The use of segmented linear models to analyze gene array time course experiments

2021 ◽  
Author(s):  
Bailu Xu
Keyword(s):  
Time Course ◽  
Linear Models ◽  
Gene Array

scholarly journals The effect of a prototype hydromulch on soil water evaporation under controlled laboratory conditions

2020 ◽  
Vol 68 (4) ◽  
pp. 404-410
Author(s):  
Antoni M.C. Verdú ◽  
M. Teresa Mas ◽  
Ramon Josa ◽  
Marta Ginovart
Keyword(s):  
Water Content ◽  
Soil Water ◽  
Soil Water Content ◽  
Time Course ◽  
Linear Models ◽  
Water Evaporation ◽  
Mechanical Resistance ◽  
Evaporation Process ◽  
Soil Columns ◽  
Dry Conditions

AbstractOrganic hydromulches can be an interesting alternative for weed control in perennial crops, but can also reduce soil water evaporation. To examine the effect of a hydromulch layer on soil water content in dry conditions laboratory experiments were conducted at constant 25°C, 40% air RH. Both for small soil containers with a short time course and for larger soil columns (with two sensors at depths of 6 cm and 11 cm) with a longer time course, the presence and also the thickness of hydromulch were significant factors for the temporal evolution of soil water content. Two distinct stages of the evaporation process, the first or initial stage and the last or final stage, were identified, analysed and compared for these experiments. General linear models performed on the soil water content temporal evolutions showed significant differences for the first and last stages at the top and bottom of the soil columns with and without hydromulch. Hydromulch application delayed the evaporation process in comparison with the control. Moreover, the hydromulch layer, which was tested for mechanical resistance to punching, offered enough resistance to prevent its perforation by the sprouts of weed rhizomes.

scholarly journals The same ultra-rapid parallel brain dynamics underpin the production and perception of speech

2021 ◽  
Author(s):  
Amie Fairs ◽  
Amandine Michelas ◽  
Sophie Dufour ◽  
Kristof Strijkers
Keyword(s):  
Language Processing ◽  
Time Course ◽  
Linear Models ◽  
Temporal Dynamics ◽  
Building Blocks ◽  
Naming Task ◽  
Stimulus Onset ◽  
Language Models ◽  
Mixed Linear Models ◽  
Listening Task

AbstractThe temporal dynamics by which linguistic information becomes available is one of the key properties to understand how language is organised in the brain. An unresolved debate between different brain language models is whether words, the building blocks of language, are activated in a sequential or parallel manner. In this study we approached this issue from a novel perspective by directly comparing the time course of word component activation in speech production versus perception. In an overt object naming task and a passive listening task we analysed with mixed linear models at the single-trial level the event-related brain potentials elicited by the same lexico-semantic and phonological word knowledge in the two language modalities. Results revealed that both word components manifested simultaneously as early as 75 ms after stimulus onset in production and perception; differences between the language modalities only became apparent after 300 ms of processing. The data provide evidence for ultra-rapid parallel dynamics of language processing and are interpreted within a neural assembly framework where words recruit the same integrated cell assemblies across production and perception. These word assemblies ignite early on in parallel and only later on reverberate in a behaviour-specific manner.

scholarly journals Hierarchical Bayesian Neural Network for Gene Expression Temporal Patterns

2004 ◽  
Vol 3 (1) ◽  
pp. 1-23 ◽  
Author(s):  
Yulan Liang ◽  
Arpad G Kelemen
Keyword(s):  
Neural Network ◽  
Gene Expression ◽  
Time Course ◽  
Gene Array ◽  
Temporal Patterns ◽  
Support Vector ◽  
Dynamic Feature ◽  
Hierarchical Bayesian ◽  
Temporal Data ◽  
Bayesian Neural Network

There are several important issues to be addressed for gene expression temporal patterns' analysis: first, the correlation structure of multidimensional temporal data; second, the numerous sources of variations with existing high level noise; and last, gene expression mostly involves heterogeneous multiple dynamic patterns. We propose a Hierarchical Bayesian Neural Network model to account for the input correlations of time course gene array data. The variations in absolute gene expression levels and the noise can be estimated with the hierarchical Bayesian setting. The network parameters and the hyperparameters were simultaneously optimized with Monte Carlo Markov Chain simulation. Results show that the proposed model and algorithm can well capture the dynamic feature of gene expression temporal patterns despite the high noise levels, the highly correlated inputs, the overwhelming interactions, and other complex features typically present in microarray data. We test and demonstrate the proposed models with yeast cell cycle temporal data sets. The model performance of Hierarchical Bayesian Neural Network was compared to other popular machine learning methods such as Nearest Neighbor, Support Vector Machine, and Self Organized Map.

Quadrature subunits in directionally selective simple cells: Spatiotemporal interactions

1997 ◽  
Vol 14 (2) ◽  
pp. 357-371 ◽  
Author(s):  
Robert C. Emerson
Keyword(s):  
Time Course ◽  
Striate Cortex ◽  
Linear Models ◽  
Linear Filter ◽  
Nonlinear Interactions ◽  
Linear Superposition ◽  
Cortical Cells ◽  
Simple Cells ◽  
Preferred Direction ◽  
Branch Model

AbstractI explore here whether linear mechanisms can explain directional selectivity (DS) in simple cells of the cat's striate cortex, a question suggested by a recent upswing in popularity of linear DS models. I chose a simple cell with a space-time inseparable receptive field (RF), i.e. one that shows gradually shifting latency across space, as the RF type most likely to depend on linear mechanisms of DS. However, measured responses of the cell to a moving bar were less modulated, and extended over a larger spatial region than predicted by two different popular “linear” models. They also were more DS in exhibiting a higher ratio of total spikes for the preferred direction. Each of the two models used for comparison has a single “branch” with a single spatiotemporally inseparable linear filter followed by a threshold, hence, a “1-branch” model. Nonlinear interactions between pairs of bars in a 2-bar linear superposition test of the cell also disagreed in time-course with those of the 1-branch models. The only model whose 1-bar and 2-bar predictions matched the measured cell (including a complete “4-branch” motion energy model that matches complex cells) has two branches that differ in phase by about 90 deg, i.e. in quadrature. Each branch has its own threshold that helps define the preceding spatiotemporal unit as a subunit even after the outputs of the two branches are summed. As subunit phases differ by only 90 deg, flashing bar responses of the 2-subunit model are similar to those of the 1-subunit model. Therefore, the number of subunits is hidden from view when testing with a conventional stationary bar. In summary, movement responses and nonlinear interactions between pairs of bars in the measured cell matched those of the 2-subunit model, while they disagreed with the popular 1-subunit model. Thus, multiple nonlinear subunits appear to be necessary for DS, even in simple cortical cells.

Ultrastructural Changes of the Symbiotic Chlorella-Like Alga Isolated from Hydra Viridis

1982 ◽  
Vol 40 ◽  
pp. 320-321
Author(s):  
K.W. Lee ◽  
R.H. Meints ◽  
D. Kuczmarski ◽  
J.L. Van Etten
Keyword(s):  
Time Course ◽  
Reciprocal Cross ◽  
Ultrastructural Level ◽  
Ultrastructural Changes ◽  
Symbiotic Relationship ◽  
Cell Recognition ◽  
Green Hydra ◽  
Different Strains ◽  
Hydra Viridis

The physiological, biochemical, and ultrastructural aspects of the symbiotic relationship between the Chlorella-like algae and the hydra have been intensively investigated. Reciprocal cross-transfer of the Chlorellalike algae between different strains of green hydra provide a system for the study of cell recognition. However, our attempts to culture the algae free of the host hydra of the Florida strain, Hydra viridis, have been consistently unsuccessful. We were, therefore, prompted to examine the isolated algae at the ultrastructural level on a time course.

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.

The time course of calcium deposition in shells of the barnacle (Balanus amphititre amphititre) during cyprid-juvenile metamorphosis

1994 ◽  
Vol 52 ◽  
pp. 178-179
Author(s):  
Nancy R. Wallace ◽  
Craig C. Freudenrich ◽  
Karl Wilbur ◽  
Peter Ingram ◽  
Ann LeFurgey
Keyword(s):  
Electron Microscopy ◽  
Scanning Electron Microscopy ◽  
Time Course ◽  
Vertical Plane ◽  
Mantle Cavity ◽  
Qualitative Assessment ◽  
Calcium Deposition ◽  
Free Swimming ◽  
Freeze Dried ◽  
Scanning Electron

The morphology of balanomorph barnacles during metamorphosis from the cyprid larval stage to the juvenile has been examined by light microscopy and scanning electron microscopy (SEM). The free-swimming cyprid attaches to a substrate, rotates 90° in the vertical plane, molts, and assumes the adult shape. The resulting metamorph is clad in soft cuticle and has an adult-like appearance with a mantle cavity, thorax with cirri, and incipient shell plates. At some time during the development from cyprid to juvenile, the barnacle begins to mineralize its shell, but it is not known whether calcification occurs before, during, or after ecdysis. To examine this issue, electron probe x-ray microanalysis (EPXMA) was used to detect calcium in cyprids and juveniles at various times during metamorphosis.Laboratory-raised, free-swimming cyprid larvae were allowed to settle on plastic coverslips in culture dishes of seawater. The cyprids were observed with a dissecting microscope, cryopreserved in liquid nitrogen-cooled liquid propane at various times (0-24 h) during metamorphosis, freeze dried, rotary carbon-coated, and examined with scanning electron microscopy (SEM). EPXMA dot maps were obtained in parallel for qualitative assessment of calcium and other elements in the carapace, wall, and opercular plates.

Arabidopsis 4-COUMAROYL-COA LIGASE 8 contributes to the biosynthesis of the benzenoid ring of coenzyme Q in peroxisomes

2019 ◽  
Vol 476 (22) ◽  
pp. 3521-3532
Author(s):  
Eric Soubeyrand ◽  
Megan Kelly ◽  
Shea A. Keene ◽  
Ann C. Bernert ◽  
Scott Latimer ◽  
...  
Keyword(s):  
Oxidative Metabolism ◽  
Time Course ◽  
Reverse Genetics ◽  
De Novo ◽  
Coenzyme Q ◽  
Control Level ◽  
Wild Type ◽  
Fluorescent Reporters ◽  
Coa Ligase ◽  
Peroxisomal Targeting

Plants have evolved the ability to derive the benzenoid moiety of the respiratory cofactor and antioxidant, ubiquinone (coenzyme Q), either from the β-oxidative metabolism of p-coumarate or from the peroxidative cleavage of kaempferol. Here, isotopic feeding assays, gene co-expression analysis and reverse genetics identified Arabidopsis 4-COUMARATE-COA LIGASE 8 (4-CL8; At5g38120) as a contributor to the β-oxidation of p-coumarate for ubiquinone biosynthesis. The enzyme is part of the same clade (V) of acyl-activating enzymes than At4g19010, a p-coumarate CoA ligase known to play a central role in the conversion of p-coumarate into 4-hydroxybenzoate. A 4-cl8 T-DNA knockout displayed a 20% decrease in ubiquinone content compared with wild-type plants, while 4-CL8 overexpression boosted ubiquinone content up to 150% of the control level. Similarly, the isotopic enrichment of ubiquinone's ring was decreased by 28% in the 4-cl8 knockout as compared with wild-type controls when Phe-[Ring-13C6] was fed to the plants. This metabolic blockage could be bypassed via the exogenous supply of 4-hydroxybenzoate, the product of p-coumarate β-oxidation. Arabidopsis 4-CL8 displays a canonical peroxisomal targeting sequence type 1, and confocal microscopy experiments using fused fluorescent reporters demonstrated that this enzyme is imported into peroxisomes. Time course feeding assays using Phe-[Ring-13C6] in a series of Arabidopsis single and double knockouts blocked in the β-oxidative metabolism of p-coumarate (4-cl8; at4g19010; at4g19010 × 4-cl8), flavonol biosynthesis (flavanone-3-hydroxylase), or both (at4g19010 × flavanone-3-hydroxylase) indicated that continuous high light treatments (500 µE m−2 s−1; 24 h) markedly stimulated the de novo biosynthesis of ubiquinone independently of kaempferol catabolism.

Short-term volume and turgor regulation in yeast

2008 ◽  
Vol 45 ◽  
pp. 147-160 ◽  
Author(s):  
Jörg Schaber ◽  
Edda Klipp
Keyword(s):  
Dynamic Model ◽  
Volume Change ◽  
Volume Regulation ◽  
Time Course ◽  
Osmotic Shock ◽  
Intracellular Concentration ◽  
Short Term ◽  
Hydrodynamic Property ◽  
Turgor Regulation ◽  
Thermodynamic Framework

Volume is a highly regulated property of cells, because it critically affects intracellular concentration. In the present chapter, we focus on the short-term volume regulation in yeast as a consequence of a shift in extracellular osmotic conditions. We review a basic thermodynamic framework to model volume and solute flows. In addition, we try to select a model for turgor, which is an important hydrodynamic property, especially in walled cells. Finally, we demonstrate the validity of the presented approach by fitting the dynamic model to a time course of volume change upon osmotic shock in yeast.

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