scholarly journals DynOmics to identify delays and co-expression patterns across time course experiments

2016 ◽  
Author(s):  
Jasmin Straube ◽  
Bevan Emma Huang ◽  
Kim-Anh Lê Cao
Keyword(s):  
Time Course ◽  
Expression Patterns ◽  
Time Integration ◽  
Omics Data ◽  
Multiple Sources ◽  
Combining Data ◽  
The Difference ◽  
Changes Over Time ◽  
High Degree ◽  
Molecular Expression

ABSTRACTDynamic changes in biological systems can be captured by measuring molecular expression from different levels (e.g., genes and proteins) across time. Integration of such data aims to identify molecules that show similar expression changes over time; such molecules may be co-regulated and thus involved in similar biological processes. Combining data sources presents a systematic approach to study molecular behaviour. It can compensate for missing data in one source, and can reduce false positives when multiple sources highlight the same pathways. However, integrative approaches must accommodate the challenges inherent in ‘omics’ data, including high-dimensionality, noise, and timing differences in expression. As current methods for identification of co-expression cannot cope with this level of complexity, we developed a novel algorithm called DynOmics. DynOmics is based on the fast Fourier transform, from which the difference in expression initiation between trajectories can be estimated. This delay can then be used to realign the trajectories and identify those which show a high degree of correlation. Through extensive simulations, we demonstrate that DynOmics is efficient and accurate compared to existing approaches. We consider two case studies highlighting its application, identifying regulatory relationships across ‘omics’ data within an organism and for comparative gene expression analysis across organisms.

Destruction of Actin Filaments by Osmium Tetroxide

1977 ◽  
Vol 35 ◽  
pp. 466-467
Author(s):  
P. Maupin-Szamier ◽  
T. D. Pollard
Keyword(s):  
Actin Filaments ◽  
Time Course ◽  
Osmium Tetroxide ◽  
Rabbit Muscle ◽  
Muscle Actin ◽  
Sodium Phosphate Buffer ◽  
Transmission Electron ◽  
The Difference ◽  
Rates Of Decay ◽  
Short Time

We have studied the destruction of rabbit muscle actin filaments by osmium tetroxide (OSO4) to develop methods which will preserve the structure of actin filaments during preparation for transmission electron microscopy.Negatively stained F-actin, which appears as smooth, gently curved filaments in control samples (Fig. 1a), acquire an angular, distorted profile and break into progressively shorter pieces after exposure to OSO4 (Fig. 1b,c). We followed the time course of the reaction with viscometry since it is a simple, quantitative method to assess filament integrity. The difference in rates of decay in viscosity of polymerized actin solutions after the addition of four concentrations of OSO4 is illustrated in Fig. 2. Viscometry indicated that the rate of actin filament destruction is also dependent upon temperature, buffer type, buffer concentration, and pH, and requires the continued presence of OSO4. The conditions most favorable to filament preservation are fixation in a low concentration of OSO4 for a short time at 0°C in 100mM sodium phosphate buffer, pH 6.0.

scholarly journals Generational Differences in Support and Care of Individuals Diagnosed With Severe Mental Illness

2020 ◽  
Vol 4 (Supplement_1) ◽  
pp. 94-94
Author(s):  
Deborah Finkel ◽  
Per Bulöw ◽  
Pia Bulöw ◽  
Monika Wilińska ◽  
Cristina Joy Torgé ◽  
...  
Keyword(s):  
Social Support ◽  
Mental Illness ◽  
Severe Mental Illness ◽  
Social Services ◽  
Generational Differences ◽  
System A ◽  
Care Systems ◽  
The Difference ◽  
Changes Over Time ◽  
Age Range

Abstract As part of the process of de-institutionalizing the Swedish mental health care system, a reform was implemented in 1995 moving responsibility for social support for people with severe mental illness (SMI) from the county to social services in the municipalities. In many ways, older people with SMI were neglected in this changing landscape of psychiatric care. To investigate possible generational differences in support experiences, two nonoverlapping cohorts were created from surveys conducted every fifth year between 1996 and 2011 in one middle-sized municipality in the south of Sweden, aiming to detect the needs for social support. Cohort 1 includes everyone detected at the 1996 survey aged 65 and 79 years (N = 92). Cohort 2 includes individuals first detected at the 2011 survey who were aged 65 to 79 (N = 104). Results indicates significant differences between the two cohorts in diagnosis, reflecting changes over time in diagnostic tendencies. Cohort 1 was on average 10 years older than Cohort 2, even within the restricted age range. After correcting for age, there were no differences between the two cohorts in education, functioning (CAN and GAF), or marital status. Although Cohort 1 experienced more days of institutionalization than Cohort 2 (median = 424.5 days vs. 382 days), the difference was not statistically significant. Cohort 2 had significantly higher additional subsidies and disposable income, as well as significantly higher income from other sources after retirement. Results indicate the changing demands that older adults with SMI will place on care systems.

scholarly journals Analysis of Transcriptional Changes in Different Brassica napus Synthetic Allopolyploids

Genes ◽  
2021 ◽  
Vol 12 (1) ◽  
pp. 82
Author(s):  
Yunxiao Wei ◽  
Guoliang Li ◽  
Shujiang Zhang ◽  
Shifan Zhang ◽  
Hui Zhang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Brassica Napus ◽  
Differentially Expressed Genes ◽  
Expression Patterns ◽  
Female Parent ◽  
Enrichment Analysis ◽  
Differentially Expressed ◽  
Transcriptional Changes ◽  
Aa Genome ◽  
High Degree

Allopolyploidy is an evolutionary and mechanistically intriguing process involving the reconciliation of two or more sets of diverged genomes and regulatory interactions, resulting in new phenotypes. In this study, we explored the gene expression patterns of eight F2 synthetic Brassica napus using RNA sequencing. We found that B. napus allopolyploid formation was accompanied by extensive changes in gene expression. A comparison between F2 and the parent shows a certain proportion of differentially expressed genes (DEG) and activation\silent gene, and the two genomes (female parent (AA)\male parent (CC) genomes) showed significant differences in response to whole-genome duplication (WGD); non-additively expressed genes represented a small portion, while Gene Ontology (GO) enrichment analysis showed that it played an important role in responding to WGD. Besides, genome-wide expression level dominance (ELD) was biased toward the AA genome, and the parental expression pattern of most genes showed a high degree of conservation. Moreover, gene expression showed differences among eight individuals and was consistent with the results of a cluster analysis of traits. Furthermore, the differential expression of waxy synthetic pathways and flowering pathway genes could explain the performance of traits. Collectively, gene expression of the newly formed allopolyploid changed dramatically, and this was different among the selfing offspring, which could be a prominent cause of the trait separation. Our data provide novel insights into the relationship between the expression of differentially expressed genes and trait segregation and provide clues into the evolution of allopolyploids.

scholarly journals Analysis of Radiation Damage in Light Water Reactors: Comparison of Cluster Analysis Methods for the Analysis of Atom Probe Data

2017 ◽  
Vol 23 (2) ◽  
pp. 366-375 ◽  
Author(s):  
Jonathan M. Hyde ◽  
Gérald DaCosta ◽  
Constantinos Hatzoglou ◽  
Hannah Weekes ◽  
Bertrand Radiguet ◽  
...  
Keyword(s):  
Cluster Analysis ◽  
Radiation Damage ◽  
Defect Formation ◽  
Chemical Species ◽  
Atom Probe ◽  
Three Dimensions ◽  
Multiple Sources ◽  
Damage Models ◽  
Combining Data ◽  
Water Reactors

AbstractIrradiation of reactor pressure vessel (RPV) steels causes the formation of nanoscale microstructural features (termed radiation damage), which affect the mechanical properties of the vessel. A key tool for characterizing these nanoscale features is atom probe tomography (APT), due to its high spatial resolution and the ability to identify different chemical species in three dimensions. Microstructural observations using APT can underpin development of a mechanistic understanding of defect formation. However, with atom probe analyses there are currently multiple methods for analyzing the data. This can result in inconsistencies between results obtained from different researchers and unnecessary scatter when combining data from multiple sources. This makes interpretation of results more complex and calibration of radiation damage models challenging. In this work simulations of a range of different microstructures are used to directly compare different cluster analysis algorithms and identify their strengths and weaknesses.

scholarly journals Jonckheere–Terpstra–Kendall-based non-parametric analysis of temporal differential gene expression

2021 ◽  
Vol 3 (1) ◽  
Author(s):  
Hitoshi Iuchi ◽  
Michiaki Hamada
Keyword(s):  
Gene Expression ◽  
Time Series ◽  
Time Course ◽  
Time Series Data ◽  
Expression Patterns ◽  
Detection Methods ◽  
Series Data ◽  
Expression Levels ◽  
Over Time ◽  
Non Parametric

Abstract Time-course experiments using parallel sequencers have the potential to uncover gradual changes in cells over time that cannot be observed in a two-point comparison. An essential step in time-series data analysis is the identification of temporal differentially expressed genes (TEGs) under two conditions (e.g. control versus case). Model-based approaches, which are typical TEG detection methods, often set one parameter (e.g. degree or degree of freedom) for one dataset. This approach risks modeling of linearly increasing genes with higher-order functions, or fitting of cyclic gene expression with linear functions, thereby leading to false positives/negatives. Here, we present a Jonckheere–Terpstra–Kendall (JTK)-based non-parametric algorithm for TEG detection. Benchmarks, using simulation data, show that the JTK-based approach outperforms existing methods, especially in long time-series experiments. Additionally, application of JTK in the analysis of time-series RNA-seq data from seven tissue types, across developmental stages in mouse and rat, suggested that the wave pattern contributes to the TEG identification of JTK, not the difference in expression levels. This result suggests that JTK is a suitable algorithm when focusing on expression patterns over time rather than expression levels, such as comparisons between different species. These results show that JTK is an excellent candidate for TEG detection.

Gebruiksaspecten van het uitroeppartikel wat in het Nederlands en Fries

2020 ◽  
Vol 136 (4) ◽  
pp. 189-209
Author(s):  
Henk Wolf
Keyword(s):  
The Core ◽  
The Difference ◽  
Lexical Phrase ◽  
High Degree ◽  
Lexical Phrases

Abstract Both Dutch and (West) Frisian make use of the exclamative particle wat (‘how’), that adds an element of surprise about a high degree of something to the semantics of the sentence. In this paper I will first show the similarities between the use of the particle in the two languages. I will demonstrate that, in Dutch, its use is largely confined to constructions that are semantically scalable, whereas in Frisian this restriction is far less strict. I will explain the difference by showing that Dutch wat is a syntactic amplifier of lexical phrases, whereas Frisian wat has developed into a pragmatic amplifier of the core predicate. I will try to account for that difference by showing how homophonous words absent in Dutch are likely to have influenced the use of Frisian wat, and how Dutch prosody strengthens the connection between wat and the amplified lexical phrase, whereas Frisian prosody weakens it. Finally, I will show that the system described as ‘Frisian’ is occasionally found in varieties of Dutch too

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