scholarly journals Variable selection from a feature representing protein sequences: a case of classification on bacterial type IV secreted effectors

2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Jian Zhang ◽  
Lixin Lv ◽  
Donglei Lu ◽  
Denan Kong ◽  
Mohammed Abdoh Ali Al-Alashaari ◽  
...  
Keyword(s):  
Variable Selection ◽  
Protein Sequences ◽  
Biological Research ◽  
Protein Classification ◽  
Ensemble Classifiers ◽  
Type Iv ◽  
Protein Prediction ◽  
Kernel Set ◽  
Bacterial Type

Abstract Background Classification of certain proteins with specific functions is momentous for biological research. Encoding approaches of protein sequences for feature extraction play an important role in protein classification. Many computational methods (namely classifiers) are used for classification on protein sequences according to various encoding approaches. Commonly, protein sequences keep certain labels corresponding to different categories of biological functions (e.g., bacterial type IV secreted effectors or not), which makes protein prediction a fantasy. As to protein prediction, a kernel set of protein sequences keeping certain labels certified by biological experiments should be existent in advance. However, it has been hardly ever seen in prevailing researches. Therefore, unsupervised learning rather than supervised learning (e.g. classification) should be considered. As to protein classification, various classifiers may help to evaluate the effectiveness of different encoding approaches. Besides, variable selection from an encoded feature representing protein sequences is an important issue that also needs to be considered. Results Focusing on the latter problem, we propose a new method for variable selection from an encoded feature representing protein sequences. Taking a benchmark dataset containing 1947 protein sequences as a case, experiments are made to identify bacterial type IV secreted effectors (T4SE) from protein sequences, which are composed of 399 T4SE and 1548 non-T4SE. Comparable and quantified results are obtained only using certain components of the encoded feature, i.e., position-specific scoring matix, and that indicates the effectiveness of our method. Conclusions Certain variables other than an encoded feature they belong to do work for discrimination between different types of proteins. In addition, ensemble classifiers with an automatic assignment of different base classifiers do achieve a better classification result.

scholarly journals Variable Selection from a Feature Representing Protein Sequences: A Case of Classification on Bacterial Type IV Secreted Effectors

2020 ◽  
Author(s):  
Jian Zhang ◽  
Lixin Lv ◽  
Donglei Lu ◽  
Denan Kong ◽  
Mohammed Abdoh Ali Al-Alashaari ◽  
...  
Keyword(s):  
Variable Selection ◽  
Protein Sequences ◽  
Biological Research ◽  
Protein Classification ◽  
Ensemble Classifiers ◽  
Type Iv ◽  
Protein Prediction ◽  
Kernel Set ◽  
Bacterial Type

Abstract Background: Classification of certain proteins with specific functions is momentous for biological research. Encoding approaches of protein sequences for feature extraction play an important role in protein classification. Many computational methods (namely classifiers) are used for classification on protein sequences according to various encoding approaches. Commonly, protein sequences keep certain labels corresponding to different categories of biological functions (e.g., bacterial type IV secreted effectors or not), which makes protein prediction a fantasy. As to protein prediction, a kernel set of protein sequences keeping certain labels certified by biological experiments should be existent in advance. However, it has been hardly ever seen in prevailing researches. Therefore, unsupervised learning rather than supervised learning (e.g. classification) should be considered. As to protein classification, various classifiers may help to evaluate the effectiveness of different encoding approaches. Besides, variable selection from an encoded feature representing protein sequences is an important issue that also needs to be considered.Results: Focusing on the latter problem, we propose a new method for variable selection from an encoded feature representing protein sequences. Taking a benchmark dataset as a case, experiments are made to identify bacterial type IV secreted effectors from protein sequences, which indicates the effectiveness of our method. Conclusions: Certain variables other than an encoded feature they belong to do work for discrimination between different types of proteins. In addition, ensemble classifiers with an automatic assignment of different base classifiers do achieve a better classification result.

MRI analysis and surgical treatment of Wassel Type IV duplicated thumbs

2021 ◽  
pp. 175319342098321
Author(s):  
Anyuan Wang ◽  
Jian Ding ◽  
Long Wang ◽  
Tinggang Chu ◽  
Zhipeng Wu ◽  
...  
Keyword(s):  
Type A ◽  
Surgical Reconstruction ◽  
Mri Findings ◽  
Level Of Evidence ◽  
Type D ◽  
Type Iv ◽  
Secondary Operations ◽  
Type C

We present the MRI findings for 39 Wassel Type IV duplicated thumbs in 38 patients. We found that MRI revealed the morphology of the cartilaginous connection between the thumb anlages and the location of the deviation corresponding to the classification of Horii, which allowed precise preoperative planning of corrective osteotomies. All 39 thumbs were available for follow-up after surgical reconstruction at a mean of 29 months (range 25 to 39). Four out of nine Horii Type A cases and all 12 Type B, as well as the six Type C and the six Type D cases, achieved good results according to the Tada scoring system. Five Type A cases achieved fair results with residual stiffness of the interphalangeal joint. No secondary operations were needed. We conclude that MRI proved useful in subclassifying Wassel Type IV duplicated thumbs and may aid in planning the osteotomies needed for their reconstruction. Level of evidence: IV

scholarly journals Two type IV secretion systems with different functions in Burkholderia cenocepacia K56-2

Microbiology ◽  
2009 ◽  
Vol 155 (12) ◽  
pp. 4005-4013 ◽  
Author(s):  
Ruifu Zhang ◽  
John J. LiPuma ◽  
Carlos F. Gonzalez
Keyword(s):  
Type Iv Secretion ◽  
Burkholderia Cenocepacia ◽  
Target Cells ◽  
Secretion Systems ◽  
Type Iv ◽  
Plasmid Mobilization ◽  
Type Iv Secretion Systems ◽  
Derivative Plasmid ◽  
Chromosome Ii ◽  
Bacterial Type

Bacterial type IV secretion systems (T4SS) perform two fundamental functions related to pathogenesis: the delivery of effector molecules to eukaryotic target cells, and genetic exchange. Two T4SSs have been identified in Burkholderia cenocepacia K56-2, a representative of the ET12 lineage of the B. cepacia complex (Bcc). The plant tissue watersoaking (Ptw) T4SS encoded on a resident 92 kb plasmid is a chimera composed of VirB/D4 and F-specific subunits, and is responsible for the translocation of effector(s) that have been linked to the Ptw phenotype. The bc-VirB/D4 system located on chromosome II displays homology to the VirB/D4 T4SS of Agrobacterium tumefaciens. In contrast to the Ptw T4SS, the bc-VirB/D4 T4SS was found to be dispensable for Ptw effector(s) secretion, but was found to be involved in plasmid mobilization. The fertility inhibitor Osa did not affect the secretion of Ptw effector(s) via the Ptw system, but did disrupt the mobilization of a RSF1010 derivative plasmid.

scholarly journals STUDIES ON EXPERIMENTAL PNEUMONIA

1920 ◽  
Vol 31 (5) ◽  
pp. 499-518 ◽  
Author(s):  
Francis G. Blake ◽  
Russell L. Cecil
Keyword(s):  
Great Majority ◽  
Sudden Onset ◽  
Epidemic Disease ◽  
Lobar Pneumonia ◽  
Type Iv ◽  
Immunological Classification ◽  
To Come ◽  
Characteristic Picture ◽  
Pneumococcus Type

Spontaneous pneumonia occurred to a considerable extent among stock monkeys at the Army Medical School. This pneumonia occurred chiefly in the form of an epidemic outbreak shortly after the arrival of a large shipment of monkeys, and was shown to be due in large part to transmission of infection from monkey to monkey, either directly or indirectly. That spread of the epidemic was facilitated by overcrowding was indicated by the fact that in a subsequent shipment of monkeys, which were kept in pairs in separate cages and were not allowed to come into contact with the monkeys among which the epidemic occurred, no cases of spontaneous pneumonia developed. The close analogy between the epidemic of lobar pneumonia that occurred among the monkeys and similar epidemics of lobar pneumonia that occurred during the war among certain groups of newly drafted troops shortly after their arrival at camp is very striking, and would seem to indicate that pneumococcus pneumonia may become an epidemic disease among groups of susceptible individuals when they are assembled under conditions that facilitate the ready transfer of infection from individual to individual. Bacteriological examination showed the spontaneous pneumonia to be due in the great majority of cases to infection with Pneumococcus Type IV. Immunological classification of the strains of pneurnococci by cross-agglutination tests showed that the majority fell into two biological groups. Two cases were apparently caused by Streptococcus hæmolyticus, two by Streptococcus viridans. The clinical course of spontaneous pneumococcus pneumonia in monkeys was characterized by sudden onset, high sustained temperature, leucocytosis, rapid respiration with expiratory grunt, cough, physical signs of consolidation, invasion of the blood by pneurnococci, and termination in death or recovery by crisis about the 7th to 9th day. In a few instances the disease was complicated by acute fibrinopurulent pericarditis, by empyema, and by purulent meningitis. It was, therefore, clinically identical with lobar pneumonia experimentally produced in monkeys and with lobar pneumonia in man. Study of the pathology of spontaneous pneumococcus pneumonia in monkeys showed that it presented the characteristic picture of lobar pneumonia, both macroscopically and microscopically, and was in all respects comparable with the pathology of lobar pneumonia experimentally produced in monkeys and of lobar pneumonia in man.

scholarly journals Disarming Bacterial Type IV Secretion

2012 ◽  
Vol 19 (8) ◽  
pp. 934-936 ◽  
Author(s):  
Todd A. Cameron ◽  
Patricia C. Zambryski
Keyword(s):  
Type Iv Secretion ◽  
Type Iv ◽  
Bacterial Type

scholarly journals HMMER Cut-off Threshold Tool (HMMERCTTER): Supervised classification of superfamily protein sequences with a reliable cut-off threshold

PLoS ONE ◽  
2018 ◽  
Vol 13 (3) ◽  
pp. e0193757 ◽  
Author(s):  
Inti Anabela Pagnuco ◽  
María Victoria Revuelta ◽  
Hernán Gabriel Bondino ◽  
Marcel Brun ◽  
Arjen ten Have
Keyword(s):  
Supervised Classification ◽  
Protein Sequences

scholarly journals Classification of Human Daily Activities Using Ensemble Methods Based on Smartphone Inertial Sensors

Sensors ◽  
2018 ◽  
Vol 18 (12) ◽  
pp. 4132 ◽  
Author(s):  
Ku Ku Abd. Rahim ◽  
I. Elamvazuthi ◽  
Lila Izhar ◽  
Genci Capi
Keyword(s):  
Activity Recognition ◽  
Inertial Sensors ◽  
Wearable Sensors ◽  
Ensemble Methods ◽  
Daily Activities ◽  
Support Vector ◽  
Random Subspace ◽  
Ensemble Classifiers ◽  
Accuracy Rate

Increasing interest in analyzing human gait using various wearable sensors, which is known as Human Activity Recognition (HAR), can be found in recent research. Sensors such as accelerometers and gyroscopes are widely used in HAR. Recently, high interest has been shown in the use of wearable sensors in numerous applications such as rehabilitation, computer games, animation, filmmaking, and biomechanics. In this paper, classification of human daily activities using Ensemble Methods based on data acquired from smartphone inertial sensors involving about 30 subjects with six different activities is discussed. The six daily activities are walking, walking upstairs, walking downstairs, sitting, standing and lying. It involved three stages of activity recognition; namely, data signal processing (filtering and segmentation), feature extraction and classification. Five types of ensemble classifiers utilized are Bagging, Adaboost, Rotation forest, Ensembles of nested dichotomies (END) and Random subspace. These ensemble classifiers employed Support vector machine (SVM) and Random forest (RF) as the base learners of the ensemble classifiers. The data classification is evaluated with the holdout and 10-fold cross-validation evaluation methods. The performance of each human daily activity was measured in terms of precision, recall, F-measure, and receiver operating characteristic (ROC) curve. In addition, the performance is also measured based on the comparison of overall accuracy rate of classification between different ensemble classifiers and base learners. It was observed that overall, SVM produced better accuracy rate with 99.22% compared to RF with 97.91% based on a random subspace ensemble classifier.

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