scholarly journals mPies: a novel metaproteomics tool for the creation of relevant protein databases and automatized protein annotation

2019 ◽  
Vol 14 (1) ◽  
Author(s):  
Johannes Werner ◽  
Augustin Géron ◽  
Jules Kerssemakers ◽  
Sabine Matallana-Surget
Keyword(s):  
Input Data ◽  
Rapid Development ◽  
Protein Annotation ◽  
Group Level ◽  
Protein Databases ◽  
Protein Inference ◽  
Protein Group ◽  
The Creation ◽  
Public Repositories ◽  
First Time

Abstract Metaproteomics allows to decipher the structure and functionality of microbial communities. Despite its rapid development, crucial steps such as the creation of standardized protein search databases and reliable protein annotation remain challenging. To overcome those critical steps, we developed a new program named mPies (metaProteomics in environmental sciences). mPies allows the creation of protein databases derived from assembled or unassembled metagenomes, and/or public repositories based on taxon IDs, gene or protein names. For the first time, mPies facilitates the automatization of reliable taxonomic and functional consensus annotations at the protein group level, minimizing the well-known protein inference issue, which is commonly encountered in metaproteomics. mPies’ workflow is highly customizable with regards to input data, workflow steps, and parameter adjustment. mPies is implemented in Python 3/Snakemake and freely available on GitHub: https://github.com/johanneswerner/mPies/. Reviewer This article was reviewed by Dr. Wilson Wen Bin Goh.

scholarly journals mPies: a novel metaproteomics tool for the creation of relevant protein databases and automatized protein annotation

2019 ◽  
Author(s):  
Johannes Werner ◽  
Augustin Geron ◽  
Jules Kerssemakers ◽  
Sabine Matallana-Surget
Keyword(s):  
Input Data ◽  
Rapid Development ◽  
Protein Annotation ◽  
Group Level ◽  
Protein Databases ◽  
Protein Inference ◽  
Protein Group ◽  
The Creation ◽  
Public Repositories ◽  
First Time

AbstractMetaproteomics allows to decipher the structure and functionality of microbial communities. Despite its rapid development, crucial steps such as the creation of standardized protein search databases and reliable protein annotation remain challenging. To overcome those critical steps, we developed a new program named mPies (metaProteomics in environmental sciences). mPies allows the creation of protein databases derived from assembled or unassembled metagenomes, and/or public repositories based on taxon IDs, gene or protein names. For the first time, mPies facilitates the automatization of reliable taxonomic and functional consensus annotations at the protein group level, minimizing the well-known protein inference issue which is commonly encountered in metaproteomics. mPies’ workflow is highly customizable with regards to input data, workflow steps, and parameter adjustment. mPies is implemented in Python 3/Snakemake and freely available on GitHub: https://github.com/johanneswerner/mPies/.

scholarly journals Automated Confirmation of Protein Annotation Using NLP and the UniProtKB Database

2020 ◽  
Vol 11 (1) ◽  
pp. 24
Author(s):  
Jin Tao ◽  
Kelly Brayton ◽  
Shira Broschat
Keyword(s):  
Language Processing ◽  
Fine Tuning ◽  
Support Vector ◽  
Protein Annotation ◽  
Computing Power ◽  
Journal Publication ◽  
Novel Approach ◽  
Uniprotkb Database ◽  
Public Repositories ◽  
Annotation Errors

Advances in genome sequencing technology and computing power have brought about the explosive growth of sequenced genomes in public repositories with a concomitant increase in annotation errors. Many protein sequences are annotated using computational analysis rather than experimental verification, leading to inaccuracies in annotation. Confirmation of existing protein annotations is urgently needed before misannotation becomes even more prevalent due to error propagation. In this work we present a novel approach for automatically confirming the existence of manually curated information with experimental evidence of protein annotation. Our ensemble learning method uses a combination of recurrent convolutional neural network, logistic regression, and support vector machine models. Natural language processing in the form of word embeddings is used with journal publication titles retrieved from the UniProtKB database. Importantly, we use recall as our most significant metric to ensure the maximum number of verifications possible; results are reported to a human curator for confirmation. Our ensemble model achieves 91.25% recall, 71.26% accuracy, 65.19% precision, and an F1 score of 76.05% and outperforms the Bidirectional Encoder Representations from Transformers for Biomedical Text Mining (BioBERT) model with fine-tuning using the same data.

The abolition of the liturgical chorēgia and the creation of the agōnothesia in Athens: new considerations on a debated issue

2020 ◽  
Vol 140 ◽  
pp. 34-68
Author(s):  
Delphine Ackermann ◽  
Clément Sarrazanas
Keyword(s):  
Fourth Century ◽  
Democratic Government ◽  
Ancient Source ◽  
The Creation ◽  
The Government ◽  
First Time ◽  
New Look

Abstract:No ancient source indicates when the agōnothesia, attested for the first time in 307/6 BC, was introduced in Athens. Scholars have long attributed its creation, along with the abolition of the liturgical chorēgia, to the government of Demetrius of Phalerum (317–307 BC), motivated by oligarchic ideology and a desire to preserve the wealth of rich citizens. This traditional thesis has recently been challenged, with some scholars attributing the creation of the agōnothesia to the restored democratic government of 307 BC and others to the government of Phocion (322–318 BC). A new look at epigraphical and literary documents hitherto neglected or imperfectly understood (especially from the Attic demes) allows the authors to establish that the liturgical chorēgia disappeared at the beginning of the government of Demetrius of Phalerum, around 316 BC. The institution of the agōnothesia had a precedent (hitherto overlooked) in Lycurgan Athens with the new festival of the Amphiaraia of 331 BC. Both measures were in fact consensual and must not be interpreted as strictly oligarchic in inspiration. The creation of the agōnothesia was above all a pragmatic response on Athens’ part to the major changes that occurred in the agonistic world in the late fourth century.

FC14-01 - Internal losses and the creation of “Nowhere land”: psychodynamic themes of adults with ADHD discovered during drama-therapy

2011 ◽  
Vol 26 (S2) ◽  
pp. 1893-1893
Author(s):  
I. Manor ◽  
G. Yazpan
Keyword(s):  
Drama Therapy ◽  
Transitional Space ◽  
Men And Women ◽  
The Past ◽  
Chronic Disorder ◽  
Pharmacological Aspect ◽  
Inner Self ◽  
Socioeconomic Strata ◽  
The Creation ◽  
First Time

ADHD is a well-known, chronic disorder that persists in adulthood. During the past 20 years its existence in adults is becoming clearer, yet its dynamic aspects are rarely discussed. The treatment of adults is vital, as much as that of children; however the literature discussing it, especially its non-pharmacological aspect, is scarce.We describe the results of our treatment with drama-therapy of two groups of adults with ADHD. These groups included 11 adults (from both groups), men and women, from most socioeconomic strata, aged ≥ 60 yrs., who were diagnosed as suffering from ADHD and were treated for it for the first time in their life. Drama-therapy was selected as we believed it to be a useful method with associative, distracted ADHD patients, since it enabled the use of transitional space through non-verbal images and acts.This presentation discusses the basic themes with which patients began therapy. Interestingly, all patients, however different, shared the same themes that were built on self doubt and the pre-presumption of disappointment. The impairment related to ADHD, that was felt, but not understood, led to a strong experience of heavy losses, which we tried to define separately: of a clear path, of control, of the inner perception of borders and of the loss of an integrative inner self. All these losses were accumulated in the transitional space in a place we named “Nowhere land”.We would like to present these themes of losses and of becoming lost and to discuss their meaning.

Professional Information Needs of Library Specialists in Russia

2021 ◽  
Vol 70 (1) ◽  
pp. 7-20
Author(s):  
Marina Y. Neshcheret
Keyword(s):  
Information Needs ◽  
Rapid Development ◽  
Information Service ◽  
Library Science ◽  
Information Process ◽  
Cultural Workers ◽  
Use Of Resources ◽  
The Creation ◽  
Professional Information ◽  
Comprehensive Study

The article is devoted to the comprehensive study of the professional information needs (IN) of specialists of the central libraries of the subjects of the Russian Federation. The rapid development of high technologies in the field of accumulation, transmission and processing of information, the creation of modern telecommunications systems have led to the emergence of fundamentally new opportunities for organizing the information process. This, in turn, led to the qualitative growth of IN specialists, including those employed in the field of library activities. The specific features of IN library specialists are determined by their place and role in the modern process of cultural activity, industry orientation, nature of work and specialization. During 2018—2019, the Centre for Research of Problems of the Development of Libraries in the Information Society of the Russian State Library carried out research aimed at comprehensive study of the information needs of cultural workers employed in the library sphere. At the first stage of the research, there was comprehended the existing experience of studying professional information needs in the national library science. At the second stage, using the method of questionnaire survey, information needs of library specialists were studied in order to identify the most rational forms and methods of providing them. The analysis of the survey results made it possible to identify the sources of professional information, to reveal information resources that have the greatest importance and characterize specific features of librarians’ information needs.The author concludes on the need to expand the access to full-text databases and electronic versions of periodicals for library staff. The creation of integrated information centre could help providing library professionals with professional information. Currently, the function of such a centre is performed by the National Electronic Library, which includes the professional section for library specialists. The results of the study form theoretical and methodological basis for the rational use of resources and potential of libraries in providing information to professional information needs of library specialists and determine the prospects for further research related to improving the forms and methods of information service for this category of users.

Education as Arikara Spiritual Renewal and Cultural Evolution

2014 ◽  
Vol 54 (3) ◽  
pp. 303-322 ◽  
Author(s):  
KuuNUx TeeRIt Kroupa
Keyword(s):  
Deep Understanding ◽  
Cultural Development ◽  
Human Beings ◽  
Old People ◽  
New Beginning ◽  
The People ◽  
History Of ◽  
The Creation ◽  
First Time ◽  
The Universe

In May 2009, the Arikara returned to the land of their ancestors along the Missouri River in South Dakota. For the first time in more than a half century, a Medicine Lodge was built for ceremony. The lodge has returned from its dormant state to regain its permanent place in Arikara culture. This event will be remembered as a significant moment in the history of the Arikara because it symbolizes a new beginning and hope for the people. Following this historic event, Arikara spiritual leader Jasper Young Bear offered to share his experience and deep insight into Arikara thought: You have to know that the universe is the Creator's dream, the Creator's mind, everything from the stars all the way to the deepest part of the ocean, to the most microscopic particle of the creation, to the creation itself, on a macro level, on a micro level. You have to understand all of those aspects to understand what the lodge represents. The lodge is a fractal, a symbolic representation of the universe itself. How do we as human beings try to make sense of that? That understanding, of how the power in the universe flows, was gifted to us through millennia of prayer and cultural development… It is important for us to internalize our stories, internalize the star knowledge, internalize those things and make that your way, make that your belief, because we're going to play it out inside the lodge. It only lives by us guys interacting with it and praying with it and bringing it to life… We're going to play out the wise sayings of the old people… So you see that it's an Arikara worldview. A learning process of how the universe functions is what you're actually experiencing [inside the Medicine Lodge]. What the old people were describing was the functioning of how we believed the universe behaves. And we had a deep, deep understanding of what that meant and how it was for us. So that's what you're actually seeing in the Medicine Lodge.

Believable and Effective AI Agents in Virtual Worlds

2012 ◽  
Vol 4 (2) ◽  
pp. 37-59 ◽  
Author(s):  
Iskander Umarov ◽  
Maxim Mozgovoy
Keyword(s):  
Artificial Intelligence ◽  
Video Games ◽  
Virtual Worlds ◽  
Rapid Development ◽  
Virtual Agents ◽  
High Ability ◽  
Topic Area ◽  
Human Likeness ◽  
New Challenges ◽  
The Creation

The rapid development of complex virtual worlds (most notably, in 3D computer and video games) introduces new challenges for the creation of virtual agents, controlled by artificial intelligence (AI) systems. Two important subproblems in this topic area which need to be addressed are (a) believability and (b) effectiveness of agents’ behavior, i.e., human-likeness of the characters and high ability to achieving their own goals. In this paper, the authors study current approaches to believability and effectiveness of AI behavior in virtual worlds. They examine the concepts of believability and effectiveness, and analyze several successful attempts to address these challenges.

scholarly journals Методы оценки продуктивности представителей рода эхинацея (Echinacea Moench) прегенеративного периода онтогенеза

2013 ◽  
pp. 24-30
Author(s):  
С. В. Поспелов
Keyword(s):  
Regression Models ◽  
Input Data ◽  
Growing Season ◽  
Echinacea Purpurea ◽  
System Productivity ◽  
Aerial Parts ◽  
Purple Coneflower ◽  
Echinacea Pallida ◽  
First Time

За багаторічними дослідженнями ехінацеї пурпурової (Echinacea purpurea (L.) Moench,) сорту Зірка Миколи Вавилова та ехінацеї блідої (Echinacea pallida (Nutt.) Nutt.) сорту Красуня Прерій вперше розроблені й запатентовані методи визначення продуктивності рослин прегенеративного періоду онтогенезу. Методики засновані на регресійних моделях із високими коефіцієнтами детермінації, на підставі яких можна без пошкодження рослин провести оцінку продуктивності надземної частини та кореневої системи протягом веґетаційного періоду. Вихідними даними для розрахунків слугують показники довжини і ширини листковоїпластинки, їх кількість, а також сума температур вище 5 0С і кількість діб від сівби. On the basis of long-term researches of Purple Coneflower (Echinacea purpurea (L.) Moench) variety «Zirka Mykoly Vavylova» and Pale Coneflower (Echinacea pallida (Nutt.) variety «Krasunja Preriy» for the first time ever there were developed and patented the methods for determining the efficiency of plants in pregenesic period of ontogeny. The foundation of methodology was made on the studies of regression models with high coefficients of determination which allow to make the estimation of aerial parts and root system productivity for the whole growing season without damaging the plants. The input data for the calculation are the indicators of the length and width of the leaf blade, the amount and the sum of temperatures above + 5 ºC and the number of days from sowing.

scholarly journals Spatial models of adjusted precipitation for Canada at varying time scales

2021 ◽  
Author(s):  
Heather MacDonald ◽  
Daniel W. McKenney ◽  
Xiaolan L. Wang ◽  
John Pedlar ◽  
Pia Papadopol ◽  
...  
Keyword(s):  
Time Scales ◽  
Input Data ◽  
Snow Water Equivalent ◽  
Spatial Models ◽  
Total Precipitation ◽  
Spline Surfaces ◽  
Monthly Total Precipitation ◽  
Monthly Total ◽  
Snow Water ◽  
First Time

AbstractThis study presents spatial models (i.e., thin plate spatially continuous spline surfaces) of adjusted precipitation for Canada at daily, pentad (5-day), and monthly time scales from 1900 to 2015. The input data include manual observations from 3346 stations that were adjusted previously to correct for snow water equivalent (SWE) conversion and various gauge-related issues. In addition to the 42,331 models for daily total precipitation and 1392 monthly total precipitation models 8395 pentad models were developed for the first time, depicting mean precipitation for 73 pentads annually. For much of Canada, mapped precipitation values from this study were higher than those from the corresponding unadjusted models (i.e., models fitted to the unadjusted data), reflecting predominantly the effects of the adjustments to the input data. Error estimates compared favourably to the corresponding unadjusted models. For example, Root generalized cross validation (GCV) estimate (a measure of predictive error) at the daily time scale was 3.6 mm on average for the 1960 to 2003 period as compared to 3.7 mm for the unadjusted models over the same period. There was a dry bias in the predictions relative to recorded values of between 1% and 6.7% of the average precipitations amounts for all time scales. Mean absolute predictive errors of the daily, pentad, and monthly models were 2.5 mm (52.7%), 0.9 mm (37.4%), and 11.2 mm (19.3%), respectively. In general, the model skill was closely tied to the density of the station network. The current adjusted models are available in grid form at ~2-10 km resolutions.

scholarly journals Digital Content of Modern Media as a Sphere for the Formation of Digital Etiquette in the Context of Transmedia

2021 ◽  
Vol 16 (1) ◽  
pp. 177-184
Author(s):  
Marfitsyna Arina R. ◽  
Keyword(s):  
Mass Media ◽  
Rapid Development ◽  
Synthesis Method ◽  
Digital Content ◽  
Transmedia Storytelling ◽  
Modern Media ◽  
Key Characteristics ◽  
The Creation ◽  
Modern Mass ◽  
Transformation Processes

The topicality of the article is determined by the fact that it examines the specifics of modern digital content in the context of the transformation processes, which take place in modern media in the context of transmedia that influence the formation of digital etiquette. The rapid development of the technical and technological components of communication contributes to the constant transformation of digital etiquette and this is one of the problems of modern transmedia space, which actualizes the identification of the content features of digital content, the role of the axiological component of modern media materials, the definition of effective ways of their representation that corresponds with the needs of the modern digital audience. The aim of the research is to describe the key characteristics of digital content in modern media that promote the formation of digital etiquette. The novelty of the article is in the concept analysis of print media, television and radio broadcasting in the context of transmedia according to the approach of the general key characteristics of the current digital content that contribute to the formation of digital etiquette and have the prospect of further research. The methodological basis was the scientific works of media theorists in Russian and foreign scientific communities. During the work on the article in the field of researching the content of modern mass media and the transformation processes that take place in the media, the author used the methods of analysis and comparison, the synthesis method was applied in terms of discussing the research results, formulating conclusions. The results of the research show that today not only adaptation in the digital environment is required but also close integration with all processes of the digital development of society is necessary for the successful functioning of modern media. The typical key features for modern digital content, which are the environment for the formation of digital etiquette, were identified during the research. It includes the ability to consume content through various gadgets; creation of interactive materials that satisfy the demands of a certain audience and give the right to participate in the creation of content and to choose it; the creation of complex multi-component materials that are endowed with the features of the project and also the transmedia narrative pattern. The article represents the interest to practicing journalists, as well as to researchers in the sphere of development of digital journalism, transmedia storytelling, digital content features and digital etiquette. Keywords: journalism, digital content, mass media transformation, transmedia, storytelling, digital etiquette

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