Non-metric similarity search of tandem mass spectra including posttranslational modifications

AbstractIn biological applications, the tandem mass spectrometry is a widely used method for determining protein and peptide sequences from an “in vitro” sample. The sequences are not determined directly, but they must be interpreted from the mass spectra, which is the output of the mass spectrometer. This work is focused on a similarity-search approach to mass spectra interpretation, where the parameterized Hausdorff distance (dHP) is used as the similarity. In order to provide an efficient similarity search under dHP, the metric access methods and the TriGen algorithm (controlling the metricity of dHP) are employed. Moreover, the search model based on the dHP supports posttranslational modifications (PTMs) in the query mass spectra, what is typically a problem when an indexing approach is used. Our approach can be utilized as a coarse filter by any other database approach for mass spectra interpretation

Vplyv ročníka a biostimulátorov na obsah mastných kyselín v hybridoch slnečnice ročnej

Sunflower (Helianthus annuus L.) is grown in Slovak growing conditions for edible oil of high quality, its composition of unsaturated fatty acids affects the human health positively. Influence of year, hybrids (Marbelia CS and Reasun DS5) and biostimulating preparations (Florone and Fertisiline) on yield, oil content, and amount of selected fatty acids (oleic, linoleic, palmitic, and stearic acids) was find out in this study. Also evaluate the relationship within the achieved yield and oil content with the obtained amount of selected fatty acids. Field small-plot experiments were established by randomized split plot method during the growing years of 2018 and 2019. The experimental field is situated in a warm maize production area, while the course of weather conditions during individual growing seasons was different. On an average for experimental period of 2018-2019, more favorable course of temperatures and precipitation was recorded in 2018. Significantly higher achene yield (3.29±0.35 t/ha) and a higher amount of selected fatty acids (oleic acid 62.11±4.33%; linoleic acid 45.32±4.62%; palmitic acid 5.26±0.33%; stearic acid 4.21±0.20%) were found in Reasun DS-5 hybrid. Both biostimulating preparations had a significant effect on the yield and oleic acid content, when both biostimulators were applied in BBCH 15 and BBCH 55. The amount of linoleic acid decreased by both biostimulating applications in BBCH 15 (Florone 33.88±10.57%; Fertilisine 34.11±13.37%) and BBCH 15, 55 ((Florone 34.08±12.34%; Fertisiline 34.26±13.40%) compared by control treatments (38.43±6.01%). The contents of linoleic acid on treated variants by both preparations in BBCH 55 (Florone 38.26±9.47%; Fertisiline 39.03±8.95%) were statistically nonsignificant with comparison to untreated control. The height of yield was negatively correlated (r= -0.310; P<0.01) with the oil content in the average of 2018 and 2019. A significant positive correlation was found in the relationships between the yield and palmitic acid (r=0.35; P<0.01), linoleic acid and palmitic acid, and stearic acid (r=0.51; P<0.01) (r=0.86; P<0.01), palmitic acid and stearic acid (r=0.45; P<0.01).Slnečnica ročná (Helianthus annuus L.) je v našich podmienkach pestovaná hlavne pre získavanie vysoko kvalitného jedlého oleja, ktorého zloženie nenasýtených mastných kyselín pozitívne vplýva na zdravie človeka. V tejto štúdii bolo cieľom zistiť vplyv ročníka, hybridov (Marbelia CS a Reasun DS-5) a biostimulačných prípravkov (Florone a Fertisiline) na úrodu, obsah oleja a množstvo vybraných mastných kyselín (kyselina olejová, linolová, palmitová a steárová). Taktiež zhodnotiť vzťah v rámci dosiahnutej úrody a obsahu oleja so získaným množstvom vybraných mastných kyselín. Poľné maloparcelové experimenty boli založené metódou kolmo delených blokov a v náhodnom usporiadaní počas pestovateľských rokov 2018 a 2019. Pokusné stanovište je situované v teplej kukuričnej výrobnej oblasti, pričom priebeh poveternostných podmienok počas jednotlivých pestovateľských období bol rozdielny. V priemere za sledované obdobie bol štatisticky preukazne vhodnejší priebeh teplôt a zrážok zaznamenaný v roku 2018. V priemere štatisticky preukazne vyššia úroda nažiek (3,29±0,35 t.ha-1) a vyšší obsah vybraných mastných kyselín (kyselina olejová 62,11±4,33 %; kyselina linolová 45,32±4,62 %; kyselina palmitová 5,26±0,33 %; kyselina steárová 4,21±0,20 %) boli zistené pri hybride Reasun DS-5. Použitím biostimulačných prípravkov bola úroda v priemere za sledované obdobie ovplyvnená štatisticky preukazne, pri aplikácii oboch prípravkov (Florone a Fertisiline) v rastovej fáze BBCH 15 aj BBCH 55 (fáza 6-8 listov a fáza kvitnutia), rovnako tak aj množstvo kyseliny olejovej. Obsah kyseliny linolovej klesol po aplikácii oboch prípravkov v rastovej fáze BBCH 15 (Florone 33,88±10,57 %; Fertilisine 34,11±13,37 %) a BBCH 15, 55 (Florone 34,08±12,34 %; Fertisiline 34,26±13,40 %) v porovnaní s kontrolným variantom (38,43±6,01 %). Obsahy získanej kyseliny linolovej na variantoch ošetrených vo fáze BBCH 55 (Florone 38,26±9,47 %; Fertisiline 39,03±8,95 %) boli štatisticky nepreukazné v porovnaní s kontrolou. Výška úrody negatívne korelovala (r= -0,310; P<0,01) s obsahom získaného oleja v priemere rokov 2018 a 2019. Významná pozitívna korelácia bola zistená pri vzťahoch úroda a kyselina palmitová (r=0.35; P<0.01), kyselina linolová a kyselina palmitová, a steárová (r=0.51; P<0.01) (r=0.86; P<0.01), kyselina palmitová a kyselina steárová (r=0.45; P<0.01)

Protein Sequences Identification using NM-tree

ABSTRACT We have generalized a method for tandem mass spectra interpretation, based on the parameterized Hausdorff distance dHP . Instead of just peptides (short pieces of proteins), in this paper we describe the interpretation of whole protein sequences. For this purpose, we employ the recently introduced NM-tree to index the database of hypothetical mass spectra for exact or fast approximate search. The NM-tree combines the M-tree with the TriGen algorithm in a way that allows to dynamically control the retrieval precision at query time. A scheme for protein sequences identification using the NM-tree is proposed

Current and Future Issues in BPM Research: A European Perspective from the ERCIS Meeting 2010

Business process management (BPM) is a still-emerging field in the academic discipline of Information Systems (IS). This article reflects on a workshop on current and future issues in BPM research that was conducted by seventeen IS researchers from eight European countries as part of the 2010 annual meeting of the European Research Center for Information Systems (ERCIS). The results of this workshop suggest that BPM research can meaningfully contribute to investigating a broad variety of phenomena that are of interest to IS scholars, ranging from rather technical (e.g., the implementation of software architectures) to managerial (e.g., the impact of organizational culture on process performance). It further becomes noticeable that BPM researchers can make use of several research strategies, including qualitative, quantitative, and design-oriented approaches. The article offers the participants’ outlook on the future of BPM research and combines their opinions with research results from the academic literature on BPM, with the goal of contributing to establishing BPM as a distinct field of research in the IS discipline

Metric indexing in information retrieval

Import 20/04/2006Prezenční výpůjčkaVŠB - Technická univerzita Ostrava. Fakulta elektrotechniky a informatiky. Katedra (456) informatik

Metrické indexování vektorových modelů v oblasti information retrieval

Abstrakt. Pro vektorové modely v oblasti Information Retrieval dosud nebylo navrženo efektivní indexovací schéma. Absence efektivní implementace vektorového modelu znemožňuje jeho použití pro velké kolekce dokumentů. V tomto příspěvku je shrnut současný stav problematiky a dále je zde představeno metrické indexování vektorových modelů, kterým se v rámci svého doktorského studia převážně zabývám. Oblast Information Retrieval [BaNe99] (dále IR, v českém prostředí oblast dokumentografických informačních systémů [PSH98]) se zabývá metodami vyhledávání v rozsáhlých kolekcích dokumentů. V minulosti byl kladen hlavní důraz na vyhledávání v kolekcích textů (tzv. Text Retrieval [Be99]). V současné době sílící multimedialní trend rozšiřuje hranice IR také do oblasti vyhledávání v multimediálních databázích, tj. vyhledávání v kolekcích dokumentů obsahujících XML, obrázky, audio, video, časové sekvence, DNA, atd. Kvalitativním rámcem oblasti IR je návrh modelů pro vyhledávání. V současnosti existují tři klasické modely a jejich modifikace. Kvalitativně nejlepš

NM-Tree: Flexible Approximate Similarity Search in Metric and Non-metric Spaces.

Abstract. So far, an efficient similarity search in multimedia databases has been carried out by metric access methods (MAMs), where the utilized similarity measure had to satisfy the metric properties (reflexivity, non-negativity, symmetry, triangle inequality). Recently, the introduction of TriGen algorithm (turning any nonmetric into metric) enabled MAMs to perform also nonmetric similarity search. Moreover, it simultaneously enabled faster approximate search (either metric or nonmetric). However, a simple application of TriGen as the first step before MAMs&apos; indexing assumes a fixed &quot;approximation level&quot;, that is, a user-defined tolerance of retrieval precision is preset for the whole index lifetime. In this paper, we push the similarity search forward; we propose the NMtree (nonmetric tree) -a modification of M-tree which natively aggregates the TriGen algorithm to support flexible approximate nonmetric or metric search. Specifically, at query time the NM-tree provides a user-defined level of retrieval efficiency/precision trade-off. We show the NM-tree could be used for general (non)metric search, while the desired retrieval precision can be flexibly tuned on-demand

analysis and indexing—Indexing methods

metric access method