scholarly journals Optimal classification of protein sequences and selection of representative sets from multiple alignments: application to homologous families and lessons for structural genomics

2001 ◽  
Vol 14 (4) ◽  
pp. 209-217 ◽  
Author(s):  
Alex C. W. May
2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Andre Then ◽  
Karel Mácha ◽  
Bashar Ibrahim ◽  
Stefan Schuster

Abstract The classification of proteinogenic amino acids is crucial for understanding their commonalities as well as their differences to provide a hint for why life settled on the usage of precisely those amino acids. It is also crucial for predicting electrostatic, hydrophobic, stacking and other interactions, for assessing conservation in multiple alignments and many other applications. While several methods have been proposed to find “the” optimal classification, they have several shortcomings, such as the lack of efficiency and interpretability or an unnecessarily high number of discriminating features. In this study, we propose a novel method involving a repeated binary separation via a minimum amount of five features (such as hydrophobicity or volume) expressed by numerical values for amino acid characteristics. The features are extracted from the AAindex database. By simple separation at the medians, we successfully derive the five properties volume, electron–ion-interaction potential, hydrophobicity, α-helix propensity, and π-helix propensity. We extend our analysis to separations other than by the median. We further score our combinations based on how natural the separations are.


2019 ◽  
Vol 1 (7) ◽  
pp. 19-23
Author(s):  
S. I. Surkichin ◽  
N. V. Gryazeva ◽  
L. S. Kholupova ◽  
N. V. Bochkova

The article provides an overview of the use of photodynamic therapy for photodamage of the skin. The causes, pathogenesis and clinical manifestations of skin photodamage are considered. The definition, principle of action of photodynamic therapy, including the sources of light used, the classification of photosensitizers and their main characteristics are given. Analyzed studies that show the effectiveness and comparative evaluation in the selection of various light sources and photosensitizing agents for photodynamic therapy in patients with clinical manifestations of photodamage.


2020 ◽  
Vol 3 (152) ◽  
pp. 92-99
Author(s):  
S. M. Geiko ◽  
◽  
O. D. Lauta

The article provides a philosophical analysis of the tropological theory of the history of H. White. The researcher claims that history is a specific kind of literature, and the historical works is the connection of a certain set of research and narrative operations. The first type of operation answers the question of why the event happened this way and not the other. The second operation is the social description, the narrative of events, the intellectual act of organizing the actual material. According to H. White, this is where the set of ideas and preferences of the researcher begin to work, mainly of a literary and historical nature. Explanations are the main mechanism that becomes the common thread of the narrative. The are implemented through using plot (romantic, satire, comic and tragic) and trope systems – the main stylistic forms of text organization (metaphor, metonymy, synecdoche, irony). The latter decisively influenced for result of the work historians. Historiographical style follows the tropological model, the selection of which is determined by the historian’s individual language practice. When the choice is made, the imagination is ready to create a narrative. Therefore, the historical understanding, according to H. White, can only be tropological. H. White proposes a new methodology for historical research. During the discourse, adequate speech is created to analyze historical phenomena, which the philosopher defines as prefigurative tropological movement. This is how history is revealed through the art of anthropology. Thus, H. White’s tropical history theory offers modern science f meaningful and metatheoretically significant. The structure of concepts on which the classification of historiographical styles can be based and the predictive function of philosophy regarding historical knowledge can be refined.


2011 ◽  
Vol 8 (1) ◽  
pp. 201-210
Author(s):  
R.M. Bogdanov

The problem of determining the repair sections of the main oil pipeline is solved, basing on the classification of images using distance functions and the clustering principle, The criteria characterizing the cluster are determined by certain given values, based on a comparison with which the defect is assigned to a given cluster, procedures for the redistribution of defects in cluster zones are provided, and the cluster zones parameters are being changed. Calculations are demonstrating the range of defect density variation depending on pipeline sections and the universal capabilities of linear objects configuration with arbitrary density, provided by cluster analysis.


1997 ◽  
Vol 3 (S2) ◽  
pp. 341-342
Author(s):  
Sara E. Miller

Negative staining is the most frequently used procedure for preparing particulate specimens, e.g., cell organelles, macromolecules, and viruses, for electron microscopy (Figs. 1-4). The main advantage is that it is rapid, requiring only minutes of preparation time. Another is that it avoids some of the harsh chemicals, e.g., organic solvents, used in thin sectioning. Also, it does not require advanced technical skill. It is widely used in virology, both in classification of viruses as well as diagnosis of viral diseases. Notwithstanding the necessity for fairly high particle counts, virus identification by negative staining is advantageous in not requiring specific reagents such as antibodies, nucleic acid probes, or protein standards which necessitate prior knowledge of potential pathogens for selection of the proper reagent. Furthermore, it does not require viable virions as does growth in tissue culture. Another procedure that uses negative contrasting is ultrathin cryosectioning (Fig. 5).In 1954 Farrant was the first to publish negatively stained material, ferritin particles.


2021 ◽  
Vol 11 (9) ◽  
pp. 3836
Author(s):  
Valeri Gitis ◽  
Alexander Derendyaev ◽  
Konstantin Petrov ◽  
Eugene Yurkov ◽  
Sergey Pirogov ◽  
...  

Prostate cancer is the second most frequent malignancy (after lung cancer). Preoperative staging of PCa is the basis for the selection of adequate treatment tactics. In particular, an urgent problem is the classification of indolent and aggressive forms of PCa in patients with the initial stages of the tumor process. To solve this problem, we propose to use a new binary classification machine-learning method. The proposed method of monotonic functions uses a model in which the disease’s form is determined by the severity of the patient’s condition. It is assumed that the patient’s condition is the easier, the less the deviation of the indicators from the normal values inherent in healthy people. This assumption means that the severity (form) of the disease can be represented by monotonic functions from the values of the deviation of the patient’s indicators beyond the normal range. The method is used to solve the problem of classifying patients with indolent and aggressive forms of prostate cancer according to pretreatment data. The learning algorithm is nonparametric. At the same time, it allows an explanation of the classification results in the form of a logical function. To do this, you should indicate to the algorithm either the threshold value of the probability of successful classification of patients with an indolent form of PCa, or the threshold value of the probability of misclassification of patients with an aggressive form of PCa disease. The examples of logical rules given in the article show that they are quite simple and can be easily interpreted in terms of preoperative indicators of the form of the disease.


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