Empirical methods
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In this paper, we present a review of how the various aspects of any study using an eye tracker (such as the instrument, methodology, environment, participant, etc.) affect the quality of the recorded eye-tracking data and the obtained eye-movement and gaze measures. We take this review to represent the empirical foundation for reporting guidelines of any study involving an eye tracker. We compare this empirical foundation to five existing reporting guidelines and to a database of 207 published eye-tracking studies. We find that reporting guidelines vary substantially and do not match with actual reporting practices. We end by deriving a minimal, flexible reporting guideline based on empirical research (Section "An empirically based minimal reporting guideline").
- Klíčová slova
- Data quality, Eye movements, Eye tracking, Replicability, Reporting guidelines, Reporting practices, Reporting standards, Reproducibility,
- MeSH
- empirický výzkum MeSH
- lidé MeSH
- pohyby očí * MeSH
- technologie sledování pohybu očí * MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- odvolaná publikace MeSH
- přehledy MeSH
- Research Support, N.I.H., Extramural MeSH
A large part of psychology has become an empirical science that assumes that there might exist one set of research methods suitable for psychological research in all human cultures. Research questions, methods, and theories formulated from one cultural perspective are not thoroughly introspectively examined when being used in another cultural environment. This leads to research that answers questions that are not meaningful in such environments. Research coming from the lexical hypothesis tradition is given as an example. The original research in English language decided that the lexicon was enough to represent language structures for the purpose of examining how language reflects personality; however, some languages might use specific grammatical structures to reflect personality, so the lexicon is not enough to adequately represent these languages. Despite this, researchers still follow the research method developed for the English language. The Czech and Korean languages are examples of this approach. A solution to this problem is the thorough use of introspection during the formulation of research questions.
- Klíčová slova
- Big five, Copypasting fallacy, Czech, Empirical research, Introspection, Korean, Lexical hypothesis,
- MeSH
- jazyk (prostředek komunikace) * MeSH
- kultura MeSH
- lidé MeSH
- psychologie metody MeSH
- výzkumný projekt * MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- Geografické názvy
- Česká republika MeSH
- Korejská republika MeSH
A detailed quantum chemical study on five peptides (WG, WGG, FGG, GGF and GFA) containing the residues phenylalanyl (F), glycyl (G), tryptophyl (W) and alanyl (A) -- where F and W are of aromatic character -- is presented. When investigating isolated small peptides, the dispersion interaction is the dominant attractive force in the peptide backbone-aromatic side chain intramolecular interaction. Consequently, an accurate theoretical study of these systems requires the use of a methodology covering properly the London dispersion forces. For this reason we have assessed the performance of the MP2, SCS-MP2, MP3, TPSS-D, PBE-D, M06-2X, BH&H, TPSS, B3LYP, tight-binding DFT-D methods and ff99 empirical force field compared to CCSD(T)/complete basis set (CBS) limit benchmark data. All the DFT techniques with a '-D' symbol have been augmented by empirical dispersion energy while the M06-2X functional was parameterized to cover the London dispersion energy. For the systems here studied we have concluded that the use of the ff99 force field is not recommended mainly due to problems concerning the assignment of reliable atomic charges. Tight-binding DFT-D is efficient as a screening tool providing reliable geometries. Among the DFT functionals, the M06-2X and TPSS-D show the best performance what is explained by the fact that both procedures cover the dispersion energy. The B3LYP and TPSS functionals-not covering this energy-fail systematically. Both, electronic energies and geometries obtained by means of the wave-function theory methods compare satisfactorily with the CCSD(T)/CBS benchmark data.
The currently practiced methods of significance testing in microarray gene expression profiling are highly unstable and tend to be very low in power. These undesirable properties are due to the nature of multiple testing procedures, as well as extremely strong and long-ranged correlations between gene expression levels. In an earlier publication, we identified a special structure in gene expression data that produces a sequence of weakly dependent random variables. This structure, termed the delta-sequence, lies at the heart of a new methodology for selecting differentially expressed genes in nonoverlapping gene pairs. The proposed method has two distinct advantages: (1) it leads to dramatic gains in terms of the mean numbers of true and false discoveries, and in the stability of the results of testing; and (2) its outcomes are entirely free from the log-additive array-specific technical noise. We demonstrate the usefulness of this approach in conjunction with the nonparametric empirical Bayes method. The proposed modification of the empirical Bayes method leads to significant improvements in its performance. The new paradigm arising from the existence of the delta-sequence in biological data offers considerable scope for future developments in this area of methodological research.
The limits on maximum information that can be transferred by single neurons may help us to understand how sensory and other information is being processed in the brain. According to the efficient-coding hypothesis (Barlow, Sensory Comunication, MIT press, Cambridge, 1961), neurons are adapted to the statistical properties of the signals to which they are exposed. In this paper we employ methods of information theory to calculate, both exactly (numerically) and approximately, the ultimate limits on reliable information transmission for an empirical neuronal model. We couple information transfer with the metabolic cost of neuronal activity and determine the optimal information-to-metabolic cost ratios. We find that the optimal input distribution is discrete with only six points of support, both with and without a metabolic constraint. However, we also find that many different input distributions achieve mutual information close to capacity, which implies that the precise structure of the capacity-achieving input is of lesser importance than the value of capacity.
- MeSH
- adenosintrifosfát metabolismus MeSH
- akční potenciály fyziologie MeSH
- informační teorie * MeSH
- lidé MeSH
- modely neurologické * MeSH
- mozek cytologie fyziologie MeSH
- nervový přenos MeSH
- neurony metabolismus MeSH
- zvířata MeSH
- Check Tag
- lidé MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Názvy látek
- adenosintrifosfát MeSH
The description of hydrogen bonds in the density-functional tight-binding (DFTB) method continues to be a challenging task because the approximations that make the method computationally efficient compromise already the first-order electrostatic contribution to the interaction. So far, the best results have been achieved with fully empirical corrections such as the recently reparametrized DFTB3-D3H4 method. This approach has, however, important limitations that arise from its independence of the actual electronic structure. Here, we present a novel correction denoted as D3H5, which is integrated deeper in the DFTB method, correcting the problem at the place of its origin. It is applied within the self-consistent evaluation of electrostatic interactions, where it empirically models the missing contributions of atomic multipoles and polarization. Despite being very simple and using fewer parameters than D3H4, it is both more accurate and more robust. In data sets of small model systems, it yields errors below 1 kcal/mol, and it performs comparably well in larger systems. Unlike D3H4, it can describe cooperativity in H-bond networks, which makes it more transferable to more complex systems.
- Publikační typ
- časopisecké články MeSH
Explaining broad molecular, phenotypic and species biodiversity patterns necessitates a unifying framework spanning multiple evolutionary scales. Here we argue that although substantial effort has been made to reconcile microevolution and macroevolution, much work remains to identify the links between biological processes at play. We highlight four major questions of evolutionary biology whose solutions require conceptual bridges between micro and macroevolution. We review potential avenues for future research to establish how mechanisms at one scale (drift, mutation, migration, selection) translate to processes at the other scale (speciation, extinction, biogeographic dispersal) and vice versa. We propose ways in which current comparative methods to infer molecular evolution, phenotypic evolution and species diversification could be improved to specifically address these questions. We conclude that researchers are in a better position than ever before to build a synthesis to understand how microevolutionary dynamics unfold over millions of years.
BACKGROUND: Integration of multi-omics data can provide a more complex view of the biological system consisting of different interconnected molecular components, the crucial aspect for developing novel personalised therapeutic strategies for complex diseases. Various tools have been developed to integrate multi-omics data. However, an efficient multi-omics framework for regulatory network inference at the genome level that incorporates prior knowledge is still to emerge. RESULTS: We present IntOMICS, an efficient integrative framework based on Bayesian networks. IntOMICS systematically analyses gene expression, DNA methylation, copy number variation and biological prior knowledge to infer regulatory networks. IntOMICS complements the missing biological prior knowledge by so-called empirical biological knowledge, estimated from the available experimental data. Regulatory networks derived from IntOMICS provide deeper insights into the complex flow of genetic information on top of the increasing accuracy trend compared to a published algorithm designed exclusively for gene expression data. The ability to capture relevant crosstalks between multi-omics modalities is verified using known associations in microsatellite stable/instable colon cancer samples. Additionally, IntOMICS performance is compared with two algorithms for multi-omics regulatory network inference that can also incorporate prior knowledge in the inference framework. IntOMICS is also applied to detect potential predictive biomarkers in microsatellite stable stage III colon cancer samples. CONCLUSIONS: We provide IntOMICS, a framework for multi-omics data integration using a novel approach to biological knowledge discovery. IntOMICS is a powerful resource for exploratory systems biology and can provide valuable insights into the complex mechanisms of biological processes that have a vital role in personalised medicine.
- Klíčová slova
- Bayesian networks, Integrative analysis, Knowledge discovery, Multimodal omics, Regulatory networks,
- MeSH
- algoritmy MeSH
- Bayesova věta MeSH
- genové regulační sítě MeSH
- lidé MeSH
- nádory tračníku * MeSH
- systémová biologie metody MeSH
- variabilita počtu kopií segmentů DNA * MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
