scholarly journals Integrated modeling of peptide digestion and detection for the prediction of proteotypic peptides in targeted proteomics

2018 ◽  
Author(s):  
Zhiqiang Gao ◽  
Cheng Chang ◽  
Yunping Zhu ◽  
Yan Fu
Keyword(s):  
Shotgun Proteomics ◽  
Mass Spectrometry Data ◽  
Supplementary Information ◽  
Targeted Proteomics ◽  
Proteolytic Digestion ◽  
Peptide Detection ◽  
Close Relationship ◽  
Proteotypic Peptide ◽  
Peptide Prediction ◽  
Selection Of

ABSTRACTMotivationThe selection of proteotypic peptides, i.e., detectable unique representatives of proteins of interest, is a key step in targeted shotgun proteomics. To date, much effort has been made to predict proteotypic peptides in the absence of mass spectrometry data. However, the performance of existing tools is still unsatisfactory. One crucial reason is their neglect of the close relationship between protein proteolytic digestion and peptide detection.ResultsWe present an algorithm (named AP3) that firstly considers peptide digestion probability as a feature for proteotypic peptide prediction and demonstrated peptide digestion probability is the most important feature for accurate prediction of proteotypic peptides. AP3 showed higher accuracy than existing tools and accurately predicted the proteotypic peptides for a targeted proteomics assay, showing its great potential for assisting the design of targeted proteomics experiments.Availability and ImplementationFreely available at http://fugroup.amss.ac.cn/software/AP3/[email protected] or [email protected] InformationSupplementary data are available at Bioinformatics online.

Tutoring Process in Emotionally Intelligent Tutoring Systems

2016 ◽  
pp. 1094-1110 ◽  
Author(s):  
Sintija Petrovica
Keyword(s):  
Intelligent Tutoring Systems ◽  
Emotional State ◽  
Intelligent Tutoring ◽  
Point Of View ◽  
Research Groups ◽  
Tutoring Systems ◽  
Knowledge States ◽  
Close Relationship ◽  
Emotionally Intelligent ◽  
Selection Of

Research has shown that emotions can influence learning in situations when students have to analyze, reason, make conclusions, apply acquired knowledge, answer questions, solve tasks, and provide explanations. A number of research groups inspired by the close relationship between emotions and learning have been working to develop emotionally intelligent tutoring systems. Despite the research carried out so far, a problem how to adapt tutoring not only to a student's knowledge state but also to his/her emotional state has been disregarded. The paper aims to examine to what extent the tutoring process and tutoring strategies are adapted to students' emotional and knowledge states in these systems. It also presents a study on how to influence student's emotions looking from the pedagogical point of view and provides general guidelines for selection of tutoring strategies to influence and regulate student's emotions.

scholarly journals XMAn v2—a database of Homo sapiens mutated peptides

2019 ◽  
Author(s):  
Marcela Aguilera Flores ◽  
Iulia M Lazar
Keyword(s):  
Mass Spectrometry ◽  
Tandem Mass Spectrometry ◽  
Homo Sapiens ◽  
Amino Acid Sequences ◽  
Mass Spectrometry Data ◽  
Supplementary Information ◽  
Tandem Mass ◽  
Mass Spectrometry Detection ◽  
Nonsense Mutations ◽  
Tandem Mass Spectrometry Data

Abstract Summary The ‘Unknown Mutation Analysis (XMAn)’ database is a compilation of Homo sapiens mutated peptides in FASTA format, that was constructed for facilitating the identification of protein sequence alterations by tandem mass spectrometry detection. The database comprises 2 539 031 non-redundant mutated entries from 17 599 proteins, of which 2 377 103 are missense and 161 928 are nonsense mutations. It can be used in conjunction with search engines that seek the identification of peptide amino acid sequences by matching experimental tandem mass spectrometry data to theoretical sequences from a database. Availability and implementation XMAn v2 can be accessed from github.com/lazarlab/XMAnv2. Supplementary information Supplementary data are available at Bioinformatics online.

Tutoring Process in Emotionally Intelligent Tutoring Systems

2014 ◽  
Vol 4 (1) ◽  
pp. 72-85 ◽  
Author(s):  
Sintija Petrovica
Keyword(s):  
Intelligent Tutoring Systems ◽  
Emotional State ◽  
Intelligent Tutoring ◽  
Point Of View ◽  
Research Groups ◽  
Tutoring Systems ◽  
Knowledge States ◽  
Close Relationship ◽  
Emotionally Intelligent ◽  
Selection Of

Research has shown that emotions can influence learning in situations when students have to analyze, reason, make conclusions, apply acquired knowledge, answer questions, solve tasks, and provide explanations. A number of research groups inspired by the close relationship between emotions and learning have been working to develop emotionally intelligent tutoring systems. Despite the research carried out so far, a problem how to adapt tutoring not only to a student's knowledge state but also to his/her emotional state has been disregarded. The paper aims to examine to what extent the tutoring process and tutoring strategies are adapted to students' emotional and knowledge states in these systems. It also presents a study on how to influence student's emotions looking from the pedagogical point of view and provides general guidelines for selection of tutoring strategies to influence and regulate student's emotions.

QuanTest2: benchmarking multiple sequence alignments using secondary structure prediction

2019 ◽  
Author(s):  
Fabian Sievers ◽  
Desmond G Higgins
Keyword(s):  
Secondary Structure ◽  
Structure Prediction ◽  
Secondary Structure Prediction ◽  
Reference Sequence ◽  
Supplementary Information ◽  
Sequence Alignments ◽  
Multiple Sequence ◽  
Multiple Sequence Alignments ◽  
Reference Sequences ◽  
Selection Of

Abstract Motivation Secondary structure prediction accuracy (SSPA) in the QuanTest benchmark can be used to measure accuracy of a multiple sequence alignment. SSPA correlates well with the sum-of-pairs score, if the results are averaged over many alignments but not on an alignment-by-alignment basis. This is due to a sub-optimal selection of reference and non-reference sequences in QuanTest. Results We develop an improved strategy for selecting reference and non-reference sequences for a new benchmark, QuanTest2. In QuanTest2, SSPA and SP correlate better on an alignment-by-alignment basis than in QuanTest. Guide-trees for QuanTest2 are more balanced with respect to reference sequences than in QuanTest. QuanTest2 scores correlate well with other well-established benchmarks. Availability and implementation QuanTest2 is available at http://bioinf.ucd.ie/quantest2.tar, comprises of reference and non-reference sequence sets and a scoring script. Supplementary information Supplementary data are available at Bioinformatics online

scholarly journals Genetic Divergence Studies in Tomato Genotypes Grown under Low-Cost Polyhouse Conditions

2021 ◽  
pp. 309-313
Author(s):  
Rakesh Kumar ◽  
Anil Bhushan ◽  
R. K. Samnotra ◽  
Tuhina Dey ◽  
Manmohan Sharma ◽  
...  
Keyword(s):  
Fruit Set ◽  
Low Cost ◽  
Fruit Weight ◽  
Solid Content ◽  
Soluble Solid Content ◽  
Close Relationship ◽  
Cluster Distance ◽  
Soluble Solid ◽  
Tomato Genotypes ◽  
Selection Of

Assessment of genetic diversity was made for sixteen yields and yield contributing traits in twenty-one tomato genotypes using D2 statistics. These genotypes were grouped into five clusters by the use of the Tocher method. Cluster I was the most significant, comprising 13 genotypes (Pusa Ruby, CLN2123A1 Red, PKM-1, IIHR-2042, Marglobe, EC 163605, Hawaii 7998, Palam Pink, EC 521038, Punjab Rakthak, EC 163383, Arka Abha and IIVR BT-10) followed by Cluster II  with 5 genotypes (EC 163611, Punjab Sartaj, EC 160885, Punjab Barkha Bahar  and Roma). Other Clusters (II, IV and V) were solitary ones (EC 249515, Kashi Chayan, DVRT-2). Cluster II recorded a maximum intra cluster distance of 3521.73 followed by cluster I (2796.45), whereas, cluster II, IV and V had zero intra cluster distance. The inter cluster D2 value also ranged widely, with a minimum value of 4082.34 between cluster I and IV, indicating a close relationship among the genotypes included. The maximum inter cluster D2 value (23102.20) between cluster II and V indicates high diversity among the genotypes in the clusters. Hence,   maximum contribution towards divergence was observed by average fruit weight (14%) followed by fruit set percentage (12%), number of flowers per cluster (8%), fruit yield per plant (7%), number of fruits per truss (6 %) and total soluble solid content (6 %). Hence, due importance could be given to the selection of genotypes for further improvement based on these traits.

scholarly journals Shotgun proteomics of SARS-CoV-2 infected cells and its application to the optimisation of whole viral particle antigen production for vaccines

2020 ◽  
Author(s):  
Lucia Grenga ◽  
Fabrice Gallais ◽  
Olivier Pible ◽  
Jean-Charles Gaillard ◽  
Duarte Gouveia ◽  
...  
Keyword(s):  
Drug Targets ◽  
Shotgun Proteomics ◽  
Mass Spectrometry Data ◽  
Effective Vaccine ◽  
Development Activity ◽  
Technology Platforms ◽  
Viral Particles ◽  
Infected Cells ◽  
The Right ◽  
Cell Proteome

AbstractSevere acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) has resulted in a pandemic and continues to spread quickly around the globe. Currently, no effective vaccine is available to prevent COVID-19 and an intense global development activity is in progress. In this context, the different technology platforms face several challenges resulting from the involvement of a new virus still not fully characterised. Finding of the right conditions for virus amplification for the development of vaccines based on inactivated or attenuated whole viral particles is among them. Here, we describe the establishment of a workflow based on shotgun tandem mass spectrometry data to guide the optimisation of the conditions for viral amplification. In parallel, we analysed the dynamic of the host cell proteome following SARS-CoV-2 infection providing a global overview of biological processes modulated by the virus and that could be further explored to identify drug targets to address the pandemic.

scholarly journals Faktor-Faktor Yang Berhubungan Dengan Pemilihan Tempat Pertolongan Persalinan Pada Ibu Bersalin

2020 ◽  
Vol 8 (1) ◽  
pp. 69-77
Author(s):  
Pawiliyah Pawiliyah ◽  
Epi Susanti
Keyword(s):  
Public Health ◽  
Health Center ◽  
Sampling Technique ◽  
Chi Square ◽  
Cross Sectional ◽  
Place Of Delivery ◽  
Public Health Center ◽  
Close Relationship ◽  
The Right ◽  
Selection Of

Labor events are physiological events whose processes can run smoothly and safely if the helper in labor can monitor labor to detect complications early. The purpose  of this study was to look at the factors related to the selection of Birth assistance places for labor mothers in Lingkar Timur Public Health Center of Bengkulu City. This study used descriptive correlational using Cross Sectional design. The sample in this study was taken by using purposive sampling technique that is taking as many as 78 samples. Data were tested using the chi-square test. To determine the closeness of the relationship, a contingency coefficient (C) test has been used. There is a relationship between age with the selection of birth assistance places in labor mothers in the Lingkar Timur Public Health Center in Bengkulu City with p=0,000 0,05 a close relationship category. There is a relationship of parity with the selection of birth places in delivery mothers in the Lingkar Timur Public Health Center Work Area with p=0,003 0,05 medium relationship category. There is an educational relationship with the selection of birth places in delivery mothers in Lingkar Timur Public Health Center with p=0,000 0,05 in the category of close relationships. There is a relationship between the complication of labor and the choice of place of delivery assistance for women giving birth in Lingkar Timur Public Health Center of Bengkulu City with p=0,000 0,05 a close relationship category. Based on the results of the study recommends the importance of health promotion such as Antenatal care, conducting pregnant mothers class programs, so that pregnant women get information and knowledge about their pregnancy conditions and can choose the right place of delivery according to their pregnancy conditions.

scholarly journals Combining high resolution and exact calibration to boost statistical power: A well-calibrated score function for high-resolution MS2 data

2018 ◽  
Author(s):  
Andy Lin ◽  
J. Jeffry Howbert ◽  
William Stafford Noble
Keyword(s):  
Mass Spectrometry ◽  
High Resolution ◽  
Statistical Power ◽  
State Of The Art ◽  
Score Function ◽  
Shotgun Proteomics ◽  
Database Search ◽  
Mass Spectrometry Data ◽  
P Value ◽  
Score Functions

AbstractTo achieve accurate assignment of peptide sequences to observed fragmentation spectra, a shotgun proteomics database search tool must make good use of the very high resolution information produced by state-of-the-art mass spectrometers. However, making use of this information while also ensuring that the search engine’s scores are well calibrated—i.e., that the score assigned to one spectrum can be meaningfully compared to the score assigned to a different spectrum—has proven to be challenging. Here, we describe a database search score function, the “residue evidence” (res-ev) score, that achieves both of these goals simultaneously. We also demonstrate how to combine calibrated res-ev scores with calibrated XCorr scores to produce a “combined p-value” score function. We provide a benchmark consisting of four mass spectrometry data sets, which we use to compare the combined p-value to the score functions used by several existing search engines. Our results suggest that the combined p-value achieves state-of-the-art performance, generally outperforming MS Amanda and Morpheus and performing comparably to MS-GF+. The res-ev and combined p-value score functions are freely available as part of the Tide search engine in the Crux mass spectrometry toolkit (http://crux.ms).

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