Search results for " data analysis"
showing 10 items of 231 documents
Metabolic flux understanding of Pichia pastoris grown on heterogenous culture media
2014
[EN] Within the emergent field of Systems Biology, mathematical models obtained from physical chemical laws (the so-called first principles-based models) of microbial systems are employed to discern the principles that govern cellular behaviour and achieve a predictive understanding of cellular functions. The reliance on this biochemical knowledge has the drawback that some of the assumptions (specific kinetics of the reaction system, unknown dynamics and values of the model parameters) may not be valid for all the metabolic possible states of the network. In this uncertainty context, the combined use of fundamental knowledge and data measured in the fermentation that describe the behaviour…
Reinterpretation of Classic Proton Charge Form Factor Measurements
2020
In 1963, a proton radius of $0.805(11)~\mathrm{fm}$ was extracted from electron scattering data and this classic value has been used in the standard dipole parameterization of the form factor. In trying to reproduce this classic result, we discovered that there was a sign error in the original analysis and that the authors should have found a value of $0.851(19)~\mathrm{fm}$. We additionally made use of modern computing power to find a robust function for extracting the radius using this 1963 data's spacing and uncertainty. This optimal function, the Pad\'{e} $(0,1)$ approximant, also gives a result which is consistent with the modern high precision proton radius extractions.
Quantitative and qualitative analysis of the mental models deployed by undergraduate students in explaining thermally activated phenomena
2017
In this contribution we describe a research aimed at pointing out the quality of mental models undergraduate engineering students deploy when asked to create explanations for phenomena/processes and/or use a given model in the same context. Student responses to a specially designed written questionnaire are initially analyzed using researcher-generated categories of reasoning, based on the Physics Education Research literature on student understanding of the relevant physics content. The inferred students’ mental models about the analyzed phenomena are categorized as practical, descriptive, or explanatory, based on an analysis of student responses to the questionnaire. A qualitative analysi…
GeneTonic: an R/Bioconductor package for streamlining the interpretation of RNA-seq data
2021
AbstractBackgroundThe interpretation of results from transcriptome profiling experiments via RNA sequencing (RNA-seq) can be a complex task, where the essential information is distributed among different tabular and list formats - normalized expression values, results from differential expression analysis, and results from functional enrichment analyses. A number of tools and databases are widely used for the purpose of identification of relevant functional patterns, yet often their contextualization within the data and results at hand is not straightforward, especially if these analytic components are not combined together efficiently.ResultsWe developed the GeneTonic software package, whi…
Feature selection on a dataset of protein families: from exploratory data analysis to statistical variable importance
2016
Proteins are characterized by several typologies of features (structural, geometrical, energy). Most of these features are expected to be similar within a protein family. We are interested to detect which features can identify proteins that belong to a family, as well as to define the boundaries among families. Some features are redundant: they could generate noise in identifying which variables are essential as a fingerprint and, consequently, if they are related or not to a function of a protein family. We defined an original approach to analyze protein features for defining their relationships and peculiarities within protein families. A multistep approach has been mainly performed in R …
Investigating the quality of mental models deployed by undergraduate engineering students in creating explanations: The case of thermally activated p…
2013
This paper describes a method aimed at pointing out the quality of the mental models undergraduate engineering students deploy when asked to create explanations for phenomena or processes and/or use a given model in the same context. Student responses to a specially designed written questionnaire are quantitatively analyzed using researcher-generated categories of reasoning, based on the physics education research literature on student understanding of the relevant physics content. The use of statistical implicative analysis tools allows us to successfully identify clusters of students with respect to the similarity to the reasoning categories, defined as ``practical or everyday,'' ``descri…
Observation of time-invariant coherence in a room temperature quantum simulator
2015
The ability to live in coherent superpositions is a signature trait of quantum systems and constitutes an irreplaceable resource for quantum-enhanced technologies. However, decoherence effects usually destroy quantum superpositions. It has been recently predicted that, in a composite quantum system exposed to dephasing noise, quantum coherence in a transversal reference basis can stay protected for indefinite time. This can occur for a class of quantum states independently of the measure used to quantify coherence, and requires no control on the system during the dynamics. Here, such an invariant coherence phenomenon is observed experimentally in two different setups based on nuclear magnet…
Negative Probabilities and Contextuality
2015
There has been a growing interest, both in physics and psychology, in understanding contextuality in experimentally observed quantities. Different approaches have been proposed to deal with contextual systems, and a promising one is contextuality-by-default, put forth by Dzhafarov and Kujala. The goal of this paper is to present a tutorial on a different approach: negative probabilities. We do so by presenting the overall theory of negative probabilities in a way that is consistent with contextuality-by-default and by examining with this theory some simple examples where contextuality appears, both in physics and psychology.
From time series to complex networks: the visibility graph
2008
In this work we present a simple and fast computational method, the visibility algorithm , that converts a time series into a graph. The constructed graph inherits several properties of the series in its structure. Thereby, periodic series convert into regular graphs, and random series do so into random graphs. Moreover, fractal series convert into scale-free networks, enhancing the fact that power law degree distributions are related to fractality, something highly discussed recently. Some remarkable examples and analytical tools are outlined to test the method's reliability. Many different measures, recently developed in the complex network theory, could by means of this new approach cha…
Bayesian Analysis of a Future Beta Decay Experiment's Sensitivity to Neutrino Mass Scale and Ordering
2021
Bayesian modeling techniques enable sensitivity analyses that incorporate detailed expectations regarding future experiments. A model-based approach also allows one to evaluate inferences and predicted outcomes, by calibrating (or measuring) the consequences incurred when certain results are reported. We present procedures for calibrating predictions of an experiment's sensitivity to both continuous and discrete parameters. Using these procedures and a new Bayesian model of the $\beta$-decay spectrum, we assess a high-precision $\beta$-decay experiment's sensitivity to the neutrino mass scale and ordering, for one assumed design scenario. We find that such an experiment could measure the el…