scholarly journals GeneHummus: A pipeline to define gene families and their expression in legumes and beyond

2018 ◽  
Author(s):  
Jose V. Die ◽  
Moamen Mahmoud Elmassry ◽  
Kimberly Hathaway LeBlanc ◽  
Olaitan I. Awe ◽  
Allissa Dillman ◽  
...  
Keyword(s):  
Large Scale ◽  
Rapid Development ◽  
High Specificity ◽  
Gene Families ◽  
Model Systems ◽  
Auxin Receptor ◽  
Plant Gene ◽  
Sequencing Technologies ◽  
Specificity And Sensitivity ◽  
The Impact

AbstractDuring the last decade, plant biotechnological laboratories have sparked a monumental revolution with the rapid development of next sequencing technologies at affordable prices. Soon, these sequencing technologies and assembling of whole genomes will extend beyond the plant computational biologists and become commonplace within the plant biology disciplines. The current availability of large-scale genomic resources for non-traditional plant model systems (the so-called ‘orphan crops’) is enabling the construction of high-density integrated physical and genetic linkage maps with potential applications in plant breeding. The newly available fully sequenced plant genomes represent an incredible opportunity for comparative analyses that may reveal new aspects of genome biology and evolution. Analysis of the expansion and evolution of gene families across species is a common approach to infer biological functions. To date, the extent and role of gene families in plants has only been partially addressed and many gene families remain to be investigated. Manual identification of gene families is highly time-consuming and laborious, requiring an iterative process of manual and computational analysis to identify members of a given family, typically combining numerous BLAST searches and manually cleaning data. Due to the increasing abundance of genome sequences and the agronomical interest in plant gene families, the field needs a clear, automated annotation tool. Here, we present the GeneHummus pipeline, a step-by-step R-based pipeline for the identification, characterization and expression analysis of plant gene families. The impact of this pipeline comes from a reduction in hands-on annotation time combined with high specificity and sensitivity in extracting only proteins from the RefSeq database and providing the conserved domain architectures based on SPARCLE. As a case study we focused on the auxin receptor factors gene (ARF) family in Cicer arietinum (chickpea) and other legumes. We anticipate that our pipeline should be suitable for any plant gene family, and likely other gene families, vastly improving the speed and ease of genomic data processing.

scholarly journals OncoThreads: Visualization of Large Scale Longitudinal Cancer Molecular Data

2021 ◽  
Author(s):  
Theresa A Harbig ◽  
Sabrina Nusrat ◽  
Tali Mazor ◽  
Qianwen Wang ◽  
Alexander Thomson ◽  
...  
Keyword(s):  
Longitudinal Data ◽  
Large Scale ◽  
Cancer Genomics ◽  
Temporal Patterns ◽  
Molecular Data ◽  
Liquid Biopsies ◽  
Sequencing Technologies ◽  
Molecular Features ◽  
Wide Range ◽  
The Impact

Molecular profiling of patient tumors and liquid biopsies over time with next-generation sequencing technologies and new immuno-profile assays are becoming part of standard research and clinical practice. With the wealth of new longitudinal data, there is a critical need for visualizations for cancer researchers to explore and interpret temporal patterns not just in a single patient but across cohorts. To address this need we developed OncoThreads, a tool for the visualization of longitudinal clinical and cancer genomics and other molecular data in patient cohorts. The tool visualizes patient cohorts as temporal heatmaps and Sankey diagrams that support the interactive exploration and ranking of a wide range of clinical and molecular features. This allows analysts to discover temporal patterns in longitudinal data, such as the impact of mutations on response to a treatment, e.g. emergence of resistant clones. We demonstrate the functionality of OncoThreads using a cohort of 23 glioma patients sampled at 2-4 timepoints. OncoThreads is freely available at http://oncothreads.gehlenborglab.org and implemented in Javascript using the cBioPortal web API as a backend.

Detection of sand deposition in pipeline using percussion, voice recognition, and support vector machine

2020 ◽  
Vol 19 (6) ◽  
pp. 2075-2090 ◽  
Author(s):  
Hao Cheng ◽  
Furui Wang ◽  
Linsheng Huo ◽  
Gangbing Song
Keyword(s):  
Support Vector Machine ◽  
Large Scale ◽  
Rapid Development ◽  
Voice Recognition ◽  
Support Vector ◽  
Machine Model ◽  
Frequency Scale ◽  
Removal Time ◽  
The Impact ◽  
Non Destructive

Deposits prevention and removal in pipeline has great importance to ensure pipeline operation. Selecting a suitable removal time based on the composition and mass of the deposits not only reduces cost but also improves efficiency. In this article, we develop a new non-destructive approach using the percussion method and voice recognition with support vector machine to detect the sandy deposits in the steel pipeline. Particularly, as the mass of sandy deposits in the pipeline changes, the impact-induced sound signals will be different. A commonly used voice recognition feature, Mel-Frequency Cepstrum Coefficients, which represent the result of a cosine transform of the real logarithm of the short-term energy spectrum on a Mel-frequency scale, is adopted in this research and Mel-Frequency Cepstrum Coefficients are extracted from the obtained sound signals. A support vector machine model was employed to identify the sandy deposits with different mass values by classifying energy summation and Mel-Frequency Cepstrum Coefficients. In addition, the classification accuracies of energy summation and Mel-Frequency Cepstrum Coefficients are compared. The experimental results demonstrated that Mel-Frequency Cepstrum Coefficients perform better in pipeline deposits detection and have great potential in acoustic recognition for structural health monitoring. In addition, the proposed Mel-Frequency Cepstrum Coefficients–based pipeline deposits monitoring model can estimate the deposits in the pipeline with high accuracy. Moreover, compared with current non-destructive deposits detection approaches, the percussion method is easy to implement. With the rapid development of artificial intelligence and acoustic recognition, the proposed method can realize higher accuracy and higher speed in the detection of pipeline deposits, and has great application potential in the future. In addition, the proposed percussion method can enable robotic-based inspection for large-scale implementation.

scholarly journals SARS-CoV-2 S1 and N-based serological assays reveal rapid seroconversion and induction of specific antibody response in COVID-19 patients

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Abdullah Algaissi ◽  
Mohamed A. Alfaleh ◽  
Sharif Hala ◽  
Turki S. Abujamel ◽  
Sawsan S. Alamri ◽  
...  
Keyword(s):  
Antibody Response ◽  
Specific Antibody ◽  
Large Scale ◽  
Disease Onset ◽  
High Specificity ◽  
Epidemiological Studies ◽  
Cross Reactivity ◽  
Enzyme Linked Immunosorbent Assay ◽  
Specificity And Sensitivity ◽  
Human Coronaviruses

Abstract As the Coronavirus Disease 2019 (COVID-19), which is caused by the novel SARS-CoV-2, continues to spread rapidly around the world, there is a need for well validated serological assays that allow the detection of viral specific antibody responses in COVID-19 patients or recovered individuals. In this study, we established and used multiple indirect Enzyme Linked Immunosorbent Assay (ELISA)-based serological assays to study the antibody response in COVID-19 patients. In order to validate the assays we determined the cut off values, sensitivity and specificity of the assays using sera collected from pre-pandemic healthy controls, COVID-19 patients at different time points after disease-onset, and seropositive sera to other human coronaviruses (CoVs). The developed SARS-CoV-2 S1 subunit of the spike glycoprotein and nucleocapsid (N)-based ELISAs not only showed high specificity and sensitivity but also did not show any cross-reactivity with other CoVs. We also show that all RT-PCR confirmed COVID-19 patients tested in our study developed both virus specific IgM and IgG antibodies as early as week one after disease onset. Our data also suggest that the inclusion of both S1 and N in serological testing would capture as many potential SARS-CoV-2 positive cases as possible than using any of them alone. This is specifically important for tracing contacts and cases and conducting large-scale epidemiological studies to understand the true extent of virus spread in populations.

scholarly journals DNA Sequence Signatures for Rapid Detection of Six Target Bacterial Pathogens Using PCR Assays

2015 ◽  
Vol 8 ◽  
pp. MBI.S29736 ◽  
Author(s):  
Kenjiro Nagamine ◽  
Guo-Chiuan Hung ◽  
Bingjie Li ◽  
Shyh-Ching Lo
Keyword(s):  
Safety Concern ◽  
Rapid Development ◽  
High Sensitivity ◽  
High Specificity ◽  
Clostridium Tetani ◽  
Specificity And Sensitivity ◽  
Wide Range ◽  
Pcr Assays ◽  
Primer Sets ◽  
Species Specific

Using Streptococcus pyogenes as a model, we previously established a stepwise computational workflow to effectively identify species-specific DNA signatures that could be used as PCR primer sets to detect target bacteria with high specificity and sensitivity. In this study, we extended the workflow for the rapid development of PCR assays targeting Enterococcus faecalis, Enterococcus faecium, Clostridium perfringens, Clostridium difficile, Clostridium tetani, and Staphylococcus aureus, which are of safety concern for human tissue intended for transplantation. Twenty-one primer sets that had sensitivity of detecting 5–50 fg DNA from target bacteria with high specificity were selected. These selected primer sets can be used in a PCR array for detecting target bacteria with high sensitivity and specificity. The workflow could be widely applicable for the rapid development of PCR-based assays for a wide range of target bacteria, including those of biothreat agents.

scholarly journals SARS-CoV-2 S1 and N-Based Serological Assays Reveal Rapid Seroconversion and Induction of Specific Antibody Response in COVID-19 Patients

2020 ◽  
Author(s):  
Abdullah Algaissi ◽  
Mohamed A. Alfaleh ◽  
Sherif Hala ◽  
Turki S. Abujamel ◽  
Sawsan S. Alamri ◽  
...  
Keyword(s):  
Antibody Response ◽  
Specific Antibody ◽  
Large Scale ◽  
Disease Onset ◽  
High Specificity ◽  
Epidemiological Studies ◽  
Cross Reactivity ◽  
Enzyme Linked Immunosorbent Assay ◽  
Specificity And Sensitivity ◽  
Human Coronaviruses

As the coronavirus disease 2019 (COVID-19), which is caused by the novel SARS-CoV-2, continues to spread rapidly around the world, there is a need for well validated serological assays that allow the detection of viral specific antibody responses in COVID-19 patients or recovered individuals. In this study, we established and used multiple indirect Enzyme Linked Immunosorbent Assay (ELISA)-based serological assays to study the antibody response in COVID-19 patients. In order to validate the assays we determined the cut off values, sensitivity and specificity of the assays using sera collected from pre-pandemic healthy controls, COVID-19 patients at different time points after disease-onset, and seropositive sera to other human coronaviruses. The developed SARS-CoV-2 S1 subunit of the spike glycoprotein and nucleocapsid (N)-based ELISAs not only showed high specificity and sensitivity but also did not show any cross-reactivity with other CoVs. We also show that all RT-PCR confirmed COVID-19 patients tested in our study developed both virus specific IgM and IgG antibodies as early as week one after disease onset. Our data also suggest that the inclusion of both S1 and N in serological testing would capture as many potential SARS-CoV-2 positive cases as possible than using any of them alone. This is specifically important for tracing contacts and cases and conducting large-scale epidemiological studies to understand the true extent of virus spread in populations.

scholarly journals Multiple Indirect ELISAs for Serological Detection of SARS-CoV-2 Antibodies

2020 ◽  
Author(s):  
Abdullah Algaissi ◽  
Mohamed A. Alfaleh ◽  
Sherif Hala ◽  
Turki S. Abujamel ◽  
Sawsan S. Alamari ◽  
...  
Keyword(s):  
Antibody Response ◽  
Large Scale ◽  
Disease Onset ◽  
High Specificity ◽  
Epidemiological Studies ◽  
Cross Reactivity ◽  
Enzyme Linked Immunosorbent Assay ◽  
Serological Tests ◽  
Specificity And Sensitivity ◽  
Novel Coronavirus

As the coronavirus disease 2019 (COVID-19), which is caused by the novel coronavirus SARS-CoV-2, continues to spread rapidly around the world, there is an urgent need for validated serological assays to evaluate viral specific antibody responses in COVID-19 patients or recovered individuals. In this study, we established and used indirect Enzyme Linked Immunosorbent Assay (ELISA)-based serological tests to study the antibody response in COVID-19 patients. In order to validate the assays, we determined the cut-off values, sensitivity and specificity of the developed assays using sera collected from COVID-19 patients in Saudi Arabia at different time points after disease onset, as well as sera that are seropositive to other human CoVs; namely MERS-CoV, hCoV-OC43, hCoV-NL63, hCoV-229E, and hCoV-HKU1. The SARS-CoV-2 S1 subunit of the spike glycoprotein and nucleocapsid (N) ELISAs that we developed here not only showed high specificity and sensitivity, but also did not show any cross-reactivity with other CoVs. We also showed that all RT-PCR confirmed COVID-19 patients included in our study developed both virus specific IgM and IgG as early as one week after the onset of disease. The availability of these validated assays will enable us to determine the nature and duration of the antibody response mounted in response to SARS-CoV-2 infection. It will also allow conducting large-scale epidemiological studies to determine evidence of previous exposure to the virus and assess the true extent of virus spread within communities.

The Role of Social Networking in Civilizational Development

2013 ◽  
pp. 1193-1217
Author(s):  
Andrew Targowski
Keyword(s):  
Social Networks ◽  
Social Networking ◽  
21St Century ◽  
Large Scale ◽  
Rapid Development ◽  
World Government ◽  
Electronic Culture ◽  
The Impact ◽  
Further Development

This study defines the nature, scope, pace, and consequences of the rapid development of social networking in the 21st century. The impact of INFOCO systems upon civilizational development is investigated and predicted for the future. Such concepts as Global Virtual Society, Global Virtual Nation, Virtual Nation, Virtual Users, National Virtual Citizens, and Global Virtual Citizens are defined. Their electronic culture is defined, too. Finally some recommendations for further research are provided. In particular, the question of whether the concept of one world government is good or bad for mankind should be answered soon, in order to properly steer the further development of large-scale social networks.

Impact of broadband power line communication on high frequency equipment using impact analysis

Frequenz ◽  
2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Yuzhe Zhou
Keyword(s):  
Communication Technology ◽  
Communication System ◽  
High Frequency ◽  
Large Scale ◽  
Impact Analysis ◽  
Rapid Development ◽  
Power Line ◽  
Power Line Communication ◽  
The Impact ◽  
Carrier Communication

Abstract With the rapid development of broadband carrier communication technology, the power line communication market is growing. However, the frequency band of power line communication overlaps with other radio services, mainly the High Frequency (HF) radio services. In addition, power line communication may have electromagnetic leakage in the open air. Large-scale power line communication system will give a much greater interference to some critical HF radio services. In this paper, the standards and researches relative to the power line communication system are reviewed. Based on existing studies, impact analysis which includes the impact probability and severity of the power line communication system on HF equipment is proposed. In addition, explicit explanations are provided. The proposed impact analysis methods are applied to simulations and evaluations. Numerical results demonstrate that a large-scale power line communication system will cause additional ambient noise, which affects the performance and reliability of HF equipment with a high probability.

scholarly journals A comprehensive review and model of putative prodromal features of bipolar affective disorder

2010 ◽  
Vol 41 (8) ◽  
pp. 1567-1577 ◽  
Author(s):  
O. D. Howes ◽  
S. Lim ◽  
G. Theologos ◽  
A. R. Yung ◽  
G. M. Goodwin ◽  
...  
Keyword(s):  
Large Scale ◽  
Bipolar Affective Disorder ◽  
High Specificity ◽  
Current Evidence ◽  
Inclusion Criteria ◽  
Comprehensive Review ◽  
Specificity And Sensitivity ◽  
Comprehensive Search ◽  
Characteristic Features ◽  
Key Questions

BackgroundIdentifying prodromal features that predate the onset of bipolar disorder (BD) may enable the prevention of BD and aid early intervention. This review addresses two key questions: Is there a bipolar prodrome? And, if there is, what are its characteristic features?MethodA comprehensive search of databases (PubMed, Medline, EMBASE and PsycINFO) supplemented by hand searches was used to identify studies of symptoms preceding the onset of BD.ResultsFifty-nine studies were identified, of which 14 met inclusion criteria. Symptoms can predate the onset of BD by months to years and can be categorized as attenuated forms of BD symptoms, general symptoms common to a range of mental disorders, and personality traits, particularly cyclothymia. Two studies provided sufficient data to enable sensitivity and specificity to be calculated. Specificity of several of the features was high (>90%) but sensitivity was generally low (all <60%). We propose a model based on the findings in the studies reviewed to illustrate the potential trajectory to BD and the points at which it may be possible to intervene.ConclusionsClinical features preceding the onset of BD can be identified. However, conclusions about whether there is a distinct prodrome to BD are restricted by the limitations of current evidence. The high specificity of some features suggests they may be useful in clinical practice. Large-scale longitudinal studies are needed to validate these features and characterize their specificity and sensitivity in independent samples.

scholarly journals VPsero: Rapid Serotyping of Vibrio parahaemolyticus Using Serogroup-Specific Genes Based on Whole-Genome Sequencing Data

2021 ◽  
Vol 12 ◽  
Author(s):  
Shengzhe Bian ◽  
Yangyang Jia ◽  
Qiuyao Zhan ◽  
Nai-Kei Wong ◽  
Qinghua Hu ◽  
...  
Keyword(s):  
Vibrio Parahaemolyticus ◽  
High Throughput Sequencing ◽  
Capsular Polysaccharide ◽  
High Specificity ◽  
Gene Clusters ◽  
Whole Genome Sequencing Data ◽  
Sequencing Data ◽  
Sequencing Technologies ◽  
Marine Habitats ◽  
Specificity And Sensitivity

Vibrio parahaemolyticus has emerged as a significant enteropathogen in human and marine habitats worldwide, notably in regions where aquaculture products constitute a major nutritional source. It is a growing cause of diseases including gastroenteritis, wound infections, and septicemia. Serotyping assays use commercially available antisera to identify V. parahaemolyticus strains, but this approach is limited by high costs, complicated procedures, cross-immunoreactivity, and often subjective interpretation. By leveraging high-throughput sequencing technologies, we developed an in silico method based on comparison of gene clusters for lipopolysaccharide (LPSgc) and capsular polysaccharide (CPSgc) by firstly using the unique-gene strategy. The algorithm, VPsero, which exploits serogroup-specific genes as markers, covers 43 K and all 12 O serogroups in serotyping assays. VPsero is capable of predicting serotypes from assembled draft genomes, outputting LPSgc/CPSgc sequences, and recognizing possible novel serogroups or populations. Our tool displays high specificity and sensitivity in prediction toward V. parahaemolyticus strains, with an average sensitivity in serogroup prediction of 0.910 for O and 0.961 for K serogroups and a corresponding average specificity of 0.990 for O and 0.998 for K serogroups.

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