MiCId GUI: The Graphical User Interface for MiCId, a Fast Microorganism Classification and Identification Workflow with Accurate Statistics and High Recall.

Although many user-friendly workflows exist for identifications of peptides and proteins in mass-spectrometry-based proteomics, there is a need of easy to use, fast, and accurate workflows for identifications of microorganisms, antimicrobial resistant proteins, and biomass estimation. Identification of microorganisms is a computationally demanding task that requires querying thousands of MS/MS spectra in a database containing thousands to tens of thousands of microorganisms. Existing software can't handle such a task in a time efficient manner, taking hours to process a single MS/MS experiment. Another paramount factor to consider is the necessity of accurate statistical significance to properly control the proportion of false discoveries among the identified microorganisms, and antimicrobial-resistant proteins, and to provide robust biomass estimation. Recently, we have developed Microorganism Classification and Identification (MiCId) workflow that assigns accurate statistical significance to identified microorganisms, antimicrobial-resistant proteins, and biomass estimation. MiCId's workflow is also computationally efficient, taking about 6-17 minutes to process a tandem mass-spectrometry (MS/MS) experiment using computer resources that are available in most laptop and desktop computers, making it a portable workflow. To make data analysis accessible to a broader range of users, beyond users familiar with the Linux environment, we have developed a graphical user interface (GUI) for MiCId's workflow. The GUI brings to users all the functionality of MiCId's workflow in a friendly interface along with tools for data analysis, visualization, and to export results.

A graphical user interface for RAId, a knowledge integrated proteomics analysis suite with accurate statistics.

OBJECTIVE: RAId is a software package that has been actively developed for the past 10 years for computationally and visually analyzing MS/MS data. Founded on rigorous statistical methods, RAId's core program computes accurate E-values for peptides and proteins identified during database searches. Making this robust tool readily accessible for the proteomics community by developing a graphical user interface (GUI) is our main goal here. RESULTS: We have constructed a graphical user interface to facilitate the use of RAId on users' local machines. Written in Java, RAId_GUI not only makes easy executions of RAId but also provides tools for data/spectra visualization, MS-product analysis, molecular isotopic distribution analysis, and graphing the retrieval versus the proportion of false discoveries. The results viewer displays and allows the users to download the analyses results. Both the knowledge-integrated organismal databases and the code package (containing source code, the graphical user interface, and a user manual) are available for download at https://www.ncbi.nlm.nih.gov/CBBresearch/Yu/downloads/raid.html .

[Periodontal health status in patients with diabetes mellitus type 1, from 18 to 30 years-old, from Santiago de Chile]. / Estado de salud periodontal en diabéticos tipo 1, de 18 a 30 años de edad, de Santiago de Chile.

BACKGROUND: The prevalence of periodontal diseases, gingivitis and periodontitis, is higher in diabetic patients and can have severe functional and esthetic consequences early in their lives. AIM: To evaluate the prevalence of periodontal disease in type 1 diabetics, aged between 18 and 30 years old, living in Santiago de Chile. SUBJECTS AND METHODS: One hundred male and female type 1 diabetics were examined. Glycated hemoglobin A1c, microalbuminuria, and fundoscopy were assessed in a sample of 52 subjects, separated in two groups according to the presence of periodontal disease. RESULTS: The prevalence of gingivitis was 22%, periodontitis 41%. Only 37% of subjects were free of periodontal disease. When compared with patients without periodontal disease, in the group of patients with the disease there was a higher proportion of subjects with diabetes lasting more than 10 years (28 and 55% respectively) and a higher proportion of patients with chronic complications of diabetes (42 and 58% respectively). CONCLUSIONS: A high prevalence of periodontal diseases was observed in this sample of diabetic patients. A long history of diabetes and the presence of chronic complications were risk factors for these diseases in the analyzed sample.