Allergen false-detection using official bioinformatic algorithms.
Ontology highlight
ABSTRACT:
SUBMITTER: Herman RA
PROVIDER: S-EPMC7289518 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:Protein allergens can be related by cross-reactivity. Allergens that share relevant sequence can cross-react, those lacking sufficient similarity in their IgE antibody-binding epitopes do not cross-react. Cross-reactivity is based on shared epitopes that is based on shared sequence and higher level structure (charge and shape). Epitopes are important in predicting cross-reactivity potential and may provide the potential to establish criteria that identify homology among allergens. Selected allergen's IgE-binding epitope sequences were used to determine how the FASTA algorithm could be used to identify a threshold of significance. A statistical measure (expectation value, E-value) was used to identify a threshold specific to identifying cross-reactivity potential. Peanut Ara h 1 and Ara h 2, shrimp tropomyosin Pen a 1, and birch tree pollen allergen, Bet v 1 were sources of known epitopes. Each epitope or set of epitopes was inserted into random amino acid sequence to create hypothetical proteins used as queries to an allergen database. Alignments with allergens were noted for the ability to match the epitope's source allergen as well as any cross-reactive or other homologous allergens. A FASTA expectation value range (1 × 10-5 -1 × 10-6 ) was identified that could act as a threshold to help identify cross-reactivity potential.
| S-EPMC5573986 | biostudies-literature
Project description:The use of faked identities is a current issue for both physical and online security. In this paper, we test the differences between subjects who report their true identity and the ones who give fake identity responding to control, simple, and complex questions. Asking complex questions is a new procedure for increasing liars' cognitive load, which is presented in this paper for the first time. The experiment consisted in an identity verification task, during which response time and errors were collected. Twenty participants were instructed to lie about their identity, whereas the other 20 were asked to respond truthfully. Different machine learning (ML) models were trained, reaching an accuracy level around 90-95% in distinguishing liars from truth tellers based on error rate and response time. Then, to evaluate the generalization and replicability of these models, a new sample of 10 participants were tested and classified, obtaining an accuracy between 80 and 90%. In short, results indicate that liars may be efficiently distinguished from truth tellers on the basis of their response times and errors to complex questions, with an adequate generalization accuracy of the classification models.
| S-EPMC5845552 | biostudies-literature
Project description:Solar energetic particle (SEP) events are known to occur following solar flares and coronal mass ejections (CMEs). However, some high-energy solar events do not result in SEPs being detected at Earth, and it is these types of event which may be termed "false alarms". We define two simple SEP forecasting algorithms based upon the occurrence of a magnetically well-connected CME with a speed in excess of 1500kms-1 (a "fast" CME) or a well-connected X-class flare and analyse them with respect to historical datasets. We compare the parameters of those solar events which produced an enhancement of >40MeV protons at Earth (an "SEP event") and the parameters of false alarms. We find that an SEP forecasting algorithm based solely upon the occurrence of a well-connected fast CME produces fewer false alarms (28.8%) than an algorithm which is based solely upon a well-connected X-class flare (50.6%). Both algorithms fail to forecast a relatively high percentage of SEP events (53.2% and 50.6%, respectively). Our analysis of the historical datasets shows that false-alarm X-class flares were either not associated with any CME, or were associated with a CME slower than 500kms-1 ; false-alarm fast CMEs tended to be associated with flare classes lower than M3. A better approach to forecasting would be an algorithm which takes as its base the occurrence of both CMEs and flares. We define a new forecasting algorithm which uses a combination of CME and flare parameters, and we show that the false-alarm ratio is similar to that for the algorithm based upon fast CMEs (29.6%), but the percentage of SEP events not forecast is reduced to 32.4%. Lists of the solar events which gave rise to >40MeV protons and the false alarms have been derived and are made available to aid further study. Electronic Supplementary Material:The online version of this article (doi:10.1007/s11207-017-1196-y) contains supplementary material, which is available to authorized users.
| S-EPMC6953974 | biostudies-literature
Project description:PurposeClinical genome sequencing (cGS) followed by orthogonal confirmatory testing is standard practice. While orthogonal testing significantly improves specificity, it also results in increased turnaround time and cost of testing. The purpose of this study is to evaluate machine learning models trained to identify false positive variants in cGS data to reduce the need for orthogonal testing.MethodsWe sequenced five reference human genome samples characterized by the Genome in a Bottle Consortium (GIAB) and compared the results with an established set of variants for each genome referred to as a truth set. We then trained machine learning models to identify variants that were labeled as false positives.ResultsAfter training, the models identified 99.5% of the false positive heterozygous single-nucleotide variants (SNVs) and heterozygous insertions/deletions variants (indels) while reducing confirmatory testing of nonactionable, nonprimary SNVs by 85% and indels by 75%. Employing the algorithm in clinical practice reduced overall orthogonal testing using dideoxynucleotide (Sanger) sequencing by 71%.ConclusionOur results indicate that a low false positive call rate can be maintained while significantly reducing the need for confirmatory testing. The framework that generated our models and results is publicly available at https://github.com/HudsonAlpha/STEVE .
| S-EPMC8257489 | biostudies-literature
Project description:Ransomware-related cyber-attacks have been on the rise over the last decade, disturbing organizations considerably. Developing new and better ways to detect this type of malware is necessary. This research applies dynamic analysis and machine learning to identify the ever-evolving ransomware signatures using selected dynamic features. Since most of the attributes are shared by diverse ransomware-affected samples, our study can be used for detecting current and even new variants of the threat. This research has the following objectives: (1) Execute experiments with encryptor and locker ransomware combined with goodware to generate JSON files with dynamic parameters using a sandbox. (2) Analyze and select the most relevant and non-redundant dynamic features for identifying encryptor and locker ransomware from goodware. (3) Generate and make public a dynamic features dataset that includes these selected parameters for samples of different artifacts. (4) Apply the dynamic feature dataset to obtain models with machine learning algorithms. Five platforms, 20 ransomware, and 20 goodware artifacts were evaluated. The final feature dataset is composed of 2000 registers of 50 characteristics each. This dataset allows for a machine learning detection with a 10-fold cross-evaluation with an average accuracy superior to 0.99 for gradient boosted regression trees, random forest, and neural networks.
| S-EPMC9920393 | biostudies-literature
Project description:Schizophrenia is a group of severe neurodevelopmental disorders. Identification of peripheral diagnostic biomarkers is an effective approach to improving diagnosis of schizophrenia. In this study, four datasets of schizophrenia patients' blood or serum samples were downloaded from the GEO database and merged and de-batched for the analyses of differentially expressed genes (DEGs) and weighted gene co-expression network analysis (WCGNA). The WGCNA analysis showed that the cyan module, among 9 modules, was significantly related to schizophrenia, which subsequently yielded 317 schizophrenia-related key genes by comparing with the DEGs. The enrichment analyses on these key genes indicated a strong correlation with immune-related processes. The CIBERSORT algorithm was adopted to analyze immune cell infiltration, which revealed differences in eosinophils, M0 macrophages, resting mast cells, and gamma delta T cells. Furthermore, by comparing with the immune genes obtained from online databases, 95 immune-related key genes for schizophrenia were screened out. Moreover, machine learning algorithms including Random Forest, LASSO, and SVM-RFE were used to further screen immune-related hub genes of schizophrenia. Finally, CLIC3 was found as an immune-related hub gene of schizophrenia by the three machine learning algorithms. A schizophrenia rat model was established to validate CLIC3 expression and found that CLIC3 levels were reduced in the model rat plasma and brains in a brain-regional dependent manner, but can be reversed by an antipsychotic drug risperidone. In conclusion, using various bioinformatic and biological methods, this study found an immune-related hub gene of schizophrenia - CLIC3 that might be a potential diagnostic biomarker and therapeutic target for schizophrenia.
| S-EPMC10568181 | biostudies-literature
Project description:Detecting small moving targets against a cluttered background in visual data is a challenging task. The main problems include spatio-temporal target contrast enhancement, background suppression and accurate target segmentation. When targets are at great distances from a non-stationary camera, the difficulty of these challenges increases. In such cases the moving camera can introduce large spatial changes between frames which may cause issues in temporal algorithms; furthermore targets can approach a single pixel, thereby affecting spatial methods. Previous literature has shown that biologically inspired methods, based on the vision systems of insects, are robust to such conditions. It has also been shown that the use of divisive optic-flow inhibition with these methods enhances the detectability of small targets. However, the location within the visual pathway the inhibition should be applied was ambiguous. In this paper, we investigated the tunings of some of the optic-flow filters and use of a nonlinear transform on the optic-flow signal to modify motion responses for the purpose of suppressing false positives and enhancing small target detection. Additionally, we looked at multiple locations within the biologically inspired vision (BIV) algorithm where inhibition could further enhance detection performance, and look at driving the nonlinear transform with a global motion estimate. To get a better understanding of how the BIV algorithm performs, we compared to other state-of-the-art target detection algorithms, and look at how their performance can be enhanced with the optic-flow inhibition. Our explicit use of the nonlinear inhibition allows for the incorporation of a wider dynamic range of inhibiting signals, along with spatio-temporal filter refinement, which further increases target-background discrimination in the presence of camera motion. Extensive experiments shows that our proposed approach achieves an improvement of 25% over linearly conditioned inhibition schemes and 2.33 times the detection performance of the BIV model without inhibition. Moreover, our approach achieves between 10 and 104 times better detection performance compared to any conventional state-of-the-art moving object detection algorithm applied to the same, highly cluttered and moving scenes. Applying the nonlinear inhibition to other algorithms showed that their performance can be increased by up to 22 times. These findings show that the application of optic-flow- based signal suppression should be applied to enhance target detection from moving platforms. Furthermore, they indicate where best to look for evidence of such signals within the insect brain.
| S-EPMC9691501 | biostudies-literature
Project description:BackgroundThe analysis of differential splicing (DS) is crucial for understanding physiological processes in cells and organs. In particular, aberrant transcripts are known to be involved in various diseases including cancer. A widely used technique for studying DS are exon arrays. Over the last decade a variety of algorithms for the detection of DS events from exon arrays has been developed. However, no comprehensive, comparative evaluation including sensitivity to the most important data features has been conducted so far. To this end, we created multiple data sets based on simulated data to assess strengths and weaknesses of seven published methods as well as a newly developed method, KLAS. Additionally, we evaluated all methods on two cancer data sets that comprised RT-PCR validated results.ResultsOur studies indicated ARH as the most robust methods when integrating the results over all scenarios and data sets. Nevertheless, special cases or requirements favor other methods. While FIRMA was highly sensitive according to experimental data, SplicingCompass, MIDAS and ANOSVA showed high specificity throughout the scenarios. On experimental data ARH, FIRMA, MIDAS, and KLAS performed best.ConclusionsEach method shows different characteristics regarding sensitivity, specificity, interference to certain data settings and robustness over multiple data sets. While some methods can be considered as generally good choices over all data sets and scenarios, other methods show heterogeneous prediction quality on the different data sets. The adequate method has to be chosen carefully and with a defined study aim in mind.
| S-EPMC4391533 | biostudies-literature
Project description:Fabry disease is a congenital lysosomal storage disease, and most of these cases develop organ damage in middle age. There are some promising therapeutic options for this disorder, which can stabilize the progression of the disease. However, a long delay in diagnosis prevents early intervention, resulting in treatment failure. Because Fabry disease is a rare disease, it is not well recognized and disease specific screening tests are rarely performed. Hence, a novel approach to for detecting patients with a widely practiced clinical test is crucial for the early detection of the disease. Recently, decision support systems based on artificial intelligence (AI) have been developed in many clinical fields. However, the construction of these models requires datasets from a large number of samples; this aspect is one of the main obstacles in AI-based approaches for rare diseases. In this study, with a novel image amplification method to construct the dataset for AI-model training, we built the deep neural-network model to detect Fabry cases from their urine samples. Sensitivity, specificity, and the AUC of the models on validation dataset were 0.902 (95% CI, 0.900-0.903), 0.977 (0.950-0.980), and 0.968 (0.964-0.972), respectively. This model could also extract disease-specific findings that are interpretable with human recognition. These results indicate that we can apply novel AI models for rare diseases based on this image amplification method we developed. We expect this approach could contribute to the diagnosis of Fabry disease.SynopsisThis is the first reported AI-based decision support system to detect undiagnosed Fabry cases, and our new image amplification method will contribute to the AI models for other rare disorders.
| S-EPMC9523392 | biostudies-literature
Project description:In order to characterise new bacteriocins produced by Streptococcus mutans we perform a complete bioinformatic analyses by scanning the genome sequence of strains UA159 and NN2025. By searching in the adjacent genomic context of the two-component signal transduction system we predicted the existence of many putative new bacteriocins' maturation pathways and some of them were only exclusive to a group of Streptococcus. Computational genomic and proteomic analysis combined to predictive functionnal analysis represent an alternative way for rapid identification of new putative bacteriocins as well as new potential antimicrobial drugs compared to the more traditional methods of drugs discovery using antagonism tests.
| S-EPMC3162582 | biostudies-literature