scholarly journals In-Silico Tool for Predicting, Scanning, and Designing Defensins

2021 ◽  
Vol 12 ◽  
Author(s):  
Dilraj Kaur ◽  
Sumeet Patiyal ◽  
Chakit Arora ◽  
Ritesh Singh ◽  
Gaurav Lodhi ◽  
...  
Keyword(s):  
Accurate Method ◽  
Support Vector ◽  
Host Defense Peptides ◽  
Web Based ◽  
Wide Range ◽  
Learning Technique ◽  
Living Species ◽  
The Difference ◽  
Validation Set ◽  
Available Information

Defensins are host defense peptides present in nearly all living species, which play a crucial role in innate immunity. These peptides provide protection to the host, either by killing microbes directly or indirectly by activating the immune system. In the era of antibiotic resistance, there is a need to develop a fast and accurate method for predicting defensins. In this study, a systematic attempt has been made to develop models for predicting defensins from available information on defensins. We created a dataset of defensins and non-defensins called the main dataset that contains 1,036 defensins and 1,035 AMPs (antimicrobial peptides, or non-defensins) to understand the difference between defensins and AMPs. Our analysis indicates that certain residues like Cys, Arg, and Tyr are more abundant in defensins in comparison to AMPs. We developed machine learning technique-based models on the main dataset using a wide range of peptide features. Our SVM (support vector machine)-based model discriminates defensins and AMPs with MCC of 0.88 and AUC of 0.98 on the validation set of the main dataset. In addition, we created an alternate dataset that consists of 1,036 defensins and 1,054 non-defensins obtained from Swiss-Prot. Models were also developed on the alternate dataset to predict defensins. Our SVM-based model achieved maximum MCC of 0.96 with AUC of 0.99 on the validation set of the alternate dataset. All models were trained, tested, and validated using standard protocols. Finally, we developed a web-based service “DefPred” to predict defensins, scan defensins in proteins, and design the best defensins from their analogs. The stand-alone software and web server of DefPred are available at https://webs.iiitd.edu.in/raghava/defpred.

I. On a determination of the boiling point of sulphur, and on a method of standardising platinum resistance thermometers by reference to it

1891 ◽  
Vol 49 (296-301) ◽  
pp. 56-60
Keyword(s):  
Accurate Method ◽  
Platinum Resistance Thermometer ◽  
Platinum Resistance ◽  
Resistance Thermometer ◽  
Platinum Resistance Thermometers ◽  
Resistance Thermometers ◽  
Wide Range ◽  
The Difference ◽  
Relative Measurements

Experiments by different observers have shown that electrical resistance thermometers afford the most convenient and accurate method of measuring temperature through a very wide range. By selecting a particular thermometer as the standard, and directly comparing others with it, it has been found possible to attain a degree of accuracy of the order of 0°·001 in the relative measurements between 0° and 100°C., and of the order of 0º·01 at 450°C. In a previous communication* it has been shown that, if t be the temperature by air thermometer, and if pt be the temperature by platinum resistance thermometer, the difference between them is very closely represented from 0° to 700°C. by the formula d = t - pt = δ { t /100│ 2 — - t /100} ... ( d ).

scholarly journals Image-Based Learning Approach Applied to Time Series Forecasting

2012 ◽  
Vol 10 (3) ◽  
Author(s):  
K. Ramírez-Amáro ◽  
J. C. Chimal-Eguía
Keyword(s):  
Time Series ◽  
Input Data ◽  
Data Representation ◽  
Time Series Forecasting ◽  
Support Vector ◽  
Learning Approach ◽  
New Information ◽  
New Learning ◽  
Learning Technique ◽  
The Difference

In this paper, a new learning approach based on time-series image information is presented. In order to implement this new learning technique, a novel time-series input data representation is also defined. This input data representation is based on information obtained by image axis division into boxes. The difference between this new input data representation and the classical is that this technique is not time-dependent. This new information is implemented in the new Image-Based Learning Approach (IBLA) and by means of a probabilistic mechanism this learning technique is applied to the interesting problem of time series forecasting. The experimental results indicate that by using the methodology proposed in this article, it is possible to obtain better results than with the classical techniques such as artificial neuronal networks and support vector machines.

scholarly journals COVID-Predictor: RNA Sequence based Prediction of Coronavirus

2020 ◽  
Author(s):  
Jnanendra Prasad Sarkar ◽  
Indrajit Saha ◽  
Arijit Seal ◽  
Debasree Maity
Keyword(s):  
Machine Learning ◽  
Clinical Importance ◽  
Rna Sequences ◽  
Web Based ◽  
Learning Technique ◽  
N Gram ◽  
Validation Set ◽  
Novel Coronavirus ◽  
Fold Cross Validation ◽  
Unknown Sequence

Abstract The problem of virus classification is always a subject of concern for virology or epidemiology over the decades. Moreover, the detection of highly divergent or yet unknown viruses is a major challenge despite of its clinical importance. In this situati on, the outbreak of novel coronavirus (SARS-CoV-2) and its susceptibility in different epidemic condition around the world clearly suggest that the virus is mutating to create divergent variants and making the task of virus prediction more challenging. On the other hand, despite of novel coronavirus, two more coronaviruses such as MERS and SARS-CoV-1 are already present. Therefore, the use of machine learning technique is highly required at this moment to predict the coronaviruses by considering their divergent genetic functional characteristics. Thus, we are proposing machine learning based coronavirus prediction technique, called COVID- Predictor, where 1000 of RNA sequences of SARS-CoV-1, MERS, SARS-CoV-2 and other virus are used to train a Na¨ıve Bayes classifier so that it can predict any unknown sequence of these viruses. In order to develop the COVID-Predictor, the feature vector is constructed by the motifs of the sequence generated by k-mer and n-gram techniques. The model has been validated using 10 fold cross validation in comparison with other classification techniques. The results show the superiority of our predictor by achieving average 97% accuracy on unseen validation set. The same pre-trained model has been used to design a web based application where RNA sequences of unknown viruses can be uploaded to predict class of coronavirus. The predictor, code and datasets are available here: http://www.nitttrkol.ac.in/indrajit/projects/COVID-Predictor/

Comparative Effects of High-Tech Visual Scene Displays and Low-Tech Isolated Picture Symbols on Engagement From Students With Multiple Disabilities

2019 ◽  
Vol 50 (4) ◽  
pp. 693-702 ◽  
Author(s):  
Christine Holyfield ◽  
Sydney Brooks ◽  
Allison Schluterman
Keyword(s):  
Language Learning ◽  
Augmentative And Alternative Communication ◽  
Visual Analysis ◽  
Multiple Disabilities ◽  
Visual Scene ◽  
Future Research ◽  
High Tech ◽  
Single Subject ◽  
Wide Range ◽  
The Difference

Purpose Augmentative and alternative communication (AAC) is an intervention approach that can promote communication and language in children with multiple disabilities who are beginning communicators. While a wide range of AAC technologies are available, little is known about the comparative effects of specific technology options. Given that engagement can be low for beginning communicators with multiple disabilities, the current study provides initial information about the comparative effects of 2 AAC technology options—high-tech visual scene displays (VSDs) and low-tech isolated picture symbols—on engagement. Method Three elementary-age beginning communicators with multiple disabilities participated. The study used a single-subject, alternating treatment design with each technology serving as a condition. Participants interacted with their school speech-language pathologists using each of the 2 technologies across 5 sessions in a block randomized order. Results According to visual analysis and nonoverlap of all pairs calculations, all 3 participants demonstrated more engagement with the high-tech VSDs than the low-tech isolated picture symbols as measured by their seconds of gaze toward each technology option. Despite the difference in engagement observed, there was no clear difference across the 2 conditions in engagement toward the communication partner or use of the AAC. Conclusions Clinicians can consider measuring engagement when evaluating AAC technology options for children with multiple disabilities and should consider evaluating high-tech VSDs as 1 technology option for them. Future research must explore the extent to which differences in engagement to particular AAC technologies result in differences in communication and language learning over time as might be expected.

COMBINATORIAL POLYNOMIALLY COMPUTABLE CHARACTERISTICS OF SUBSTITUTIONS AND THEIR PROPERTIES

2020 ◽  
Vol 7 (2) ◽  
pp. 34-41
Author(s):  
VLADIMIR NIKONOV ◽  
◽  
ANTON ZOBOV ◽  
Keyword(s):  
Mathematical Expectation ◽  
Point Of View ◽  
Small Range ◽  
Computational Point ◽  
Wide Range ◽  
Bijective Function ◽  
The Difference ◽  
Element Base ◽  
Selection Of

The construction and selection of a suitable bijective function, that is, substitution, is now becoming an important applied task, particularly for building block encryption systems. Many articles have suggested using different approaches to determining the quality of substitution, but most of them are highly computationally complex. The solution of this problem will significantly expand the range of methods for constructing and analyzing scheme in information protection systems. The purpose of research is to find easily measurable characteristics of substitutions, allowing to evaluate their quality, and also measures of the proximity of a particular substitutions to a random one, or its distance from it. For this purpose, several characteristics were proposed in this work: difference and polynomial, and their mathematical expectation was found, as well as variance for the difference characteristic. This allows us to make a conclusion about its quality by comparing the result of calculating the characteristic for a particular substitution with the calculated mathematical expectation. From a computational point of view, the thesises of the article are of exceptional interest due to the simplicity of the algorithm for quantifying the quality of bijective function substitutions. By its nature, the operation of calculating the difference characteristic carries out a simple summation of integer terms in a fixed and small range. Such an operation, both in the modern and in the prospective element base, is embedded in the logic of a wide range of functional elements, especially when implementing computational actions in the optical range, or on other carriers related to the field of nanotechnology.

Generalized Heterodyne Configurations for Photo-induced Force Microscopy

2019 ◽  
Author(s):  
Le Wang ◽  
Devon Jakob ◽  
Haomin Wang ◽  
Alexis Apostolos ◽  
Marcos M. Pires ◽  
...  
Keyword(s):  
Spatial Resolution ◽  
Repetition Rate ◽  
Modulation Frequency ◽  
High Harmonic ◽  
Chemical Imaging ◽  
Heterodyne Detection ◽  
Force Microscopy ◽  
Wide Range ◽  
The Difference ◽  
Afm Cantilever

<div>Infrared chemical microscopy through mechanical probing of light-matter interactions by atomic force microscopy (AFM) bypasses the diffraction limit. One increasingly popular technique is photo-induced force microscopy (PiFM), which utilizes the mechanical heterodyne signal detection between cantilever mechanical resonant oscillations and the photo induced force from light-matter interaction. So far, photo induced force microscopy has been operated in only one heterodyne configuration. In this article, we generalize heterodyne configurations of photoinduced force microscopy by introducing two new schemes: harmonic heterodyne detection and sequential heterodyne detection. In harmonic heterodyne detection, the laser repetition rate matches integer fractions of the difference between the two mechanical resonant modes of the AFM cantilever. The high harmonic of the beating from the photothermal expansion mixes with the AFM cantilever oscillation to provide PiFM signal. In sequential heterodyne detection, the combination of the repetition rate of laser pulses and polarization modulation frequency matches the difference between two AFM mechanical modes, leading to detectable PiFM signals. These two generalized heterodyne configurations for photo induced force microscopy deliver new avenues for chemical imaging and broadband spectroscopy at ~10 nm spatial resolution. They are suitable for a wide range of heterogeneous materials across various disciplines: from structured polymer film, polaritonic boron nitride materials, to isolated bacterial peptidoglycan cell walls. The generalized heterodyne configurations introduce flexibility for the implementation of PiFM and related tapping mode AFM-IR, and provide possibilities for additional modulation channel in PiFM for targeted signal extraction with nanoscale spatial resolution.</div>

Investigating the Efficacy and Cost-Effectiveness of a Web-based Self-help Program for People With Adjustment Problems After an Accident (SelFIT): Protocol for a Randomized Controlled Trial (Preprint)

2020 ◽  
Author(s):  
Julia Hegy ◽  
Noemi Anja Brog ◽  
Thomas Berger ◽  
Hansjoerg Znoj
Keyword(s):  
Health Care ◽  
Psychological Distress ◽  
Cost Effectiveness ◽  
Well Being ◽  
User Friendliness ◽  
Adjustment Problems ◽  
Health Care Consumption ◽  
Web Based ◽  
Self Help ◽  
Wide Range

BACKGROUND Accidents and the resulting injuries are one of the world’s biggest health care issues often causing long-term effects on psychological and physical health. With regard to psychological consequences, accidents can cause a wide range of burdens including adjustment problems. Although adjustment problems are among the most frequent mental health problems, there are few specific interventions available. The newly developed program SelFIT aims to remedy this situation by offering a low-threshold web-based self-help intervention for psychological distress after an accident. OBJECTIVE The overall aim is to evaluate the efficacy and cost-effectiveness of the SelFIT program plus care as usual (CAU) compared to only care as usual. Furthermore, the program’s user friendliness, acceptance and adherence are assessed. We expect that the use of SelFIT is associated with a greater reduction in psychological distress, greater improvement in mental and physical well-being, and greater cost-effectiveness compared to CAU. METHODS Adults (n=240) showing adjustment problems due to an accident they experienced between 2 weeks and 2 years before entering the study will be randomized. Participants in the intervention group receive direct access to SelFIT. The control group receives access to the program after 12 weeks. There are 6 measurement points for both groups (baseline as well as after 4, 8, 12, 24 and 36 weeks). The main outcome is a reduction in anxiety, depression and stress symptoms that indicate adjustment problems. Secondary outcomes include well-being, optimism, embitterment, self-esteem, self-efficacy, emotion regulation, pain, costs of health care consumption and productivity loss as well as the program’s adherence, acceptance and user-friendliness. RESULTS Recruitment started in December 2019 and is ongoing. CONCLUSIONS To the best of our knowledge, this is the first study examining a web-based self-help program designed to treat adjustment problems resulting from an accident. If effective, the program could complement the still limited offer of secondary and tertiary psychological prevention after an accident. CLINICALTRIAL ClinicalTrials.gov NCT03785912; https://clinicaltrials.gov/ct2/show/NCT03785912?cond=NCT03785912&draw=2&rank=1

scholarly journals Epidemiological modeling in StochSS Live!

2021 ◽  
Author(s):  
Richard Jiang ◽  
Bruno Jacob ◽  
Matthew Geiger ◽  
Sean Matthew ◽  
Bryan Rumsey ◽  
...  
Keyword(s):  
Stochastic Model ◽  
Epidemiological Model ◽  
Supplementary Information ◽  
Supplementary Data ◽  
Web Based ◽  
Epidemiological Modeling ◽  
Modeling Simulation ◽  
Wide Range ◽  
Biochemical Systems

Abstract Summary We present StochSS Live!, a web-based service for modeling, simulation and analysis of a wide range of mathematical, biological and biochemical systems. Using an epidemiological model of COVID-19, we demonstrate the power of StochSS Live! to enable researchers to quickly develop a deterministic or a discrete stochastic model, infer its parameters and analyze the results. Availability and implementation StochSS Live! is freely available at https://live.stochss.org/ Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Possibility of Human Gender Recognition Using Raman Spectra of Teeth

Molecules ◽  
2021 ◽  
Vol 26 (13) ◽  
pp. 3983
Author(s):  
Ozren Gamulin ◽  
Marko Škrabić ◽  
Kristina Serec ◽  
Matej Par ◽  
Marija Baković ◽  
...  
Keyword(s):  
Raman Spectra ◽  
Principal Component ◽  
Support Vector ◽  
Gender Recognition ◽  
Proof Of Concept ◽  
Male And Female ◽  
Tooth Type ◽  
Tooth Apex ◽  
The Difference

Gender determination of the human remains can be very challenging, especially in the case of incomplete ones. Herein, we report a proof-of-concept experiment where the possibility of gender recognition using Raman spectroscopy of teeth is investigated. Raman spectra were recorded from male and female molars and premolars on two distinct sites, tooth apex and anatomical neck. Recorded spectra were sorted into suitable datasets and initially analyzed with principal component analysis, which showed a distinction between spectra of male and female teeth. Then, reduced datasets with scores of the first 20 principal components were formed and two classification algorithms, support vector machine and artificial neural networks, were applied to form classification models for gender recognition. The obtained results showed that gender recognition with Raman spectra of teeth is possible but strongly depends both on the tooth type and spectrum recording site. The difference in classification accuracy between different tooth types and recording sites are discussed in terms of the molecular structure difference caused by the influence of masticatory loading or gender-dependent life events.

scholarly journals Ablation Analysis to Select Wearable Sensors for Classifying Standing, Walking, and Running

Sensors ◽  
2020 ◽  
Vol 21 (1) ◽  
pp. 194
Author(s):  
Sarah Gonzalez ◽  
Paul Stegall ◽  
Harvey Edwards ◽  
Leia Stirling ◽  
Ho Chit Siu
Keyword(s):  
Activity Recognition ◽  
Principal Components ◽  
Classification Accuracy ◽  
Wearable Sensors ◽  
Sensor Data ◽  
Machine Learning Techniques ◽  
Support Vector ◽  
Learning Techniques ◽  
Measurement Units ◽  
The Difference

The field of human activity recognition (HAR) often utilizes wearable sensors and machine learning techniques in order to identify the actions of the subject. This paper considers the activity recognition of walking and running while using a support vector machine (SVM) that was trained on principal components derived from wearable sensor data. An ablation analysis is performed in order to select the subset of sensors that yield the highest classification accuracy. The paper also compares principal components across trials to inform the similarity of the trials. Five subjects were instructed to perform standing, walking, running, and sprinting on a self-paced treadmill, and the data were recorded while using surface electromyography sensors (sEMGs), inertial measurement units (IMUs), and force plates. When all of the sensors were included, the SVM had over 90% classification accuracy using only the first three principal components of the data with the classes of stand, walk, and run/sprint (combined run and sprint class). It was found that sensors that were placed only on the lower leg produce higher accuracies than sensors placed on the upper leg. There was a small decrease in accuracy when the force plates are ablated, but the difference may not be operationally relevant. Using only accelerometers without sEMGs was shown to decrease the accuracy of the SVM.

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