imagery
We studied the applicability of point clouds derived from tri-stereo satellite imagery for
semantic segmentation for generalized sparse convolutional neural networks by the example of
an Austrian study area. We examined, in particular, if the distorted geometric information, in addition
to color, influences the performance of segmenting clutter, roads, buildings, trees, and vehicles. In this
regard, we trained a fully convolutional neural network that uses generalized sparse convolution
one time solely on 3D geometric information (i.e., 3D point cloud derived by dense image matching),
and twice on 3D geometric as well as color information. In the first experiment, we did not use
class weights, whereas in the second we did. We compared the results with a fully convolutional
neural network that was trained on a 2D orthophoto, and a decision tree that was once trained on
hand-crafted 3D geometric features, and once trained on hand-crafted 3D geometric as well as color
features. The decision tree using hand-crafted features has been successfully applied to aerial laser
scanning data in the literature. Hence, we compared our main interest of study, a representation
learning technique, with another representation learning technique, and a non-representation learning
technique. Our study area is located in Waldviertel, a region in Lower Austria. The territory is
a hilly region covered mainly by forests, agriculture, and grasslands. Our classes of interest are heavily
unbalanced. However, we did not use any data augmentation techniques to counter overfitting. For our
study area, we reported that geometric and color information only improves the performance of the
Generalized Sparse Convolutional Neural Network (GSCNN) on the dominant class, which leads to a
higher overall performance in our case. We also found that training the network with median class
weighting partially reverts the effects of adding color. The network also started to learn the classes
with lower occurrences. The fully convolutional neural network that was trained on the 2D orthophoto
generally outperforms the other two with a kappa score of over 90% and an average per class accuracy
of 61%. However, the decision tree trained on colors and hand-crafted geometric features has a 2%
higher accuracy for roads
Destroying activity of magnetoferritin on lysozyme amyloid fibrils
Presence of protein amyloid aggregates (oligomers, protofilaments, fibrils) is associated with many diseases as diabetes mellitus or Alzheimer's disease. The interaction between lysozyme amyloid fibrils and magnetoferritin loaded with different amount of iron atoms (168 or 532 atoms) has been investigated by small-angle X-rays scattering and thioflavin T fluorescence measurements. Results suggest that magnetoferritin caused an iron atom-concentration dependent reduction of lysozyme fibril siz
<i>In Silico</i> and <i>in Vitro</i> Study of Binding Affinity of Tripeptides to Amyloid β Fibrils: Implications for Alzheimer’s Disease
Self-assembly of Aβ peptides
into amyloid aggregates has
been suggested as the major cause of Alzheimer’s disease (AD).
Nowadays, there is no medication for AD, but experimental data indicate
that reversion of the process of amyloid aggregation reduces the symptoms
of disease. In this paper, all 8000 tripeptides were studied for their
ability to destroy Aβ fibrils. The docking method and the more
sophisticated MM-PBSA (molecular mechanics Poisson–Boltzmann
surface area) method were employed to calculate the binding affinity
and mode of tripeptides to Aβ fibrils. The ability of these
peptides to depolymerize Aβ fibrils was also investigated experimentally
using atomic force microscopy and fluorescence spectroscopy (Thioflavin
T assay). It was shown that tripeptides prefer to bind to hydrophobic
regions of 6Aβ<sub>9–40</sub> fibrils. Tripeptides WWW,
WWP, WPW and PWW were found to be the most potent binders. <i>In vitro</i> experiments showed that tight-binding tripeptides
have significant depolymerizing activities and their DC<sub>50</sub> values determined from dose–response curves were in micromolar
range. The ability of nonbinding (GAM, AAM) and weak-binding (IVL
and VLA) tripeptides to destroy Aβ fibrils was negligible. <i>In vitro</i> data of tripeptide depolymerizing activities support
the predictions obtained by molecular docking and all-atom simulation
methods. Our results suggest that presence of multiple complexes of
heterocycles forming by tryptophan and proline residues in tripeptides
is crucial for their tight binding to Aβ fibrils as well as
for extensive fibril depolymerization. We recommend PWW for further
studies as it has the lowest experimental binding constant
Binding of Glyco-Acridine Derivatives to Lysozyme Leads to Inhibition of Amyloid Fibrillization
While amyloid-related diseases are
at the center of intense research
efforts, no feasible cure is currently available for these diseases.
The experimental and computational techniques were used to study the
ability of glyco-acridines to prevent lysozyme amyloid fibrillization
in vitro. Fluorescence spectroscopy and atomic force microscopy have
shown that glyco-acridines inhibit amyloid aggregation of lysozyme;
the inhibition efficiency characterized by the half-maximal inhibition
concentration IC<sub>50</sub> was affected by the structure and concentration
of the derivative. We next investigated relationship between the binding
affinity and the inhibitory activity of the compounds. The semiempirical
quantum PM6-DH+ method provided a good correlation pointing to the
importance of quantum effects on the binding of glyco-acridine derivatives
to lysozyme. The contribution of linkers may be explained by the valence
bond theory. Our data provide a basis for the development of new small
molecule inhibitors effective in therapy of amyloid-related diseases