Search results for "Fingerprint"
showing 10 items of 215 documents
Protein and DNA fingerprinting of a soil bacterial community inoculated into three different sterile soils
2007
The functional and genetic structures of a soil bacterial community were characterized after inoculation into three different sterile soils using a protein and DNA fingerprinting method, respectively. Principal component analysis (PCA) of profiles revealed that, depending on soil characteristics, bacterial communities with similar genetic structures harbored different functional structures and thus could potentially be of differing ecological significance for soil functioning. Co-inertia analysis between protein fingerprinting data and the corresponding sets of soil physicochemical characteristics demonstrated the correlation between the functional structure of the bacterial community and s…
Sampling strategy in molecular microbial ecology: influence of soil sample size on DNA fingerprinting analysis of fungal and bacterial communities.
2003
Assessing soil microbial community structure by the use of molecular techniques requires a satisfactory sampling strategy that takes into account the high microbial diversity and the heterogeneous distribution of microorganisms in the soil matrix. The influence of the sample size of three different soil types (sand, silt and clay soils) on the DNA yield and analysis of bacterial and fungal community structure were investigated. Six sample sizes from 0.125 g to 4 g were evaluated. The genetic community structure was assessed by automated ribosomal intergenic spacer analysis (A-RISA fingerprint). Variations between bacterial (B-ARISA) and fungal (F-ARISA) community structure were quantified b…
Rapid and Nondestructive Determination of Egg Freshness Category and Marked Date of Lay using Spectral Fingerprint
2020
The potential of nondestructive prediction of egg freshness based on near-infrared (NIR) spectra fingerprints would be beneficial to quality control officers and consumers alike. In this study, handheld NIR spectrometer in the range of 740 nm to 1070 nm and chemometrics were used to simultaneously determine egg freshness based on marked date of lay for eggs stored under cold and ambient conditions. The spectra acquired from the eggs were preprocessed using multiplicative scatter correction and principal component analysis (MSC-PCA). Linear discriminant analysis (LDA) was used to build identification model to predict the category of freshness, while partial least square regression (PLS-R) wa…
Soil REE patterns as tracers of the emplacement of metal-rich anthropogenic materials. A case study in Moa (Cuba)
2019
Purpose: Are rare earth element (REE) patterns employable as tracers in human interventions of bulk soil disturbances, when high concentrations of metals are involved in the in situ soil disturbance? In terms of bulk soil disturbance, it is difficult to distinguish between bulk soil disturbances and emplacement of new earthen material. Chemical fingerprinting, in particular REE plus yttrium, is applied across many fields, but predominantlyin tracking the sources of potential environmental contaminants. Materials and methods: The REE normalised patterns (HNO 3 :HF:HCl 3:1:1 digestion, ICP-MS) of two Calcaric Cambisols were compared with those of a Geric Ferralsol (Novic, Technic) originated …
A convolutional neural network for virtual screening of molecular fingerprints
2019
In the last few years, Deep Learning (DL) gained more and more impact on drug design because it allows a huge increase of the prediction accuracy in many stages of such a complex process. In this paper a Virtual Screening (VS) procedure based on Convolutional Neural Networks (CNN) is presented, that is aimed at classifying a set of candidate compounds as regards their biological activity on a particular target protein. The model has been trained on a dataset of active/inactive compounds with respect to the Cyclin-Dependent Kinase 1 (CDK1) a very important protein family, which is heavily involved in regulating the cell cycle. One qualifying point of the proposed approach is the use of molec…
"Towards a "fingerprint" of paper network; separating forgeries from genuine by the properties of fibre structure"
2014
A novel method is introduced for distinguishing counterfeit banknotes from genuine samples. The method is based on analyzing differences in the networks of paper fibers. The main tool is a curvelet-based algorithm for measuring the distribution of overall fiber orientation and quantifying its anisotropy. The use of a couple or more appropriate parameters makes it possible to distinguish forgeries from genuine samples as concentrated point clouds in a two- or three-dimensional parameter space. Furthermore, the techniques of making watermarks is investigated by comparing genuine and counterfeit €50 banknotes. In addition, the so-called wire markings are shown to differ significantly from each…
"Master-Slave" Biological Network Alignment
2010
Performing global alignment between protein-protein interaction (PPI) networks of different organisms is important to infer knowledge about conservation across species. Known methods that perform this task operate symmetrically, that is to say, they do not assign a distinct role to the input PPI networks. However, in most cases, the input networks are indeed distinguishable on the basis of how well the corresponding organism is biologically well-characterized. For well-characterized organisms the associated PPI network supposedly encode in a sound manner all the information about their proteins and associated interactions, which is far from being the case for not well characterized ones. He…
Asymmetric Comparison and Querying of Biological Networks
2011
Comparing and querying the protein-protein interaction (PPI) networks of different organisms is important to infer knowledge about conservation across species. Known methods that perform these tasks operate symmetrically, i.e., they do not assign a distinct role to the input PPI networks. However, in most cases, the input networks are indeed distinguishable on the basis of how the corresponding organism is biologically well characterized. In this paper a new idea is developed, that is, to exploit differences in the characterization of organisms at hand in order to devise methods for comparing their PPI networks. We use the PPI network (called Master) of the best characterized organism as a …
Convolutional architectures for virtual screening
2020
Abstract Background A Virtual Screening algorithm has to adapt to the different stages of this process. Early screening needs to ensure that all bioactive compounds are ranked in the first positions despite of the number of false positives, while a second screening round is aimed at increasing the prediction accuracy. Results A novel CNN architecture is presented to this aim, which predicts bioactivity of candidate compounds on CDK1 using a combination of molecular fingerprints as their vector representation, and has been trained suitably to achieve good results as regards both enrichment factor and accuracy in different screening modes (98.55% accuracy in active-only selection, and 98.88% …
Filtered circular fingerprints improve either prediction or runtime performance while retaining interpretability.
2016
Background Even though circular fingerprints have been first introduced more than 50 years ago, they are still widely used for building highly predictive, state-of-the-art (Q)SAR models. Historically, these structural fragments were designed to search large molecular databases. Hence, to derive a compact representation, circular fingerprint fragments are often folded to comparatively short bit-strings. However, folding fingerprints introduces bit collisions, and therefore adds noise to the encoded structural information and removes its interpretability. Both representations, folded as well as unprocessed fingerprints, are often used for (Q)SAR modeling. Results We show that it can be prefer…