Graph-based Cluster Analysis to Identify Similar Questions: A Design Science Approach

Social question answering (SQA) services allow users to clarify their queries by asking questions and obtaining answers from other users. To enhance the responsiveness of such services, one can identify similar questions and, thereafter, return the answers available. However, identifying similar questions is difficult because of the complex language structure of user-generated questions. For this reason, we developed an approach to cluster similar questions based on a web of social relationships among the questions, the answers, the askers, and the answerers. To do so, we designed a graph-based cluster analysis using design science research guidelines. In evaluating the results, we found that the proposed graph-based cluster analysis is more promising than baseline methods

NLTS Hamiltonians from good quantum codes

The NLTS (No Low-Energy Trivial State) conjecture of Freedman and Hastings [2014] posits that there exist families of Hamiltonians with all low energy states of non-trivial complexity (with complexity measured by the quantum circuit depth preparing the state). We prove this conjecture by showing that the recently discovered families of constant-rate and linear-distance QLDPC codes correspond to NLTS local Hamiltonians.Comment: 12 pages, 1 figure, added funding information and discussion

Evolutionary relationships in Panicoid grasses based on plastome phylogenomics (Panicoideae; Poaceae)

Background: Panicoideae are the second largest subfamily in Poaceae (grass family), with 212 genera and approximately 3316 species. Previous studies have begun to reveal relationships within the subfamily, but largely lack resolution and/or robust support for certain tribal and subtribal groups. This study aims to resolve these relationships, as well as characterize a putative mitochondrial insert in one linage. Results: 35 newly sequenced Panicoideae plastomes were combined in a phylogenomic study with 37 other species: 15 Panicoideae and 22 from outgroups. A robust Panicoideae topology largely congruent with previous studies was obtained, but with some incongruences with previously reported subtribal relationships. A mitochondrial DNA (mtDNA) to plastid DNA (ptDNA) transfer was discovered in the Paspalum lineage. Conclusions: The phylogenomic analysis returned a topology that largely supports previous studies. Five previously recognized subtribes appear on the topology to be non-monophyletic. Additionally, evidence for mtDNA to ptDNA transfer was identified in both Paspalum fimbriatum and P. dilatatum, and suggests a single rare event that took place in a common progenitor. Finally, the framework from this study can guide larger whole plastome sampling to discern the relationships in Cyperochloeae, Steyermarkochloeae, Gynerieae, and other incertae sedis taxa that are weakly supported or unresolved.Fil: Burke, Sean V.. Northern Illinois University; Estados UnidosFil: Wysocki, William P.. Northern Illinois University; Estados UnidosFil: Zuloaga, Fernando Omar. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Botánica Darwinion. Academia Nacional de Ciencias Exactas, Físicas y Naturales. Instituto de Botánica Darwinion; ArgentinaFil: Craine, Joseph M.. Jonah Ventures; Estados UnidosFil: Pires, J. Chris. University of Missouri; Estados UnidosFil: Edger, Patrick P.. Michigan State University; Estados UnidosFil: Mayfield Jones, Dustin. Donald Danforth Plant Science Center; Estados UnidosFil: Clark, Lynn G.. Iowa State University; Estados UnidosFil: Kelchner, Scot A.. University of Idaho; Estados UnidosFil: Duvall, Melvin R.. Northern Illinois University; Estados Unido

Species Diversity and Distribution Patterns of Woody Plants in Adaba-Dodola Afromontane Forest, Oromia, Ethiopia

학위논문 (박사)-- 서울대학교 대학원 농업생명과학대학 산림과학부(산림환경학전공), 2017. 8. 박필선.p = 0.014). Jaccard coefficient of similarity showed that there was 73% of dissimilarity between standing vegetation and soil seed bank. The poor species correspondence might be emanated from many reasons. It could be due short-lived seed bank as a result of lack of dormancy mechanisms to persist in the soil, or due to endocarp dormancy (e.g. Juniperus procera and Olea europaea species) that prevented early germination, or high seed predation by animals (insects) due to fleshy nature of seeds that attract predators (e.g. Juniperus procera, Ekebergia carpesis and Podocarpus falcatus seeds) or poor viability due to soil borne fungal diseases attacks (e.g. Podocarpus falcatusrecent study of seed viability in Podocarpus falcatus showed 2.1% viability). Generally, based on soil seed bank evaluation, about 68 % of the woody species of the above ground vegetation was not represented in the seed bank. Based on the regeneration analysis, about 41.27 % of the total species was not regenerating at all, 25.40% species had fair regeneration and 9.52 % had poor regeneration status in Adaba-Dodola Afromontane forest. Moreover, the ecological dominance analysis also revealed that about 81% of the total woody species require immediate conservation priority. The important findings of the present study were that the joint effect of anthropogenic disturbances and environmental factors had been demonstrated to be a likely mechanism shaping the overall elevational pattern of species distribution, richness and diversity both in aboveground vegetation and soil seed bank. Effect of disturbance, especially cutting was found to be the main factor for the decline of species diversity at low elevations while that of the upper end elevation zone was mainly related to environmental factors rather than the disturbance activities. This implied that the observed patterns of vegetation were not attributed to a single universal explanation but rather to a combination of environmental and anthropogenic factors. Thus, it is highly important to take anthropogenic effects into account when describing ecological processes along elevational gradients. As a general conclusion, depending only on natural regeneration might not be an effective strategy for restoration of the degraded Adaba-Dodola Afromontane forest implying that enrichment planting with adaptable seedlings is required for successful vegetation restoration, especially for species having low importance value index and poor regeneration status. The forest restoration or conservation efforts need to focus both on maintaining the quantity as well as the quality (species composition) of species to diversify the species-poor sites. Mitigation of grazing and harvesting disturbances should be considered as one of the main measures that need to be taken into account in forest conservation planning in the study site.Adaba-Dodola Afromontane forest is one of the biodiversity priority areas of Ethiopia. Nevertheless, this forest is among the most degraded forests in Ethiopian Afromontane forests with remnant fragmented forest patches. Mitigation and restoration of the disturbed forests are taken as priority task for biodiversity conservation and maintaining ecosystem functions. To generate relevant information that helps for maintaining the remaining forest, this study was aimed to explore how the forest species composition, distribution pattern, richness, diversity, structure and regeneration varied with the environment and anthropogenic influences and to evaluate the relative importance of these explanatory variables at different elevation zones. Three forest sites were considered for the study. 90 plots (20 m × 20 m) were sampled along elevational gradients from two transects of about 1 km apart from all sites. Soil seed bank germination test was performed in greenhouse for six months. Two multivariate analysis models, Canonical Correspondence Analysis (CCA) and Redundancy Analysis (RDA) models, were performed to examine the relationships between vegetation patterns and explanatory variables. Species diversity indices were used to analyze the pattern of species diversity, richness and evenness. The CCA/ RDA in CANOCO and stepwise multiple regression models were used for variation partitioning among explanatory variables. Analysis of variance (ANOVA) was used for means separation among the significant response variables. Species-environment ordination computed by CCA/RDA indicated that the variations in woody plant communities were explained by environmental and disturbance factors. The environmental and anthropogenic disturbance data sets in the entire vegetation, respectively explained 19 % (p = 0.005) and 26 % (p = 0.005) of the total variations (TVE) in species diversity and 37 % (p = 0.045) and 24 % (p < 0.045) of the total variation in species richness. The species richness (R2 = 0.36p < 0.006) and diversity (R2 = 0.47p < 0.001) showed a pronounced shift at mid elevation gradient exhibiting a hump shape pattern. The mid elevation maximum richness and diversity patterns were presumed to be emanated from many factors as indicated by multivariate models and analysis of variance. One of the main reasons might be the less anthropogenic activities such as cutting, grazing, settlement and canopy openness as compared to the low and high elevation sites. The less anthropogenic disturbances in the mid elevation in turn were attributed to the high topographic roughness (steep and undulating slope) that might have limited the ease accessibility of the forest for anthropogenic activities. Moreover, the middle elevation is the transitional zone between the lower and the upper zones that might have enabled the site to share some climatic conditions from both elevation zones. According to our climate data, this site was supposed to have moderate climatic conditions (1059 mm mean annual rainfall and 11 oC mean annual temperature) that might be favorable to sustain more number of species to coexist. At low elevation, the variance partitioning models indicated that pure anthropogenic factor exerted significant (p <0.005) effect on the species diversity while pure environmental factor did not have significant effect. Cutting disturbance had the most pronounced effect on species diversity at low elevations. However, at the upper end of elevation, the multivariate model analysis indicated that only pure environment had significant influence on the decline of species diversity implying that decline of diversity at the upper end elevation zone was mainly attributed to environmental factors rather than the anthropogenic disturbances. The cool temperature at high elevation (1.7 oC mean annual minimum temperature) might have accounted for the decline of species richness and diversity by slowing the growth and regeneration rate of plants. In the soil seed bank, the largest variation in species diversity was explained by cutting (R2adj =10.8 %p = 0.038) followed by soil pH (R2adj = 5.1%p= 0.029) and aspect (R2adj = 5.0%1. INTRODUCTION 1 2. LITERATURE REVIEW 6 2.1. Vegetation classification and ordination 6 2.2. Diversity indices (Alpha, beta and gamma) 8 2.3. Forest regeneration 10 2.4. Soil seed bank 11 2.5. Forest degradation in Ethiopia: An overview 13 2.6. Patterns of floristic composition and diversity in Ethiopia 14 3. MATERIALS AND METHODS 16 3.1. Study area description 16 3.2. Site selection 32 3.3. Data collection 32 3.4. Data analysis 41 4. RESULTS AND DISCUSSION 53 4.1. Species-area curve 53 4.2. Species composition and distribution 56 4.3. Community clustering and ordination analysis 60 4.4. Species dispersion patterns 69 4.5. Alpha (α), beta (β) and gamma (γ) diversity in forest communities 73 4.6. Floristic similarities 74 4.7. Forest stand structure 75 4.8. Soil seed bank floristic composition and diversity 114 4.9. CCA-ordination analysis of plant species with environmental and disturbance factors 140 4.10. Effects of environmental and disturbance factors on species composition 145 4.11. Effects of environmental and anthropogenic factors on species richness and diversity 160 CONCLUSIONS 190 LITERATURE CITED 195 APPENDICES 228 ABSTRACT IN KOREAN 233Docto

Analytics of student interactions: towards theory-driven, actionable insights

The field of learning analytics arose as a response to the vast quantities of data that are increasingly generated about students, their engagement with learning resources, and their learning and future career outcomes. While the field began as a collage, adopting methods and theories from a variety of disciplines, it has now become a major area of research, and has had a substantial impact on practice, policy, and decision-making. Although the field supports the collection and analysis of a wide array of data, existing work has predominantly focused on the digital traces generated through interactions with technology, learning content, and other students. Yet for any analyses to support students and teachers, the measures derived from these data must (1) offer practical and actionable insight into learning processes and outcomes, and (2) be theoretically grounded. As the field has matured, a number of challenges related to these criteria have become apparent. For instance, concerns have been raised that the literature prioritises predictive modeling over ensuring that these models are capable of informing constructive actions. Furthermore, the methodological validity of much of this work has been challenged, as a swathe of recent research has found many of these models fail to replicate to novel contexts. The work presented in this thesis addresses both of these concerns. In doing so, our research is pervaded by three key concerns: firstly, ensuring that any measures developed are both structurally valid and generalise across contexts; secondly, providing actionable insight with regards to student engagement; and finally, providing representations of student interactions that are predictive of student outcomes, namely, grades and students’ persistence in their studies. This research programme is heavily indebted to the work of Vincent Tinto, who conceptually distinguishes between the interactions students have with the academic and social domains present within their educational institution. This model has been subjected to extensive empirical validation, using a range of methods and data. For instance, while some studies have relied upon survey responses, others have used social network metrics, demographic variables, and students’ time spent in class together to evaluate Tinto’s claims. This model provides a foundation for the thesis, and the work presented may be categorised into two distinct veins aligning with the academic and social aspects of integration that Tinto proposes. These two domains, Tinto argues, continually modify a student’s goals and commitments, resulting in persistence or eventual disengagement and dropout. In the former, academic domain, we present a series of novel methodologies developed for modeling student engagement with academic resources. In doing so, we assessed how an individual student’s behaviour may be modeled using hidden Markov models (HMMs) to provide representations that enable actionable insight. However, in the face of considerable individual differences and cross-course variation, the validity of such methods may be called into question. Accordingly, ensuring that any measurements of student engagement are both structurally valid, and generalise across course contexts and disciplines became a central concern. To address this, we developed our model of student engagement using sticky-HMMs, emphasised the more interpretable insight such an approach provides compared to competing models, demonstrated its cross-course generality, and assessed its structural validity through the successful prediction of student dropout. In the social domain, a critical concern was to ensure any analyses conducted were valid. Accordingly, we assessed how the diversity of social tie definitions may undermine the validity of subsequent modeling practices. We then modeled students’ social integration using graph embedding techniques, and found that not only are student embeddings predictive of their final grades, but also of their persistence in their educational institution. In keeping with Tinto’s model, our research has focused on academic and social interactions separately, but both avenues of investigation have led to the question of student disengagement and dropout, and how this may be represented and remedied through the provision of actionable insight

APPROCCI BIOINFORMATICI PER L’ANALISI DI DATI DI NEXT GENERATION SEQUENCING IN OPHRYS (ORCHIDACEAE)

Il progetto di dottorato è stato finalizzato ad ottimizzare tecniche bioinformatiche in un contesto evolutivo e di assemblare dei genomi per contribuire all’arricchimento delle banche dati per il genere non-modello Ophrys (Orchidaceae). Questo genere rappresenta una sfida aperta per i ricercatori, in quanto è caratterizzato da una rapida radiazione evolutiva che ha impedito una chiara identificazione delle specie utilizzando le tradizionali tecniche genetiche. Nel corso del Dottorato sono stati dunque affrontati due casi di studio: l’assemblaggio e l’arricchimento delle banche dati con nuovi genomi plastidiali di due specie appartenenti al genere Ophrys ed un’analisi critica più approfondita al fine di ottimizzare l’analisi dei dati GBS in un complesso di specie appartenenti al genere Ophrys. L’approccio seed-extend si è rivelato il migliore per l’assemblaggio dei genomi plastidiali. I genomi presentano 127 geni distinti di cui 25 sono duplicati perché presenti nell’Inverted Repeat. In una specie, il gene ndhF è risultato essere troncato mentre nell’altra il gene ycf1 è risultato essere parzialmente duplicato. Questo riarrangiamento ha causato lo spostamento della giunzione tra le regioni Inverted Repeat e la Small Single Copy. Entrambi i genomi plastidiali hanno 213 loci microsatellitari di cui 67 sono polimorfici e possono essere usati per analisi filogeografiche. L’analisi critica dei dati GBS è stata effettuata attraverso l’utilizzo di diverse strategie di filtraggio dei dati mancanti e dei loci eterozigoti. Usando il genoma plastidiale di una specie come riferimento, è stato possibile distinguere sei aplotipi che hanno consentito l’individuazione di due cladi filetici. Questo risultato è in linea con un’analisi filogenetica effettuata eliminando tutti i loci eterozigoti e selezionando quelli condivisi da almeno il 70% degli individui. Diversamente introducendo nell’analisi i loci eterozigoti ed analizzando quelli condivisi da almeno il 30% degli individui è stato possibile distinguere le specie. Nel complesso questi due casi di studio hanno consentito di testare e individuare strategie di analisi bioinformatica di dati genomici in un contesto evolutivo e di assemblare dei genomi per contribuire all’arricchimento delle banche dati. Tali tecniche potranno essere utilizzate per l’annotazione di genomi organellari in specie non modello e per l’analisi di dati GBS

The Cambria Connection: Identifying Ceramic Production and Community Interaction in Late Prehistoric Minnesota, AD 1050-1300

The Cambria phase (AD 1050-1300) is an archaeological complex primarily centered on the elevated terraces of the Minnesota River in south-central Minnesota. Cambria phase pottery demonstrates technical and stylistic influences from several different late prehistoric cultures, and although the Cambria phase is currently classified as part of the Initial Middle Missouri Variant, certain affinities are evident between the grit-tempered, rolled rim ceramics at Cambria and the Powell-Ramey series at Cahokia. Although this pottery is a minority ware at Cambria, it is ubiquitous in the site literature, where it is interpreted as evidence for interaction with the Mississippian world. However, the nature and degree of the relationship between the two cultural areas has never been defined clearly. This project utilizes attribute and compositional analysis to identify the range of variation in the ceramic assemblages of three sites referred to collectively as the Cambria Locality: the Cambria, Price, and Owen D. Jones sites. A theoretical framework is structured from integrating articulated facets of world systems theory, community studies and the internal frontier concept. The results are interpreted at multiple levels of analysis, but are primarily focused on understanding interaction locally amongst the three sites, and in a micro-regional context within southern Minnesota. The evidence for and mechanisms of cultural interaction with Mississippian communities are evaluated. Finally, a model is developed to explain the emergence of the Cambria Locality village sites as intra-regional migration by cultural groups trending towards sedentism and maize agriculture from other areas in southern Minnesota