2,720 research outputs found
Safe Functional Inference for Uncharacterized Viral Proteins
No full textThe explosive growth in the number of sequenced genomes has created a flood of protein sequences with unknown structure and function. A routine protocol for functional inference on an input query sequence is based on a database search for homologues. Searching a query against a non-redundant database using BLAST (or more advanced methods, e.g. PSI-BLAST) suffers from several drawbacks: (i) a local alignment often dominates the results; (ii) the reported statistical score (i.e. E-value) is often misleading; (iii) incorrect annotations may be falsely propagated. 
Several systematic methods are commonly used to assign sequences with functions on a genomic scale. In Pfam (1) and resources alike, statistical profiles (HMMs) are built from semi-manual multiple alignments of seed homologous sequences. The profiles are then used to scan genomic sequences for additional family members. The drawbacks of this scheme are: (i) only families with a predetermined seed are considered; (ii) the query must have a detectable sequence similarity to seed sequences; (iii) attention to internal relationships among the family members or the relations to other families is lacking; (iv) family membership is often set by pre-determined thresholds.
An alternative to profile or model based methods for functional inference relies on a hierarchical clustering of the protein space, as implemented in the ProtoNet approach (2). The fundamental principle is the creation of a tree that captures evolutionary relatedness among protein families. The tree construction is fully automatic, and is based only on reported BLAST similarities among clustered sequences. The tree provides protein groupings in continuous evolutionary granularities, from closely related to distant superfamilies. Clusters in the ProtoNet tree show high correspondence with homologous sequence (i.e. Pfam and InterPro), functional (i.e. E.C. classification) and structural (i.e., SCOP) families (3). A new clustering scheme (4) has provided an extensive update to the ProtoNet process, which is now based on direct clustering of all detectable sequence similarities. 
Herein, we use the ProtoNet resource to develop a methodology for a consistent and safe functional inference for remote families. We illustrate the success of our approach towards clusters of poorly characterized viral proteins. Viral sequences are characterized by a rapid evolutionary rate which drives viral families to be even more remote (sequence-similarity-wise). Thus, functional inference for viral families is apparently an unsolved task. Despite this inherent difficulty, the new ProtoNet tree scaffold reliably captures weak evolutionary connections for viral families, which were previously overlooked. We take advantage of this, and propose new functional assignments for viral protein families.

08101 Abstracts Collection – Computational Proteomics
No full textThe second Dagstuhl Seminar on emph{Computational Proteomics} took place
from March 3rd to 7th, 2008 in Schloss Dagstuhl--Leibniz Center for
Informatics. This highly international meeting brought together researchers
from computer science and from proteomics to discuss the state of the art
and future developments at the interface between experiment and theory.
This interdisciplinary exchange covered a wide range of topics, from new
experimental methods resulting in more complex data we will have to expect
in the future to purely theoretical studies of what level of experimental
accuracy is required in order to solve certain problems. A particular focus
was also on the application side, where the participants discussed more
complex experimental methodologies that are enabled by more sophisticated
computational techniques. Quantitative aspects of protein expression
analysis as well as posttranslational modifications in the context of
disease development and diagnosis were discussed. The seminar sparked a
number of new ideas and collaborations and has resulted in several joint
grant applications and paper submissions.
This paper describes the seminar topics, its goals and results. The
executive summary is followed by the abstracts of the presentations given.
Links to extended abstracts or full papers are provided, if available
Business plan for a person operating under a business name Individual Football Training Litol - Michal Zoubek
No full textBakalářská práce se zaměřuje na sestavení podnikatelského plánu pro potenciálně nově zakládanou firmu Individuální fotbalové tréninky Litol – Michal Zoubek, která by nabízela individuální fotbalové tréninky v Litoli na hřišti. Cílem práce je provést potřebné analýzy pro přípravu podnikatelského plánu a zhotovení jeho návrhu. V závěru autor odpoví na výzkumnou otázku, zda se v tomto konkrétním prostředí a trhu za konkrétních podmínek vyplatí začít podnikat. K dosažení cílů autor provede analýzy související s tématem, provede dotazníkové šetření, sestaví vlastní podnikatelský plán a závěrem odpoví na výzkumnou otázku.The bachelor thesis focuses on the preparation of a business plan for a potential newly established company Individual football training Litol – Michal Zoubek, which would offer individual football training in Litol. The aim of the thesis is to carry out the necessary analyses for the preparation of the business plan and to make a proposal. Finally, the author answers the research question whether it is worth starting a business in this particular environment and market under specific conditions. In order to achieve the objectives, the author will carry out analyses related to the topic, conduct a questionnaire survey, draw up his own business plan and finally answer the research question
Statewide congestion overview
No full textprepared by Oregon Department of Transportation, Transportation Planning Analysis Unit ; principal author: Brian Gregor ; staff support: Michal Wert, MW Consulting.Title from PDF title page.Covers OCLC #1390891081, OCLC #1378912112, OCLC #1201266716, and OCLC #1201266486.This archived document is maintained by the State Library of Oregon as part of the Oregon Documents Depository Program. It is for informational purposes and may not be suitable for legal purposes.Includes bibliographical references.Mode of access: Internet from the Oregon Government Publications Collection.Text in English
Quaint Fantasy. Apprehension of Michal Ajvaz as an Author of Magical Realism
No full textThe thesis deals with a question if it is appropriate to consider Czech writer Michal Ajvaz to be an author of magical realism. His fiction usually incorporates supernatural objects or events into a natural fictional world just as in the fiction of magical realism. The thesis analyses the nature of magic motifs and events in the studied literature, as well as literary techniques, which are used to achieve this specific kind of poetics. By examination of the canonical works of magical realism, such as the novel One Hundred Years of Solitude by G. G. Márquez, The House of the Spirits by Isabel Allende or the novel Midnight Children by S. Rushdie, we can specify the structure of this literary genre and compare it to the texts of Michal Ajvaz. In a survey, we focus on two Ajvaz's early novels - the fantastic one The Other City (1993) and the philosophical prose The Golden Age (2001). KEYWORDS Michal Ajvaz, magical realism, magic realism, postmodernism, The Other City, The Golden Ag
Poetics of affectivity by Michal Tallo
No full textMichal Tallo belongs to the young generation reviving certain aspects of anesthetic poetics, which formed in Slovak poetry at the beginning of the 1990s. Anesthetic procedures are directly related to the observed aspect of emotionality in Tallo‘s work. The paper follows the male lyrical heroes from the collections Antimita (Anti-intimacy) (2016), Δ [Delta] (Delta) (2018), Kniha tmy (The Book of Darkness) (2021), and the male characters of the short story Futbal (Football) from the book Všetko je v poriadku, všade je láska (All is well, there is love everywhere) (2024). The paper focuses primarily on one element of Michal Tallo poetics, which is called "admitted affectivity." Affectivity proves specific characteristics of the author\u27s work, which oscillate between the two extreme positions of suppressing and releasing emotions.Michal Tallo belongs to the young generation reviving certain aspects of anesthetic poetics, which formed in Slovak poetry at the beginning of the 1990s. Anesthetic procedures are directly related to the observed aspect of emotionality in Tallo‘s work. The paper follows the male lyrical heroes from the collections Antimita (Anti-intimacy) (2016), Δ [Delta] (Delta) (2018), Kniha tmy (The Book of Darkness) (2021), and the male characters of the short story Futbal (Football) from the book Všetko je v poriadku, všade je láska (All is well, there is love everywhere) (2024). The paper focuses primarily on one element of Michal Tallo poetics, which is called "admitted affectivity." Affectivity proves specific characteristics of the author\u27s work, which oscillate between the two extreme positions of suppressing and releasing emotions
Five Years of Work of Michal Baludansky Academic Society
No full textThe article covers the work of Academic Society of Michal Baludansky since its foundation day and up till now. The author reveals main directions of the society’s collaboration with universities in different countries bearing a direct relationship to the life and activities of a famous scientist and teacher Michal BaludanskyВ статье предлагается обзор основных направлений и результатов деятельности Академического общества Михаила Балудянского от его образования до настоящего времени. Охарактеризованы основные области сотрудничества общества с университетами разных стран, имеющими непосредственное отношение к жизни и деятельности знаменитого ученого и педагога Михаила Балудянског
Five Years of Work of Michal Baludansky Academic Society
No full textThe article covers the work of Academic Society of Michal Baludansky since its foundation day and up till now. The author reveals main directions of the society’s collaboration with universities in different countries bearing a direct relationship to the life and activities of a famous scientist and teacher Michal BaludanskyВ статье предлагается обзор основных направлений и результатов деятельности Академического общества Михаила Балудянского от его образования до настоящего времени. Охарактеризованы основные области сотрудничества общества с университетами разных стран, имеющими непосредственное отношение к жизни и деятельности знаменитого ученого и педагога Михаила Балудянског
Legal and Financial Problems of International Joint Custody of Children
No full textThe aim of this article is to analyze very interesting and currently up-to-date area of children living in international joint custody from the legal and financial point of view. This covers the situation when custody of a child is awarded to both parents living in different states of the European Union (or also other states). The number of marriages contracted between Czech nationals and foreign nationals and also between nationals from two different states (not necessarily inside European Union) increases every year while free movement of people is a real practice today. Because these international marriages are becoming more common they bring new problems that must be solved by contemporary law. This regulation needs to result from the knowledge of the children psychology that is affecting family law the most but also has its practical aspects in the area of taxation and payment issues that will be analyzed deeply as well.juridical problems, financial problems, international joint custody, family.
The Secrets of a Functional Synapse – From a Computational and Experimental Viewpoint
No full textAbstract Background Neuronal communication is tightly regulated in time and in space. The neuronal transmission takes place in the nerve terminal, at a specialized structure called the synapse. Following neuronal activation, an electrical signal triggers neurotransmitter (NT) release at the active zone. The process starts by the signal reaching the synapse followed by a fusion of the synaptic vesicle and diffusion of the released NT in the synaptic cleft; the NT then binds to the appropriate receptor, and as a result, a potential change at the target cell membrane is induced. The entire process lasts for only a fraction of a millisecond. An essential property of the synapse is its capacity to undergo biochemical and morphological changes, a phenomenon that is referred to as synaptic plasticity. Results In this survey, we consider the mammalian brain synapse as our model. We take a cell biological and a molecular perspective to present fundamental properties of the synapse:(i) the accurate and efficient delivery of organelles and material to and from the synapse; (ii) the coordination of gene expression that underlies a particular NT phenotype; (iii) the induction of local protein expression in a subset of stimulated synapses. We describe the computational facet and the formulation of the problem for each of these topics. Conclusion Predicting the behavior of a synapse under changing conditions must incorporate genomics and proteomics information with new approaches in computational biology.</p
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