Browse
Submit Data
Databases
API
Help

Dataset Information

18 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Time series experimental design under one-shot sampling: The importance of condition diversity.

ABSTRACT: Many biological data sets are prepared using one-shot sampling, in which each individual organism is sampled at most once. Time series therefore do not follow trajectories of individuals over time. However, samples collected at different times from individuals grown under the same conditions share the same perturbations of the biological processes, and hence behave as surrogates for multiple samples from a single individual at different times. This implies the importance of growing individuals under multiple conditions if one-shot sampling is used. This paper models the condition effect explicitly by using condition-dependent nominal mRNA production amounts for each gene, it quantifies the performance of network structure estimators both analytically and numerically, and it illustrates the difficulty in network reconstruction under one-shot sampling when the condition effect is absent. A case study of an Arabidopsis circadian clock network model is also included.

SUBMITTER: Kang X

PROVIDER: S-EPMC6822768 | biostudies-literature | 2019

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Time series experimental design under one-shot sampling: The importance of condition diversity.

Kang Xiaohan X Hajek Bruce B Wu Faqiang F Hanzawa Yoshie Y

PloS one 20191031 10

Many biological data sets are prepared using one-shot sampling, in which each individual organism is sampled at most once. Time series therefore do not follow trajectories of individuals over time. However, samples collected at different times from individuals grown under the same conditions share the same perturbations of the biological processes, and hence behave as surrogates for multiple samples from a single individual at different times. This implies the importance of growing individuals u ...[more]

PMID: 31671126

Similar Datasets

Phase Diversity Electro-optic Sampling: A new approach to single-shot terahertz waveform recording.

Project description:Recording electric field evolution in single-shot with THz bandwidth is needed in science including spectroscopy, plasmas, biology, chemistry, Free-Electron Lasers, accelerators, and material inspection. However, the potential application range depends on the possibility to achieve sub-picosecond resolution over a long time window, which is a largely open problem for single-shot techniques. To solve this problem, we present a new conceptual approach for the so-called spectral decoding technique, where a chirped laser pulse interacts with a THz signal in a Pockels crystal, and is analyzed using a grating optical spectrum analyzer. By borrowing mathematical concepts from photonic time stretch theory and radio-frequency communication, we deduce a novel dual-output electro-optic sampling system, for which the input THz signal can be numerically retrieved-with unprecedented resolution-using the so-called phase diversity technique. We show numerically and experimentally that this approach enables the recording of THz waveforms in single-shot over much longer durations and/or higher bandwidth than previous spectral decoding techniques. We present and test the proposed DEOS (Diversity Electro-Optic Sampling) design for recording 1.5 THz bandwidth THz pulses, over 20 ps duration, in single-shot. Then we demonstrate the potential of DEOS in accelerator physics by recording, in two successive shots, the shape of 200 fs RMS relativistic electron bunches at European X-FEL, over 10 ps recording windows. The designs presented here can be used directly for accelerator diagnostics, characterization of THz sources, and single-shot Time-Domain Spectroscopy.

| S-EPMC8748811 | biostudies-literature

Sampling plant diversity and rarity at landscape scales: importance of sampling time in species detectability.

Project description:Documenting and estimating species richness at regional or landscape scales has been a major emphasis for conservation efforts, as well as for the development and testing of evolutionary and ecological theory. Rarely, however, are sampling efforts assessed on how they affect detection and estimates of species richness and rarity. In this study, vascular plant richness was sampled in 356 quarter hectare time-unlimited survey plots in the boreal region of northeast Alberta. These surveys consisted of 15,856 observations of 499 vascular plant species (97 considered to be regionally rare) collected by 12 observers over a 2 year period. Average survey time for each quarter-hectare plot was 82 minutes, ranging from 20 to 194 minutes, with a positive relationship between total survey time and total plant richness. When survey time was limited to a 20-minute search, as in other Alberta biodiversity methods, 61 species were missed. Extending the survey time to 60 minutes, reduced the number of missed species to 20, while a 90-minute cut-off time resulted in the loss of 8 species. When surveys were separated by habitat type, 60 minutes of search effort sampled nearly 90% of total observed richness for all habitats. Relative to rare species, time-unlimited surveys had ? 65% higher rare plant detections post-20 minutes than during the first 20 minutes of the survey. Although exhaustive sampling was attempted, observer bias was noted among observers when a subsample of plots was re-surveyed by different observers. Our findings suggest that sampling time, combined with sample size and observer effects, should be considered in landscape-scale plant biodiversity surveys.

| S-EPMC3989307 | biostudies-literature

Gamma diversity and under-sampling together generate patterns in beta-diversity.

Project description:Beta diversity represents how species in the regional pool segregate among local communities and hence forms a link between local and regional species diversities. Therefore, the magnitude of beta diversity and its variation across geographic gradients can provide insights into mechanisms of community assembly. Along with limits on local or regional level diversities, effects of local abundance that lead to under-sampling of the regional species pool are important determinants of estimated beta diversity. We explore the effects of regional species pools, abundance distributions, and local abundance to show that patterns in beta diversity as well as the mean of species abundance distribution have distinct outcomes, depending on limits on species pools and under-sampling. We highlight the effect of under-sampling in some established relationships between gamma diversity and beta diversity using graphical methods. We then use empirical data on ant communities across an elevational gradient in the Eastern Himalayas to demonstrate a shift from effect of reduction in species pool to under-sampling at mid-elevations. Our results show that multiple processes with contrasting effects simultaneously affect patterns in beta diversity across geographic gradients.

| S-EPMC8563776 | biostudies-literature

One-shot analysis of translated mammalian lncRNAs with AHARIBO

Project description:A vast portion of the mammalian genome is transcribed as long non-coding RNAs (lncRNAs) acting in the cytoplasm with largely unknown functions. Surprisingly, lncRNAs have been shown to interact with ribosomes, encode uncharacterized proteins, or act as ribosome sponges. These functions still remain mostly undetected and understudied owing to the lack of efficient tools for genome-wide simultaneous identification of ribosome-associated lncRNAs and peptide-producing lncRNAs. Here we present AHARIBO, a method for the detection of lncRNAs either untranslated, but associated with ribosomes, or encoding small peptides. Using AHARIBO in mouse embryonic stem cells during neuronal differentiation, we isolated ribosome-protected RNA fragments, translated RNAs and corresponding de novo synthesized polypeptides. Besides identifying mRNAs under active translation and associated ribosomes, we found and distinguished lncRNAs acting as ribosome sponges or encoding micropeptides, laying the ground for a better functional understanding of hundreds lncRNAs.

2021-02-28 | GSE167865 | GEO

Experimental demonstration of the importance of competition under disturbance.

Project description:Ecologists have long recognized the roles of competition and disturbance in shaping ecological communities, and the combinatorial effects of these two factors have been the subject of substantial ecological research. Nevertheless, it is still unclear whether competition remains as an important structuring force in habitats strongly influenced by disturbance. The conventional belief remains that the importance of competition decreases with increasing disturbance, but limited theory suggests otherwise. Using protist communities established in laboratory microcosms, we demonstrate that disturbance does not diminish the importance of competition. Interspecific competition significantly increased rates of species extinction over a broad disturbance gradient, and increasing disturbance intensities increased, rather than decreased, the tempo of competitive exclusion. This community-level pattern is linked to the species-level pattern that interspecific competition led to most frequent extinctions of each species at the highest level of disturbance that the species can tolerate. Consequently, despite a strong tradeoff between competitive ability and disturbance tolerance across the competing species, species diversity generally declined with disturbance. The consistent structuring role of competition throughout the disturbance gradient underscores the need to understand competitive interactions and their consequences even in highly disturbed habitats.

| S-EPMC2919955 | biostudies-literature

Experimental condition

Project description:BY4730 cultures were exposed to medium containing dilutions of test agent (Cisplatin (Cis), 600mg/mL; Methylmethane sulfonate (MMS), 0.12% v/v; Bleomycin (Bleo), 0.15U/mL; NaCl, 10mg/mL; ethanol, 15% v/v) for 120 min. Control cultures were either mock-treated with the solvent, DMSO (for comparison to Cis, MMS, Bleo) or maintained in media (for comparison to ethanol and NaCl) for 120 mins. Sample preparation and processing procedures were performed according the Affymetrix Genechipâ Expression Analysis Technical Manual (Affymetrix, Santa Clara, CA). Briefly, total RNA was isolated from thawed cell pellets using a hot phenol protocol described by Schmitt et. al. (1990). Total RNA was converted to poly(A)+ mRNA and isolated using Oligotex mRNA kit. Double stranded cDNA was generated by using T7-(dT) 24 oligo primer (Genset Corp., San Diego, CA) and Superscript Double Stranded cDNA Synthesis Kit (Gibco BRL, Carlsbad, CA). The cDNA was used for in vitro transcription (IVT) with Enzo BioArray RNA Transcript Labeling Kit to incorporate biotinylated ribonucleotides. Biotinylated cRNA (15 mg) was fragmented in 40 mM tris-acetate, pH 8.1; 30 mM MgOAc; 100 mM KOAc. Samples were then hybridized with Affymetrix probe array Yeast Genome S98 at 45°C for 16 hours with constant rotation. Hybridized probe arrays were washed and stained using an Affymetrix GeneChipâ Fluidics Station 400 and protocol EukGE-WS2. The chips were scanned using the Affymetrix GeneArray Scanner. Keywords: repeat sample

2005-04-20 | GSE2224 | GEO

Experimental Design, Population Dynamics, and Diversity in Microbial Experimental Evolution.

Project description:In experimental evolution, laboratory-controlled conditions select for the adaptation of species, which can be monitored in real time. Despite the current popularity of such experiments, nature's most pervasive biological force was long believed to be observable only on time scales that transcend a researcher's life-span, and studying evolution by natural selection was therefore carried out solely by comparative means. Eventually, microorganisms' propensity for fast evolutionary changes proved us wrong, displaying strong evolutionary adaptations over a limited time, nowadays massively exploited in laboratory evolution experiments. Here, we formulate a guide to experimental evolution with microorganisms, explaining experimental design and discussing evolutionary dynamics and outcomes and how it is used to assess ecoevolutionary theories, improve industrially important traits, and untangle complex phenotypes. Specifically, we give a comprehensive overview of the setups used in experimental evolution. Additionally, we address population dynamics and genetic or phenotypic diversity during evolution experiments and expand upon contributing factors, such as epistasis and the consequences of (a)sexual reproduction. Dynamics and outcomes of evolution are most profoundly affected by the spatiotemporal nature of the selective environment, where changing environments might lead to generalists and structured environments could foster diversity, aided by, for example, clonal interference and negative frequency-dependent selection. We conclude with future perspectives, with an emphasis on possibilities offered by fast-paced technological progress. This work is meant to serve as an introduction to those new to the field of experimental evolution, as a guide to the budding experimentalist, and as a reference work to the seasoned expert.

| S-EPMC6094045 | biostudies-literature

Pituitary hyperplasia: case series and literature review of an under-recognised and heterogeneous condition.

Project description:Pituitary hyperplasia (PH) occurs in heterogeneous settings and remains under-recognised. Increased awareness of this condition and its natural history should circumvent unnecessary trans-sphenoidal surgery. We performed an observational case series of patients referred to a single endocrinologist over a 3-year period. Four young women were identified with PH manifesting as diffuse, symmetrical pituitary enlargement near or touching the optic apparatus on MRI. The first woman presented with primary hypothyroidism and likely had thyrotroph hyperplasia given prompt resolution with thyroxine. The second and third women were diagnosed with pathological gonadotroph hyperplasia due to primary gonadal insufficiency, with histopathological confirmation including gonadal-deficiency cells in the third case where surgery could have been avoided. The fourth woman likely had idiopathic PH, though she had concomitant polycystic ovary syndrome which is a debated cause of PH. Patients suspected of PH should undergo comprehensive hormonal, radiological and sometimes ophthalmological evaluation. This is best conducted by a specialised multidisciplinary team with preference for treatment of underlying conditions and close monitoring over surgical intervention.Normal pituitary dimensions are influenced by age and gender with the greatest pituitary heights seen in young adults and perimenopausal women.Pituitary enlargement may be seen in the settings of pregnancy, end-organ insufficiency with loss of negative feedback, and excess trophic hormone from the hypothalamus or neuroendocrine tumours.PH may be caused or exacerbated by medications including oestrogen, GNRH analogues and antipsychotics.Management involves identification of cases of idiopathic PH suitable for simple surveillance and reversal of pathological or iatrogenic causes where they exist.Surgery should be avoided in PH as it rarely progresses.

| S-EPMC4482158 | biostudies-literature

Evolution of direct reciprocity under uncertainty can explain human generosity in one-shot encounters.

Project description:Are humans too generous? The discovery that subjects choose to incur costs to allocate benefits to others in anonymous, one-shot economic games has posed an unsolved challenge to models of economic and evolutionary rationality. Using agent-based simulations, we show that such generosity is the necessary byproduct of selection on decision systems for regulating dyadic reciprocity under conditions of uncertainty. In deciding whether to engage in dyadic reciprocity, these systems must balance (i) the costs of mistaking a one-shot interaction for a repeated interaction (hence, risking a single chance of being exploited) with (ii) the far greater costs of mistaking a repeated interaction for a one-shot interaction (thereby precluding benefits from multiple future cooperative interactions). This asymmetry builds organisms naturally selected to cooperate even when exposed to cues that they are in one-shot interactions.

| S-EPMC3156224 | biostudies-other

Optimized multi-shot imaging inspection design.

Project description:The inspection of complex-shaped components, such as those enabled by additive manufacturing, is a major challenge in industrial quality assurance. A frequently adopted approach to volumetric non-destructive evaluation is X-ray computed tomography, but this has major drawbacks. Two-dimensional radiography can overcome some of these problems, but does not generally provide an inspection that is as capable. Moreover, designing a detailed inspection for a complex-shaped component is a labour-intensive task, requiring significant expert input. In response, a computational framework for optimizing the data acquisition for an image-based inspection modality has been devised. The initial objective is to advance the capabilities of radiography, but the algorithm is, in principle, also applicable to alternative types of imaging. The algorithm exploits available prior information about the inspection and simulations of the inspection modality to allow the determination of the optimal inspection configuration, including specifically component poses with respect to the imaging system. As an intermediate output, spatial maps of inspection performance are computed, for understanding spatially varying limits of detection. Key areas of innovation concern the defect detectability evaluation for arbitrarily complex indications and the creation of an application-specific optimization algorithm. Initial trials of the algorithm are presented, with good results.

| S-EPMC6127396 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data