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"Multidimensional Scaling"
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Latent Feature Extraction for Process Data via Multidimensional Scaling
Computer-based interactive items have become prevalent in recent educational assessments. In such items, detailed human–computer interactive process, known as response process, is recorded in a log file. The recorded response processes provide great opportunities to understand individuals’ problem solving processes. However, difficulties exist in analyzing these data as they are high-dimensional sequences in a nonstandard format. This paper aims at extracting useful information from response processes. In particular, we consider an exploratory analysis that extracts latent variables from process data through a multidimensional scaling framework. A dissimilarity measure is described to quantify the discrepancy between two response processes. The proposed method is applied to both simulated data and real process data from 14 PSTRE items in PIAAC 2012. A prediction procedure is used to examine the information contained in the extracted latent variables. We find that the extracted latent variables preserve a substantial amount of information in the process and have reasonable interpretability. We also empirically prove that process data contains more information than classic binary item responses in terms of out-of-sample prediction of many variables.
Journal Article
Deer-mediated changes in environment compound the direct impacts of herbivory on understorey plant communities
1. In forests of eastern North America, white-tailed deer (Odocoileus virginianus) can directly affect, via herbivory, the presence, abundance and reproductive success of many plant species. In addition, deer indirectly influence understorey communities by altering environmental conditions. 2. To examine how deer indirectly influence understorey plants via environmental modification, we sampled vegetation and environmental variables in- and outside deer exclosures (10-20 years old) located in temperate forests in northern Wisconsin and the Upper Peninsula of Michigan, USA. We assessed how excluding deer affected understorey community composition and structure, the soil and light environment, and relationships between direct and indirect effects, using non-metric multidimensional scaling (NMDS), mixed linear models and nonparametric multiplicative regression (NPMR). 3. Excluding deer altered sapling communities and several aspects of the understorey environment. Excluding deer from plots with lower overstory basal area increased sapling abundance, decreasing the amount of light available to groundlayer plants. Exclusion also reduced soil compaction and the thickness of the soil E horizon. 4. The composition of understorey communities covaried in apparent response to the environmental factors affected by exclusion. In several common species and groups, E horizon thickness, compaction, openness, and/or total (sapling and overstory) basal area were significant predictors of plant frequency. 5. Complementary analyses revealed that deer exclusion also altered the frequency distributions of several species and groups across environmental space. 6. Synthesis. Deer alter many facets of the understorey environment, such as light availability, soil compaction and thickness of the soil E horizon, which, in turn, appear to mediate variation in plant communities. Those environmental modifications likely compound direct impacts of herbivory as drivers of understorey community change. Our results provide evidence that deer effects on the environment have important implications for forest composition. Thus, we suggest a re-examination of the common assumption that understorey community shifts stem primarily from tissue removal.
Journal Article
Heterogeneity and overlap in the continuum of linguistic profile of logopenic and semantic variants of primary progressive aphasia: a Profile Analysis based on Multidimensional Scaling study
Background
Primary progressive aphasia (PPA) diagnostic criteria underestimate the complex presentation of semantic (sv) and logopenic (lv) variants, in which symptoms partially overlap, and mixed clinical presentation (mixed-PPA) and heterogenous profile (lvPPA +) are frequent. Conceptualization of similarities and differences of these clinical conditions is still scarce.
Methods
Lexical, semantic, phonological, and working memory errors from nine language tasks of sixty-seven PPA were analyzed using Profile Analysis based on Multidimensional Scaling, which allowed us to create a distributed representation of patients’ linguistic performance in a shared space. Patients had been studied with [
18
F] FDG-PET. Correlations were performed between metabolic and behavioral data.
Results
Patients’ profiles were distributed across a continuum. All PPA, but two, presented a lexical retrieval impairment, in terms of reduced production of verbs and nouns. svPPA patients occupied a fairly clumped space along the continuum, showing a preponderant semantic deficit, which correlated to fusiform gyrus hypometabolism, while only few presented working memory deficits. Adjacently, lvPPA + presented a semantic impairment combined with phonological deficits, which correlated with metabolism in the anterior fusiform gyrus and posterior middle temporal gyrus. Starting from the shared phonological deficit side, a large portion of the space was occupied by all lvPPA, showing a combination of phonological, lexical, and working memory deficits, with the latter correlating with posterior temporo-parietal hypometabolism. Mixed PPA did not show unique profile, distributing across the space.
Discussion
Different clinical PPA entities exist but overlaps are frequent. Identifying shared and unique clinical markers is critical for research and clinical practice. Further research is needed to identify the role of genetic and pathological factors in such distribution, including also higher sample size of less represented groups.
Journal Article
Multidimensional scaling methods can reconstruct genomic DNA loops using Hi-C data properties
This paper proposes multidimensional scaling (MDS) applied to high-throughput chromosome conformation capture (Hi-C) data on genomic interactions to visualize DNA loops. Currently, the mechanisms underlying the regulation of gene expression are poorly understood, and where and when DNA loops are formed remains undetermined. Previous studies have focused on reproducing the entire three-dimensional structure of chromatin; however, identifying DNA loops using these data is time-consuming and difficult. MDS is an unsupervised method for reconstructing the original coordinates from a distance matrix. Here, MDS was applied to high-throughput chromosome conformation capture (Hi-C) data on genomic interactions to visualize DNA loops. Hi-C data were converted to distances by taking the inverse to reproduce loops via MDS, and the missing values were set to zero. Using the converted data, MDS was applied to the log-transformed genomic coordinate distances and this process successfully reproduced the DNA loops in the given structure. Consequently, the reconstructed DNA loops revealed significantly more DNA-transcription factor interactions involved in DNA loop formation than those obtained from previously applied methods. Furthermore, the reconstructed DNA loops were significantly consistent with chromatin immunoprecipitation followed by sequencing (ChIP-seq) peak positions. In conclusion, the proposed method is an improvement over previous methods for identifying DNA loops.
Journal Article
Touching-untouching patterns organize action representation in the inferior parietal cortex
•Patterns of (un-)touchings of hands, objects and ground can code action categories.•Robots can effectively use these patterns to recognize and respond to human actions.•Patterns relate to perceived action similarity in Inverse Multidimensional Scaling.•Left parietal area codes patterns as shown by Representational Similarity Analyses.•Touching-Untouching sequences organize parietal action representation.
At an abstract temporospatial level, object-directed actions can be described as sequences of touchings and untouchings of objects, hands, and the ground. These sparse action codes can effectively guide automated systems like robots in recognizing and responding to human actions without the need for object identification. The aim of the current study was to investigate whether the neural processing of actions and their behavioral classification relies on the action categorization derived from the touching-untouching structure. Here we show, using a representational similarity analysis of functional MRI data from two experiments, that action representations in left anterior intraparietal sulcus (aIPS) are particularly associated with this categorization of touching-untouching structures. Within the examined action observation network, only the touching-untouching category model selectively correlated with the representational profile of the left aIPS. The behavioral results showed a significant relation between the touching-untouching structure and the observers’ judgments on the similarity of actions with weakly-informative objects. Extending prior research on touchings and untouchings as meaningful anchor points for explicit action segmentation, our findings suggest that touching-untouching sequences serve as an organizing principle in inferior parietal action representation.
Journal Article
Mapping Espoused Organizational Values
This paper develops an inventory and conceptual map of espoused organizational values. We suggest that espoused values are fundamentally different to other value forms as they are collective value statements that need to coexist as a basis for organizational activity and performance. The inventory is built from an analysis of 3112 value items espoused by 554 organizations in the UK and USA in both profit and not-for-profit sectors. We distil these value items into 85 espoused value labels, and these are assessed in terms of their similarity and difference through judgements made by 53 experienced individuals. The resulting conceptual map facilitates the evaluation of values which are espoused at the organizational level, as opposed to aggregations of personal values, an important distinction that is often ignored in the literature. This analysis identifies a number of distinct areas of emphasis occupied by espoused values. In particular, the richness of value labels that relates to broader ethical issues may be aimed at external stakeholder management, but also may have an increasing influence on organizational behaviour as they are embedded into organizational practices. By advancing our understanding of espoused values, through an analysis of those being used in practice, we provide a means by which future research into organizational values and ethical issues can progress.
Journal Article
The effect of soil sample size, for practical DNA extraction, on soil microbial diversity in different taxonomic ranks
To determine the optimal soil sample size for microbial community structure analysis, DNA extraction, microbial composition analysis, and diversity assessments were performed using soil sample sizes of 0.2, 1, and 5 g. This study focused on the relationship between soil amount and DNA extraction container volume and the alteration in microbial composition at different taxonomic ranks (order, class, and phylum). Horizontal (0.2 and 1 g) and vertical (5 g) shaking were applied during DNA extraction for practical use in a small laboratory. In the case of the 5 g soil sample, DNA extraction efficiency and the value of α-diversity index fluctuated severely, possibly because of vertical shaking. Regarding the 0.2 and 1 g soil samples, the number of taxa, Shannon–Wiener index, and Bray–Curtis dissimilarity were stable and had approximately the same values at each taxonomic rank. However, non-metric multidimensional scaling showed that the microbial compositions of these two sample sizes were different. The higher relative abundance of taxa in the case of the 0.2 g soil sample might indicate that cell wall compositions differentiated the microbial community structures in these two sample sizes due to high shear stress tolerance. The soil sample size and tube volume affected the estimated microbial community structure. A soil sample size of 0.2 g would be preferable to the other sample sizes because of the possible higher shearing force for DNA extraction and lower experimental costs due to smaller amounts of consumables. When the taxonomic rank was changed from order to phylum, some minor taxa identified at the order rank were integrated into major taxa at the phylum rank. The integration affected the value of the β-diversity index; therefore, the microbial community structure analysis, reproducibility of structures, diversity assessment, and detection of minor taxa would be influenced by the taxonomic rank applied.
Journal Article
What are emotions and how many are there?
Human emotion has been a focus of scientific research across a wide variety of scientific disciplines and, in spite of careful research dating back as far as Charles Darwin, no consensus has emerged as to what emotions are, how many there are, and whether they are sharply bounded biological processes or culturally defined processes with diffuse boundaries, changing in response to contextual factors. Recently, Cowen and Keltner published research applying what they call a “semantic space approach” to the study of emotion (Cowen in Trends Cogn Sci 22:274–276, 2018; in Proceedings of the National Academy of Sciences of the United States of America, 2017; in Am Psychol 2019). Their method finds that respondents recognize 28 emotional categories arrayed in a 27-dimensional space. These categories are not sharply bounded, but tail off into one another. Some researchers (Barrett in Trends Cogn Sci 22(2):97–99, 2018) have called their methodology into question, and recommended alternative procedures to check these results. In this article we apply an alternative, widely used methodology for generating semantic spaces to Cowen and Keltner’s emotional categories. Results of this alternative (“Galileo”) analysis conducted in the United States and Singapore support the finding that the space in which these 28 emotional categories lie is a high dimensional space, and that they are indeed not sharply bounded. Additionally however, the Galileo method finds that the underlying space is non-Euclidean and it provides information about the actual sizes of the dimensions. Results also show that some of Cowen and Keltner’s emotional categories (such as frustration) may not be best described as emotions themselves, but rather as situations in which other emotions (e.g., anger, sadness, etc.) may be generated.
Journal Article
Coevolutionary and Phylogenetic Analysis of Mimiviral Replication Machinery Suggest the Cellular Origin of Mimiviruses
Mimivirus is one of the most complex and largest viruses known. The origin and evolution of Mimivirus and other giant viruses have been a subject of intense study in the last two decades. The two prevailing hypotheses on the origin of Mimivirus and other viruses are the reduction hypothesis, which posits that viruses emerged from modern unicellular organisms; whereas the virus-first hypothesis proposes viruses as relics of precellular forms of life. In this study, to gain insights into the origin of Mimivirus, we have carried out extensive phylogenetic, correlation, and multidimensional scaling analyses of the putative proteins involved in the replication of its 1.2-Mb large genome. Correlation analysis and multidimensional scaling methods were validated using bacteriophage, bacteria, archaea, and eukaryotic replication proteins before applying to Mimivirus. We show that a large fraction of mimiviral replication proteins, including polymerase B, clamp, and clamp loaders are of eukaryotic origin and are coevolving. Although phylogenetic analysis places some components along the lineages of phage and bacteria, we show that all the replication-related genes have been homogenized and are under purifying selection. Collectively our analysis supports the idea that Mimivirus originated from a complex cellular ancestor. We hypothesize that Mimivirus has largely retained complex replication machinery reminiscent of its progenitor while losing most of the other genes related to processes such as metabolism and translation.
Journal Article