scholarly journals Towards combined semantic and lexical scores based on a new representation of textual data to extract experimental data from scientific publications

Author(s):  
Martin Lentschat ◽  
Patrice Buche ◽  
Juliette Dibie Barthelemy ◽  
Mathieu Roche
2021 ◽  
Author(s):  
◽  
Mukhlis Matti

<p>This thesis explores and evaluates MAXCCLUS, a bioinformatics clustering algorithm, which was designed to be used to cluster genes from microarray experimental data. MAXCCLUS does the clustering of genes depending on the textual data that describe the genes. MAXCCLUS attempts to create clusters of which it selects only the statistically significant clusters by running a significance test. It then attempts to generalise these clusters by using a simple greedy generalisation algorithm. We explore the behaviour of MAXCCLUS by running several clustering experiments that investigate various modifications to MAXCCLUS and its data. The thesis shows (a) that using the simple generalisation algorithm of MAXCCLUS gives better result than using an exhaustive search algorithm for generalisation, (b) the significance test that MAXCCLUS uses needs to be modified to take into consideration the dependency of some genes on other genes functionally, (c) it is advantageous to delete the non domain-relevant textual data that describe the genes but disadvantageous to add more textual data to describe the genes, and (d) that MAXCCLUS behaves poorly when it attempts to cluster genes that have adjacent categories instead of having two distinct categories only.</p>


2021 ◽  
Author(s):  
◽  
Mukhlis Matti

<p>This thesis explores and evaluates MAXCCLUS, a bioinformatics clustering algorithm, which was designed to be used to cluster genes from microarray experimental data. MAXCCLUS does the clustering of genes depending on the textual data that describe the genes. MAXCCLUS attempts to create clusters of which it selects only the statistically significant clusters by running a significance test. It then attempts to generalise these clusters by using a simple greedy generalisation algorithm. We explore the behaviour of MAXCCLUS by running several clustering experiments that investigate various modifications to MAXCCLUS and its data. The thesis shows (a) that using the simple generalisation algorithm of MAXCCLUS gives better result than using an exhaustive search algorithm for generalisation, (b) the significance test that MAXCCLUS uses needs to be modified to take into consideration the dependency of some genes on other genes functionally, (c) it is advantageous to delete the non domain-relevant textual data that describe the genes but disadvantageous to add more textual data to describe the genes, and (d) that MAXCCLUS behaves poorly when it attempts to cluster genes that have adjacent categories instead of having two distinct categories only.</p>


2019 ◽  
Vol 4 ◽  
pp. 22-32 ◽  
Author(s):  
Burkan Isgor ◽  
Ueli Angst ◽  
Mette Geiker ◽  
Ceki Halmen ◽  
Carolyn Hansson ◽  
...  

Experience has shown that many aspects of experimental design for studying steel corrosion in cementitious systems may significantly influence the obtained results. In the absence of standardized methods to study steel corrosion in concrete, researchers usually define their own test setups, which partially explains the large scatter and uncertainty in the aggregated published data. When the details of these setups are not provided adequately, experimental results cannot be interpreted in a wider context. Unfortunately, many scientific publications lack important experimental details. Therefore, this paper aims at improving the quality of reported experimental details, observations, and data in scientific publications, and raising awareness for relevant issues to improve the quality of research in the field. To this end, this paper provides a list of experimental details that have been found important by many decades of research, and which are, thus, recommended to be considered in conducting and reporting laboratory studies involving corrosion of steel embedded in cementitious systems. Finally, we propose a checklist for reporting experimental data in scientific publications.


Author(s):  
A. Gómez ◽  
P. Schabes-Retchkiman ◽  
M. José-Yacamán ◽  
T. Ocaña

The splitting effect that is observed in microdiffraction pat-terns of small metallic particles in the size range 50-500 Å can be understood using the dynamical theory of electron diffraction for the case of a crystal containing a finite wedge. For the experimental data we refer to part I of this work in these proceedings.


Author(s):  
K.B. Reuter ◽  
D.B. Williams ◽  
J.I. Goldstein

In the Fe-Ni system, although ordered FeNi and ordered Ni3Fe are experimentally well established, direct evidence for ordered Fe3Ni is unconvincing. Little experimental data for Fe3Ni exists because diffusion is sluggish at temperatures below 400°C and because alloys containing less than 29 wt% Ni undergo a martensitic transformation at room temperature. Fe-Ni phases in iron meteorites were examined in this study because iron meteorites have cooled at slow rates of about 10°C/106 years, allowing phase transformations below 400°C to occur. One low temperature transformation product, called clear taenite 2 (CT2), was of particular interest because it contains less than 30 wtZ Ni and is not martensitic. Because CT2 is only a few microns in size, the structure and Ni content were determined through electron diffraction and x-ray microanalysis. A Philips EM400T operated at 120 kV, equipped with a Tracor Northern 2000 multichannel analyzer, was used.


Author(s):  
C. C. Ahn ◽  
D. H. Pearson ◽  
P. Rez ◽  
B. Fultz

Previous experimental measurements of the total white line intensities from L2,3 energy loss spectra of 3d transition metals reported a linear dependence of the white line intensity on 3d occupancy. These results are inconsistent, however, with behavior inferred from relativistic one electron Dirac-Fock calculations, which show an initial increase followed by a decrease of total white line intensity across the 3d series. This inconsistency with experimental data is especially puzzling in light of work by Thole, et al., which successfully calculates x-ray absorption spectra of the lanthanide M4,5 white lines by employing a less rigorous Hartree-Fock calculation with relativistic corrections based on the work of Cowan. When restricted to transitions allowed by dipole selection rules, the calculated spectra of the lanthanide M4,5 white lines show a decreasing intensity as a function of Z that was consistent with the available experimental data.Here we report the results of Dirac-Fock calculations of the L2,3 white lines of the 3d and 4d elements, and compare the results to the experimental work of Pearson et al. In a previous study, similar calculations helped to account for the non-statistical behavior of L3/L2 ratios of the 3d metals. We assumed that all metals had a single 4s electron. Because these calculations provide absolute transition probabilities, to compare the calculated white line intensities to the experimental data, we normalized the calculated intensities to the intensity of the continuum above the L3 edges. The continuum intensity was obtained by Hartree-Slater calculations, and the normalization factor for the white line intensities was the integrated intensity in an energy window of fixed width and position above the L3 edge of each element.


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