scholarly journals Characterization of peptide-protein relationships in protein ambiguity groups via bipartite graphs

2021 ◽  
Author(s):  
Karin Schork ◽  
Michael Turewicz ◽  
Julian Uszkoreit ◽  
Jörg Rahnenführer ◽  
Martin Eisenacher
Keyword(s):  
Real Data ◽  
Bipartite Graphs ◽  
Data Sets ◽  
Complex Structures ◽  
Protein Databases ◽  
Protein Inference ◽  
The Relationship ◽  
Ambiguity Groups ◽  
Proteins And Peptides

Motivation: In bottom-up proteomics, proteins are enzymatically digested before measurement with mass spectrometry. The relationship between proteins and peptides can be represented by bipartite graphs. This representation is useful to aid protein inference and quantification, which is complex due to the occurrence of shared peptides. We conducted a comprehensive analysis of bipartite graphs using theoretical peptides from in silico digestion of protein databases as well as quantified peptides quantified from real data sets. Results: The graphs based on quantified peptides are smaller and have less complex structures compared to graphs using theoretical peptides. The proportion of protein nodes without unique peptides and of graphs that contain such proteins are considerably greater for real data. Large differences between the two analyzed organisms (mouse and yeast) on database as well as quantitative level have been observed. Insights of this analysis may be useful for the development of protein inference and quantification algorithms.

scholarly journals A ocupação humana antiga (11-7 mil anos atrás) do Planalto Meridional Brasileiro: caracterização geomorfológica, geológica, paleoambiental e tecnológica de sítios arqueológicos relacionados a três distintas indústrias líticas

2020 ◽  
Vol 13 (6) ◽  
pp. 2553
Author(s):  
Pedro Michelutti Cheliz ◽  
João Carlos Moreno de Sousa ◽  
Gabriela Sartori Mingatos ◽  
Mercedes Okumura ◽  
Astolfo Gomes de Mello Araujo
Keyword(s):  
Significant Variation ◽  
Raw Materials ◽  
Archaeological Sites ◽  
Data Sets ◽  
Human Settlement ◽  
Human Occupation ◽  
Natural Landscapes ◽  
Lithic Artifacts ◽  
The Relationship

Com o objetivo de ponderar conexões entre quadros naturais e a ocupação humana pré-colonial, caracterizou-se os artefatos e a contextualização geomorfológica e ambiental de quatro sítios líticos vinculados a antigos registros de grupos caçadores-coletores do sul e sudeste do Brasil, associados a três distintas indústrias líticas. Elencou-se associação dos sítios com terrenos de baixos declives e altimetrias em seus respectivos contextos (terrenos mais estáveis para fixação humana), adjacentes a córregos e próximos de faixas do terreno que registram maiores inclinações e desníveis verticais, mais propensas a apresentarem afloramentos rochosos (fontes potenciais de matérias-primas para a confecção de ferramentas lascadas). Elencou-se fontes de matérias-primas nos entornos de cada sítio e as matérias-primas associadas aos artefatos, e ponderou-se a correlação entre os dois conjuntos de dados. Analisou-se a relação dos padrões tecnológicos de artefatos líticos com a caracterização petrográfica das matérias-primas, verificando-se quais silcretes semelhantes foram usadas para produção de artefatos distintos. Ainda, verificou-se que alguns dos produtos líticos de um dos sítios analisados mostram padrões tecnológicos semelhantes, mesmo quando obtidos a partir de silcretes distintos. Caracterizou-se ausência de variação significativa dos atributos tecnológicos dos artefatos registrados em diferentes posicionamentos verticais nos perfis das unidades de escavação nas quais foram registrados, mesmo quando mostram-se associados a registros paleoambientais distintos (alternâncias entre climas mais secos que os atuais e condições caracterizadas por incrementos de umidade no intervalo de 11 a 7 mil anos atrás).Palavras chave: sítios arqueológicos líticos; Holoceno Inicial, paleoclimas, ameríndios, geoarqueologia The ancient human occupation (11-7 thousand years ago) of the Southern Brazilian Plateau: geomorphological, geological, paleoenvironmental and technological characterization of archaeological sites related to three distinct lithic industries A B S T R A C T In order to discuss connections between the natural landscapes and pre-colonial human occupation, were characterized the artifacts and the geomorphological and environmental contextualization of four lithic sites linked to ancient records of hunter-gatherer groups from the south and southeast of Brazil, associated with three distinct lithic industries. The association of sites with low slopes and altimetry in their respective contexts (more stable terrains for human settlement), adjacent to rivers and close to terrains that register greater inclinations and vertical unevenness, more likely to present rocky outcrops (potential sources of raw materials for making chipped tools) was listed. Were characterized sources of raw materials in the surroundings of each site, the raw materials associated with the artifacts, and the correlation between the two data sets was considered. The relationship between the technological standards of lithic artifacts and the petrographic characterization of the raw materials was analyzed, verifying which similar raw materials were used to produce different artifacts. Also, it was found that some of the lithic products from one of the analyzed sites show similar technological patterns, even when obtained from different raw materials. There was a lack of significant variation in the technological attributes of the artifacts recorded in different vertical positions in the profiles of the excavation units in which they were recorded, even when they are associated with different paleoenvironmental records (alternations between drier climates than current and others characterized by increments in the moisture between 11 to 7 thousand years ago).Keywords: lithic archaeological sites; Initial Holocene, paleoclimates, amerindians, geoarchaeology 

scholarly journals Characterization of Polyvinylidene Fluoride (PVDF) Electrospun Fibers Doped by Carbon Flakes

Polymers ◽  
2020 ◽  
Vol 12 (12) ◽  
pp. 2766
Author(s):  
Pavel Kaspar ◽  
Dinara Sobola ◽  
Klára Částková ◽  
Alexandr Knápek ◽  
Daniel Burda ◽  
...  
Keyword(s):  
Dielectric Constant ◽  
Thermal Degradation ◽  
Polymer Material ◽  
Polyvinylidene Fluoride ◽  
Electrospun Fibers ◽  
Complex Structures ◽  
Crystalline Phases ◽  
Points Of View ◽  
The Relationship

Polyvinylidene fluoride (PVDF) is a modern polymer material used in a wide variety of ways. Thanks to its excellent resistance to chemical or thermal degradation and low reactivity, it finds use in biology, chemistry, and electronics as well. By enriching the polymer with an easily accessible and cheap variant of graphite, it is possible to affect the ratio of crystalline phases. A correlation between the ratios of crystalline phases and different properties, like dielectric constant as well as piezo- and triboelectric properties, has been found, but the relationship between them is highly complex. These changes have been observed by a number of methods from structural, chemical and electrical points of view. Results of these methods have been documented to create a basis for further research and experimentation on the usability of this combined material in more complex structures and devices.

Demonstration of Improved Quantitative Mobility Spectrum Analysis (i-QMSA)

1997 ◽  
Vol 490 ◽  
Author(s):  
I. Vurgaftman ◽  
J. R. Meyer ◽  
C. A. Hoffman ◽  
D. Redfern ◽  
J. Antoszewski ◽  
...  
Keyword(s):  
Spectrum Analysis ◽  
Real Data ◽  
Semiconductor Materials ◽  
Data Sets ◽  
Mobility Spectrum ◽  
Data Set ◽  
Standard Tool ◽  
Field Dependent ◽  
Quantitative Mobility Spectrum Analysis

ABSTRACTWe discuss an improved quantitative mobility spectrum analysis (i-QMSA) of magnetic-field-dependent Hall and resistivity data, which can determine multiple electron and hole densities and mobilities. A fully automated computer implementation of i-QMSA is applied to a variety of synthetic and real data sets. The results show that the new algorithm increases the information available from a given data set and is suitable for use as a standard tool in the characterization of semiconductor materials and devices.

Neural Feature Abstraction from Judgments of Similarity

1998 ◽  
Vol 10 (7) ◽  
pp. 1815-1830 ◽  
Author(s):  
Michael D. Lee
Keyword(s):  
Neural Network ◽  
Multidimensional Scaling ◽  
Ad Hoc ◽  
Solution Space ◽  
Real Data ◽  
Neural Network Modeling ◽  
Data Sets ◽  
Regularization Technique ◽  
Clustering Approach ◽  
The Relationship

The common neural network modeling practice of representing the elements of a task domain in terms of a set of features lacks justification if the features are derived through some form of ad hoc preabstraction. By examining a featural similarity model related to established multidimensional scaling techniques, a neural network is developed that generates features from similarity data and attaches weights to these features. The network performs a constrained search of a continuous solution space to determine the features and uses a previously developed regularization technique to minimize the number of features it derives. The network is demonstrated on artificial data, from which it recovers known features and weights, and on two real data sets involving the similarity of a set of geometric shapes and the abstract conceptual similarities of the 10 Arabic numerals. On the basis of these results, the relationship between the multidimensional scaling approach adopted by the network and an alternative additive clustering approach to feature extraction is discussed.

A Help for Lifetime Management: Defect Characterisation Through Signal Processing of Ultrasonic Data

2003 ◽  
Author(s):  
S. Gautier ◽  
L. Cha˜tellier
Keyword(s):  
Signal Processing ◽  
Real Data ◽  
Data Sets ◽  
Height Estimation ◽  
Planar Defects ◽  
Mechanical Constraints ◽  
Processing Step ◽  
Non Destructive ◽  
Defect Characterisation

So as to detect and to characterize potential defects on cast components, a program of in-service inspections is carried out for the non destructive evaluation (NDE) of the component. A first step of inspection usually consists in detection. Still, should a defect be detected, one can be asked to prove the component still stands the mechanical constraints. Then, it is very important to be able to characterize precisely the size and the position of the defect. In the studied case, we concentrate on planar defects which are to be characterized from ultrasonic. The estimation of the height consists in measuring the time of flight between two reflectors: the diffraction and the corner echoes. But in case of small defects, the two echoes overlap and it is very difficult to give a height estimation of the defect. Then, the core of our contribution deals with the signal processing method we developed for the estimation of the height of planar defects. The use of our so-called deconvolution process now enables to obtain the height estimation of the defect, when it was impossible without processing. Processing results of real data sets are given for the inspection of representative mock-ups of homogeneous austenitic welds. In conclusion, the signal processing step turns out to be an important step in the characterization of defects and can thus contributes to maintain some components in service.

PROCESSING AND VISUALIZATION OF LIGHT MICROSCOPE IMAGES

2009 ◽  
Vol 09 (03) ◽  
pp. 369-388
Author(s):  
MAURICIO RAFAEL MAURER ◽  
HELIO PEDRINI ◽  
MARCO ANTONIO FERREIRA RANDI
Keyword(s):  
Image Analysis ◽  
Magnetic Resonance ◽  
Three Dimensional ◽  
Real Data ◽  
Data Sets ◽  
Complex Structures ◽  
X Ray ◽  
Knowledge Domains ◽  
Microscope Images ◽  
Effective Transfer

The analysis of three-dimensional structures of tissues and cellular constituents is a fundamental task in Biology and Medicine. Although three-dimensional images, acquired by light microscopes, play an important role in such knowledge domains, their analysis has not been much exploited compared to other imaging technologies, such as X-ray radiography, computerized tomography or magnetic resonance. In light microscopy, the majority of the activities involved in the image analysis (for instance, detection, counting, quantification) is still performed manually. The main difficulties among the others include the fact that the objects under investigation usually have complex structures, large number of cellular elements, shape variations and presence of noise in the acquired images. This paper describes a method for processing and visualization of images obtained with light microscopes. An effective transfer function based on the optical density of the cellular constituents is employed to generate the volumetric visualization. Several real data sets are used to demonstrate the effectiveness of the proposed method.

Skeletal elements of crinoid echinoderms: High-resolution structural and microanalytical results

1983 ◽  
Vol 41 ◽  
pp. 194-195
Author(s):  
D. F. Blake ◽  
L. F. Allard ◽  
D. R. Peacor
Keyword(s):  
High Resolution ◽  
Marine Invertebrates ◽  
Sea Urchins ◽  
Structural Features ◽  
Sea Stars ◽  
High Resolution Tem ◽  
Relationship Of ◽  
The Relationship ◽  
Insight Into

Echinodermata is a phylum of marine invertebrates which has been extant since Cambrian time (c.a. 500 m.y. before the present). Modern examples of echinoderms include sea urchins, sea stars, and sea lilies (crinoids). The endoskeletons of echinoderms are composed of plates or ossicles (Fig. 1) which are with few exceptions, porous, single crystals of high-magnesian calcite. Despite their single crystal nature, fracture surfaces do not exhibit the near-perfect {10.4} cleavage characteristic of inorganic calcite. This paradoxical mix of biogenic and inorganic features has prompted much recent work on echinoderm skeletal crystallography. Furthermore, fossil echinoderm hard parts comprise a volumetrically significant portion of some marine limestones sequences. The ultrastructural and microchemical characterization of modern skeletal material should lend insight into: 1). The nature of the biogenic processes involved, for example, the relationship of Mg heterogeneity to morphological and structural features in modern echinoderm material, and 2). The nature of the diagenetic changes undergone by their ancient, fossilized counterparts. In this study, high resolution TEM (HRTEM), high voltage TEM (HVTEM), and STEM microanalysis are used to characterize tha ultrastructural and microchemical composition of skeletal elements of the modern crinoid Neocrinus blakei.

EXELFS Studies of Carbon Fibers

1990 ◽  
Vol 48 (2) ◽  
pp. 72-73
Author(s):  
V. Serin ◽  
K. Hssein ◽  
G. Zanchi ◽  
J. Sévely
Keyword(s):  
Carbon Fibers ◽  
Energy Analysis ◽  
Electron Excitation ◽  
Complex Structures ◽  
High Modulus ◽  
Promising Technique ◽  
X Ray ◽  
Fine Structures ◽  
X Ray Absorption

The present developments of electron energy analysis in the microscopes by E.E.L.S. allow an accurate recording of the spectra and of their different complex structures associated with the inner shell electron excitation by the incident electrons (1). Among these structures, the Extended Energy Loss Fine Structures (EXELFS) are of particular interest. They are equivalent to the well known EXAFS oscillations in X-ray absorption spectroscopy. Due to the EELS characteristic, the Fourier analysis of EXELFS oscillations appears as a promising technique for the characterization of composite materials, the major constituents of which are low Z elements. Using EXELFS, we have developed a microstructural study of carbon fibers. This analysis concerns the carbon K edge, which appears in the spectra at 285 eV. The purpose of the paper is to compare the local short range order, determined by this way in the case of Courtauld HTS and P100 ex-polyacrylonitrile carbon fibers, which are high tensile strength (HTS) and high modulus (HM) fibers respectively.

Microstructural Characterization of Au-Ge-Ni based ohmic contacts to GaAs/AlGaAs modfet device

1987 ◽  
Vol 45 ◽  
pp. 326-327
Author(s):  
A.K. Rai ◽  
A.K. Petford-Long ◽  
A. Ezis ◽  
D.W. Langer
Keyword(s):  
Contact Resistance ◽  
Ohmic Contact ◽  
Ohmic Contacts ◽  
Microstructural Characterization ◽  
Almost Everywhere ◽  
Spacer Layer ◽  
Good Contact ◽  
The Relationship ◽  
Lower Contact

Considerable amount of work has been done in studying the relationship between the contact resistance and the microstructure of the Au-Ge-Ni based ohmic contacts to n-GaAs. It has been found that the lower contact resistivity is due to the presence of Ge rich and Au free regions (good contact area) in contact with GaAs. Thus in order to obtain an ohmic contact with lower contact resistance one should obtain a uniformly alloyed region of good contact areas almost everywhere. This can possibly be accomplished by utilizing various alloying schemes. In this work microstructural characterization, employing TEM techniques, of the sequentially deposited Au-Ge-Ni based ohmic contact to the MODFET device is presented.The substrate used in the present work consists of 1 μm thick buffer layer of GaAs grown on a semi-insulating GaAs substrate followed by a 25 Å spacer layer of undoped AlGaAs.

Sign in / Sign up

Export Citation Format

Share Document