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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
Diversity and ecological drivers of lichens on Kunashir Island (Kuril Islands, Russian Far East)
The purpose of this study is to examine the diversity of lichens in different communities of Kunashir Island and to identify factors influencing their distribution on the island. In total, we identified 172 species of lichens and related fungi. Ochrolechia lijiangensis and Pertusaria plittiana are new to Russia. Amandinea pelidna, Bacidina brandii, and Lecanora caesiosora are new for the Russian Far East. Thirteen species are reported for the first time for the Sakhalin Region. Six species are new for the Kuril Islands and 37 are new for Kunashir Island. Most of the identified lichens are corticolous species. The richest in the number of lichen species are Abies sachalinensis, Betula ermanii, Quercus crispula, Picea ajanensis, Acer mayrii, Alnus hirsuta, and Salix udensis (25–40 species). It is shown that at the landscape level the only significant factor for the species composition of lichens is the community type, while at the substrate level, the coniferous or deciduous nature of the substrate and the acidity of the bark have an impact.
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
Exploring the Functional Strategies Adopted by Coastal Plants Along an Ecological Gradient Using Morpho-functional Traits
Coastal dunes are characterised by strong interactions between biotic and abiotic factors along a short gradient from the shoreline to the inland region. We carried out an ecological analysis of the vegetation in a protected area of the Italian coast to evaluate the relationships among species abundance, the occurrence of morphoanatomical traits related to leaves, stems, and roots, and soil variables. Three transects were established perpendicular to the shoreline, with 27 plots distributed in the frontal dunes, backdunes, and temporarily wet dune slacks. An analysis based on community-weighted mean values showed that the pioneer communities of the frontal dunes were dominated by ruderals that are well adapted to the harsh ecological conditions of these environments, showing succulent leaves, high limb thickness values, and low values for leaf dry matter content (LDMC). The backdune vegetation was a mosaic of annual herbaceous and perennial shrub communities showing both ruderal and stresstolerant strategies (clonality, sclerified leaves, high LDMC values, root phenolics) consistent with less extreme ecological conditions. The dune slack areas were dominated by plants showing adaptations to both arid and flooded environments, such as C4 photosynthesis, amphistomatic leaves, and abundant aerenchyma in the roots. The invasive status, C4 photosynthesis, leaf trichomes, and aerenchyma in the roots were significantly correlated with soil humidity, organic matter content, and pH. These results demonstrate the usefulness of anatomical traits (including root system traits) in understanding the functional strategies adopted by plants. Invasive species tended to occupy plots with high levels of soil moisture, suggesting an avoidance strategy for the harsh environmental conditions of coastal sand dunes. Finally, we suggest including information regarding root systems into coastal monitoring programs because they are directly linked to soil parameters useful in coastal dune management and protection.
Journal Article