Explore the vast range of titles available.

Background Plasmids play a major role in the transfer of antimicrobial resistance (AMR) genes among bacteria via horizontal gene transfer. The identification of plasmids in short-read assemblies is a challenging problem and a very active research area. Plasmid binning aims at detecting, in a draft genome assembly, groups (bins) of contigs likely to originate from the same plasmid. Several methods for plasmid binning have been developed recently, such as PlasBin-flow, HyAsP, gplas, MOB-suite, and plasmidSPAdes. This motivates the problem of evaluating the performances of plasmid binning methods, either against a given ground truth or between them. Results We describe PlasEval, a novel method aimed at comparing the results of plasmid binning tools. PlasEval computes a dissimilarity measure between two sets of plasmid bins, that can originate either from two plasmid binning tools, or from a plasmid binning tool and a ground truth set of plasmid bins. The PlasEval dissimilarity accounts for the contig content of plasmid bins, the length of contigs and is repeat-aware. Moreover, the dissimilarity score computed by PlasEval is broken down into several parts, that allows to understand qualitative differences between the compared sets of plasmid bins. We illustrate the use of PlasEval by benchmarking four recently developed plasmid binning tools—PlasBin-flow, HyAsP, gplas, and MOB-recon—on a data set of 53 E. coli bacterial genomes. Conclusion Analysis of the results of plasmid binning methods using PlasEval shows that their behaviour varies significantly. PlasEval can be used to decide which specific plasmid binning method should be used for a specific dataset. The disagreement between different methods also suggests that the problem of plasmid binning on short-read contigs requires further research. We believe that PlasEval can prove to be an effective tool in this regard. PlasEval is publicly available at https://github.com/acme92/PlasEval

In the field of genome rearrangement algorithms, models accounting for gene duplication lead often to hard problems. For example, while computing the pairwise distance is tractable in most duplication-free models, the problem is NP-complete for most extensions of these models accounting for duplicated genes. Moreover, problems involving more than two genomes, such as the genome median and the Small Parsimony problem, are intractable for most duplication-free models, with some exceptions, for example the Single-Cut-or-Join (SCJ) model. We introduce a variant of the SCJ distance that accounts for duplicated genes, in the context of directed evolution from an ancestral genome to a descendant genome where orthology relations between ancestral genes and their descendant are known. Our model includes two duplication mechanisms: single-gene tandem duplication and the creation of single-gene circular chromosomes. We prove that in this model, computing the directed distance and a parsimonious evolutionary scenario in terms of SCJ and single-gene duplication events can be done in linear time. We also show that the directed median problem is tractable for this distance, while the rooted median problem, where we assume that one of the given genomes is ancestral to the median, is NP-complete. We also describe an Integer Linear Program for solving this problem. We evaluate the directed distance and rooted median algorithms on simulated data. Our results provide a simple genome rearrangement model, extending the SCJ model to account for single-gene duplications, for which we prove a mix of tractability and hardness results. For the NP-complete rooted median problem, we design a simple Integer Linear Program. Our publicly available implementation of these algorithms for the directed distance and median problems allow to solve efficiently these problems on large instances.

Background. In the field of genome rearrangement algorithms, models accounting for gene duplication lead often to hard problems. For example, while computing the pairwise distance is tractable in most duplication-free models, the problem is NP-complete for most extensions of these models accounting for duplicated genes. Moreover, problems involving more than two genomes, such as the genome median and the Small Parsimony problem, are intractable for most duplication-free models, with some exceptions, for example the Single-Cut-or-Join (SCJ) model. Results. We introduce a variant of the SCJ distance that accounts for duplicated genes, in the context of directed evolution from an ancestral genome to a descendant genome where orthology relations between ancestral genes and their descendant are known. Our model includes two duplication mechanisms: single-gene tandem duplication and the creation of single-gene circular chromosomes. We prove that in this model, computing the directed distance and a parsimonious evolutionary scenario in terms of SCJ and single-gene duplication events can be done in linear time. We also show that the directed median problem is tractable for this distance, while the rooted median problem, where we assume that one of the given genomes is ancestral to the median, is NP-complete. We also describe an Integer Linear Program for solving this problem. We evaluate the directed distance and rooted median algorithms on simulated data. Conclusion. Our results provide a simple genome rearrangement model, extending the SCJ model to account for single-gene duplications, for which we prove a mix of tractability and hardness results. For the NP-complete rooted median problem, we design a simple Integer Linear Program. Our publicly available implementation of these algorithms for the directed distance and median problems allow to solve efficiently these problems on large instances.

Plasmids play a major role in the transfer of antimicrobial resistance (AMR) genes among bacteria via horizontal gene transfer. The identification of plasmids in short-read assemblies is a challenging problem and a very active research area. Plasmid binning aims at detecting, in a draft genome assembly, groups (bins) of contigs likely to originate from the same plasmid. Several methods for plasmid binning have been developed recently, such as PlasBin-flow, HyAsP, gplas, MOB-suite, and plasmidSPAdes. This motivates the problem of evaluating the performances of plasmid binning methods, either against a given ground truth or between them. We describe PlasEval, a novel method aimed at comparing the results of plasmid binning tools. PlasEval computes a dissimilarity measure between two sets of plasmid bins, that can originate either from two plasmid binning tools, or from a plasmid binning tool and a ground truth set of plasmid bins. The PlasEval dissimilarity accounts for the contig content of plasmid bins, the length of contigs and is repeat-aware. Moreover, the dissimilarity score computed by PlasEval is broken down into several parts, that allows to understand qualitative differences between the compared sets of plasmid bins. We illustrate the use of PlasEval by benchmarking four recently developed plasmid binning tools – PlasBin-flow, HyAsP, gplas, and MOB-recon – on a data set of 54 E. coli bacterial genomes. PlasEval is freely available at https://github.com/acme92/PlasEval

- In a world saturated with travel information overload and generic recommendations, \"Tour Sentiments: A Personalized Travel Recommendation System Using AI \" emerges as a groundbreaking initiative. This project seeks to transform travel planning by harnessing the capabilities of Artificial Intelligence and real-time google Maps with street view and duration of travel. The primary goal of 'Tour Sentiments' is to create a personalized travel recommendation system that adapts to the changing emotions and preferences of travelers. By employing real-time sentiment analysis using google gemini, the system aims to offer tailored suggestions that align closely with individuals' current feelings and desires, departing from conventional one-size-fits-all approaches. Beyond mere efficiency, the ultimate vision of 'Tour Sentiments' is to elevate the travel experience, infusing it with joy, discovery, and lasting memories. Through the amalgamation of AI and sentiment analysis, the project aspires to make global exploration more accessible and captivating, setting a new standard for personalized travel guidance and enriching journeys worldwide.

Phishing attacks cause companies and individuals huge economic as well as intangible damages. Phishing attacks employ a litany of attack vectors. To deal with such attacks, counter work needs to be done in several areas. In this paper, the authors have presented a survey of literature on phishing detection and the current trends in phishing. The authors have also mentioned that phishing detection can be classified into three main categories namely, disallowing attacks to reach the users, user training, and more useful user interfaces. The goal of this paper is to cover all important aspects involved in phishing detection as compared to existing surveys on phishing detection that have focused on individual aspects. There has been a continuous increase in phishing attacks, with a sharp rise in Spear phishing and attacks over Social Media.

Introduction: Health is defined as a state of complete physical, mental, and social well-being. Awareness of orthodontic treatment varies in different regions. Undergoing orthodontic treatment to correct malocclusion would be very beneficial to children as it could help eliminate bullying by peers regarding facial appearance. This kind of bullying by peers could affect the child psychologically. Materials and Methods: A questionnaire survey was conducted in Karad Taluka in Maharashtra. A total of 378 subjects were selected. The schools were randomly selected. A questionnaire including general information, knowledge, and awareness of orthodontic treatment was prepared, and the teachers were given 15 min to fill it. Since it was a short period of time to gather information from other sources, the participants answered the questionnaire using their own knowledge. The purpose of this questionnaire, which consisted of 12 questions in both English and Marathi was to evaluate the level of knowledge the teachers had about orthodontic treatment. The purpose of the study and questionnaire forms were explained by the examiner. The responses of the teachers to the questions were recorded on a 2-point Likert scale {YES or NO}. Results: Simple descriptive statistics was applied to describe the study variables. A Chi-square test of independence was performed to check independence between answers and gender for each question. Conclusion: Within limits of this study, it may be concluded that knowledge of available treatments was more in males compared to females in rural areas.

C. elegans is commonly used in neuroscience for behaviour analysis because of it's compact nervous system with well-described connectivity. Localizing the animal and distinguishing between its head and tail are important tasks to track the worm during behavioural assays and to perform quantitative analyses. We demonstrate a neural network based approach to localize both the head and the tail of the worm in an image. To make empirical results in the paper reproducible and promote open source machine learning based solutions for C. elegans behavioural analysis, we also make our code publicly available.