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Program FACTOR at 10: Origins, development and future directions
We aim to provide a conceptual view of the origins, development and future directions of FACTOR, a popular free program for fitting the factor analysis (FA) model.
The study is organized into three parts. In the first part we discuss FACTOR in its initial period (2006-2012) as a traditional FA program with many new and cutting-edge features. The second part discusses the present period (2013-2016) in which FACTOR has developed into a comprehensive program embedded in the framework of structural equation modelling and item response theory. The third part discusses expected future developments.
at present FACTOR has attained a degree of technical development comparable to commercial software, and offers options not available elsewhere.
We discuss several shortcomings as well as points that require changes or improvements. We also discuss the functioning of FACTOR within its community of users.
Journal Article
The genetics and mechanisms of T cell acute lymphoblastic leukaemia
Key Points
T cell acute lymphoblastic leukaemia (T-ALL) is an aggressive haematological tumour resulting from the malignant transformation of T cell progenitors.
T-ALL is biologically and genetically heterogeneous with gene expression signatures that identify different clinico-biological groups associated with T cell arrest at different stages of thymocyte development.
Oncogenic NOTCH signalling resulting from activating mutations in
NOTCH1
is a major driver of T-ALL transformation.
Aberrant expression of transcription factor oncogenes as a result of chromosomal translocations and other chromosomal rearrangements is common in T-ALL.
Recurrent mutations and deletions in T-ALL frequently involve cell cycle regulators, but also transcription factors, tumour suppressors, epigenetic factors and negative regulators of NOTCH1, Janus kinase (JAK)–signal transducer and activator of transcription (STAT), PI3K and MAPK signalling.
Relapsed T-ALL is associated with a poor prognosis, and relapse-associated activating mutations in the cytosolic 5′-nucleotidase II gene,
NT5C2
, induce resistance to 6-mercaptopurine chemotherapy.
This Review discusses the increased understanding of the biology of T cell acute lymphoblastic leukaemia (T-ALL) and how this has translated into new prognostic biomarkers, improved animal models and the emergence of targeted therapies to combat this disease.
T cell acute lymphoblastic leukaemia (T-ALL) is an aggressive haematological malignancy derived from early T cell progenitors. In recent years genomic and transcriptomic studies have uncovered major oncogenic and tumour suppressor pathways involved in T-ALL transformation and identified distinct biological groups associated with prognosis. An increased understanding of T-ALL biology has already translated into new prognostic biomarkers and improved animal models of leukaemia and has opened opportunities for the development of targeted therapies for the treatment of this disease. In this Review we examine our current understanding of the molecular mechanisms of T-ALL and recent developments in the translation of these results to the clinic.
Journal Article
QQ-system and Weyl-type transfer matrices in integrable SO(2r) spin chains
A
bstract
We propose the full system of Baxter Q-functions (QQ-system) for the integrable spin chains with the symmetry of the
D
r
Lie algebra. We use this QQ-system to derive new Weyl-type formulas expressing transfer matrices in all symmetric and antisymmetric (fundamental) representations through
r
+ 1 basic Q-functions. Our functional relations are consistent with the Q-operators proposed recently by one of the authors and verified explicitly on the level of operators at small finite length.
Journal Article
Mirror channel eigenvectors of the d-dimensional fishnets
A
bstract
We present a basis of eigenvectors for the graph building operators acting along the mirror channel of planar fishnet Feynman integrals in
d
-dimensions. The eigenvectors of a fishnet lattice of length
N
depend on a set of
N
quantum numbers (
u
k
, l
k
), each associated with the rapidity and bound-state index of a lattice excitation. Each excitation is a particle in (1 + 1)-dimensions with
O
(
d
) internal symmetry, and the wave-functions are formally constructed with a set of creation/annihilation operators that satisfy the corresponding Zamolodchikovs-Faddeev algebra. These properties are proved via the representation, new to our knowledge, of the matrix elements of the fused R-matrix with
O
(
d
) symmetry as integral operators on the functions of two spacetime points. The spectral decomposition of a fishnet integral we achieved can be applied to the computation of Basso-Dixon integrals in higher dimensions.
Journal Article
Decalogue for the Factor Analysis of Test Items
Decalogue for the Factor Analysis of Test Items.
In the study of the psychometric properties of the items of a test, a fundamental aspect is the analysis of their dimensional structure. The objective of this work is to provide some guidelines that allow the factor analysis of the items to be carried out in a rigorous and systematic way.
A review of the recent psychometric literature was carried out to identify the fundamental steps to be followed in order to carry out an adequate factor analysis of the items of a test.
Ten main recommendations were identified to carry out the factorial analysis of the items of a test: adequacy of the data and the sample, univariate statistics, justification of the analysis, selection of the analyzable items, type of model, most appropriate factorial solution, estimation of the parameters, adequacy of the factorial solution, substantive coherence of the model, and final version of the test.
If the ten recommendations proposed in the current psychometric literature are systematically followed, it will be possible to optimize the quality of the tests and the decision-making based on the estimates of the scores obtained through them. These recommendations should be useful to both researchers and practitioners.
Journal Article
FACTOR: A computer program to fit the exploratory factor analysis model
Exploratory factor analysis (EFA) is one of the most widely used statistical procedures in psychological research. It is a classic technique, but statistical research into EFA is still quite active, and various new developments and methods have been presented in recent years. The authors of the most popular statistical packages, however, do not seem very interested in incorporating these new advances. We present the program FACTOR, which was designed as a general, user-friendly program for computing EFA. It implements traditional procedures and indices and incorporates the benefits of some more recent developments. Two of the traditional procedures implemented are polychoric correlations and parallel analysis, the latter of which is considered to be one of the best methods for determining the number of factors or components to be retained. Good examples of the most recent developments implemented in our program are (1) minimum rank factor analysis, which is the only factor method that allows one to compute the proportion of variance explained by each factor, and (2) the simplimax rotation method, which has proved to be the most powerful rotation method available. Of these methods, only polychoric correlations are available in some commercial programs. A copy of the software, a demo, and a short manual can be obtained free of charge from the first author.
Journal Article
Determining the equilibrium structures of nanoalloys by computational methods
Nanoalloys are bi- or multi-metallic nanoparticles with sizes in the range between 1 and 100 nm. They are the subject of intense research activity in the last decades, both in experiments and in theory/modelling. From a theoretical point of view, determining the equilibrium structure of nanoalloys at different temperatures is a quite complex task, which has stimulated the developments of specifically tailored methods and algorithms. Here, we review some recent developments in this field, considering first methods for the global optimization of nanoalloys, and then methods for studying their finite-temperature equilibrium properties.
Journal Article
Spatial variance of spring phenology in temperate deciduous forests is constrained by background climatic conditions
Leaf unfolding in temperate forests is driven by spring temperature, but little is known about the spatial variance of that temperature dependency. Here we use in situ leaf unfolding observations for eight deciduous tree species to show that the two factors that control chilling (number of cold days) and heat requirement (growing degree days at leaf unfolding, GDD
req
) only explain 30% of the spatial variance of leaf unfolding. Radiation and aridity differences among sites together explain 10% of the spatial variance of leaf unfolding date, and 40% of the variation in GDD
req
. Radiation intensity is positively correlated with GDD
req
and aridity is negatively correlated with GDD
req
spatial variance. These results suggest that leaf unfolding of temperate deciduous trees is adapted to local mean climate, including water and light availability, through altered sensitivity to spring temperature. Such adaptation of heat requirement to background climate would imply that models using constant temperature response are inherently inaccurate at local scale.
Drivers of spatial differences in leaf phenology are not as widely studied as temporal differences. Here the authors show that the spatial variation of leaf unfolding in 8 deciduous tree species in Europe can be explained by local adaptation to long-term mean climate conditions.
Journal Article
Targeting FGF19 inhibits tumor growth in colon cancer xenograft and FGF19 transgenic hepatocellular carcinoma models
Although fibroblast growth factor 19 (FGF19) can promote liver carcinogenesis in mice its involvement in human cancer is not well characterized. Here we report that FGF19 and its cognate receptor FGF receptor 4 (FGFR4) are coexpressed in primary human liver, lung and colon tumors and in a subset of human colon cancer cell lines. To test the importance of FGF19 for tumor growth, we developed an anti-FGF19 monoclonal antibody that selectively blocks the interaction of FGF19 with FGFR4. This antibody abolished FGF19-mediated activity
in vitro
and inhibited growth of colon tumor xenografts
in vivo
and effectively prevented hepatocellular carcinomas in FGF19 transgenic mice. The efficacy of the antibody in these models was linked to inhibition of FGF19-dependent activation of FGFR4, FRS2, ERK and
β
-catenin. These findings suggest that the inactivation of FGF19 could be beneficial for the treatment of colon cancer, liver cancer and other malignancies involving interaction of FGF19 and FGFR4.
Journal Article