Conservation, Comparative Genomics and Species Delimitation of the Reindeer Lichens (\u3ci\u3eCladonia\u3c/i\u3e)

The genus Cladonia represents one of the most speciose genera of lichenized fungi, with more than 500 known species encompassing a diverse array of morphologies and habits. These lichens form keystone species in many habitats, serving a variety of ecological roles. However, despite being among of the more well studied lichens, there is much still unknown or under-studied about them. As is the case with most lichen study systems, phylogenetic study has been limited to a small number of partial loci, while adoption of next-generation sequence methods has been slow. As a consequence, there are still knowledge gaps in Cladonia phylogenetics and comparative genomics. The limited application of molecular data has also left most species, even iconic and well-known taxa such as C. rangiferina, without an effective re-assessment of species boundaries with molecular data. Like all lichens, Cladonia species are also understudied in terms of conservation, with only a handful of the speciose genus assessed with IUCN Red List guidelines. In this dissertation, I take steps in addressing some of these current shortcomings over five studies; i) I review and analyze the application of traditional sequence data and the adoption of next-generation sequence data in lichens since 2000, ii) I conduct a population survey and IUCN Red List assessment for a geographically restricted and overlooked species, C. submitis, listing the species as Endangered (EN), iii) I sequence and assemble the mitochondrial genomes of multiple Cladonia species and examine the mitochondrial genome architecture and diversity of homing endonuclease genes within and among species in the genus, iv) I assess the evolutionary relationships and species boundaries of three morphologically similar and partly co-occurring species, C. rangiferina, C. oricola and C. stygia, and v) I investigate the delimitation between widely disjunct populations of C. submitis, describe the population in east Asia as C. miyabii sp. nov., and assess the species as Vulnerable (VU) under IUCN guidelines. These studies generated a wealth of assembled mitochondrial genomes and other molecular data for Cladonia, provided the first intraspecific comparison of lichen mitochondrial genomes and homing endonuclease genes, established molecular support for multiple distinct species including one new to science, and contributed to a steadily growing body of conservation assessments, of which lichens are desperately in need

Measures for explainable AI: Explanation goodness, user satisfaction, mental models, curiosity, trust, and human-AI performance

If a user is presented an AI system that portends to explain how it works, how do we know whether the explanation works and the user has achieved a pragmatic understanding of the AI? This question entails some key concepts of measurement such as explanation goodness and trust. We present methods for enabling developers and researchers to: (1) Assess the a priori goodness of explanations, (2) Assess users\u27 satisfaction with explanations, (3) Reveal user\u27s mental model of an AI system, (4) Assess user\u27s curiosity or need for explanations, (5) Assess whether the user\u27s trust and reliance on the AI are appropriate, and finally, (6) Assess how the human-XAI work system performs. The methods we present derive from our integration of extensive research literatures and our own psychometric evaluations. We point to the previous research that led to the measurement scales which we aggregated and tailored specifically for the XAI context. Scales are presented in sufficient detail to enable their use by XAI researchers. For Mental Model assessment and Work System Performance, XAI researchers have choices. We point to a number of methods, expressed in terms of methods\u27 strengths and weaknesses, and pertinent measurement issues

Effects of resistance training on classic and specific bioelectrical impedance vector analysis in elderly women

Raw bioelectrical impedance analysis (BIA) data [resistance (R); reactance (Xc)] through bioelectrical impedance vector analysis (BIVA) and phase angle (PhA) have been used to evaluate cellular function and hydration status. The purpose of this investigation was to examine the effects of resistance training (RT) on classic and specific BIVA in elderly women. Twenty women (mean ± SD; age: 71.9 ± 6.9 years; BMI: 24.5 ± 3.0 kg m(-2)) completed a 6-month RT program. Whole-body, single-frequency BIA, body geometry, and leg strength (5RM) measures were completed at baseline (t0), 3 months (t3), and 6 months (t6). The mean impedance vector displacements were compared using Hotelling's T(2) test to evaluate changes in R and Xc relative to height (R/ht; Xc/ht) or body volume (Rsp; Xcsp) estimated from the arms, legs, and trunk. 5RM, PhA, and BIVA variables were compared using ANOVA. PhA improved at t6 (p < 0.01), while 5RM improved at t3 and t6 (p < 0.01). Using classic BIVA, 6 months (T(2) = 31.6; p < 0.01), but not 3 months of RT (T(2) = 4.5; p = 0.20), resulted in significant vector migration. Using specific BIVA, 6 months (T(2) = 24.4; p < 0.01), but not 3 months of RT (T(2) = 5.5; p = 0.10), also resulted in significant vector migration. 5RM was correlated to both PhA (r = 0.48-56) and Xcsp (r = 0.45-53) at all time points. Vector displacements were likely the result of improved cellular integrity (Xcsp) and cellular health (PhA)

A longitudinal study of infants' early speech production and later letter identification

Letter identification is an early metric of reading ability that can be reliability tested before a child can decode words. We test the hypothesis that early speech production will be associated with children's later letter identification. We examined longitudinal growth in early speech production in 9 typically developing children across eight occasions, every 3 months from 9 months to 30 months. At each occasion, participants and their caregivers engaged in a speech sample in a research lab. This speech sample was transcribed for a variety of vocalizations, which were then transformed to calculate consonant-vowel ratio. Consonantvowel ratio is a measure of phonetic complexity in speech production. At the age of 72 months, children's letter knowledge was measured. A multilevel model including fixed quadratic age change and a random intercept was estimated using letter identification as a predictor of the growth in early speech production from 9±30 months, measured by the outcome of consonant-vowel ratio. Results revealed that the relation between early speech production and letter identification differed over time. For each additional letter that a child identified, their consonant-vowel ratio at the age of 9 months increased. As such, these results confirmed our hypothesis: more robust early speech production is associated with more accurate letter identification.(R01 DC006463

A biochemical approach to define the interactome for calpain2 in endothelial cells

Current repositories for protein-protein interactions and high throughput screening methods focus on individual gene products and do not consider the significance of calcium induced conformational changes. These limitations suggest the need for alternative strategies to better define the calpain2 interactome. Affinity capture coupled with LC-MS/MS and proteomic analysis of the recovered proteins provides a powerful approach to identify protein-protein interactions for the heterodimeric calpain2. CAPN2 (rat) was modified to be catalytically incompetent (C105A) and fused with a C-terminal 15 residue peptide optimized for biotinylation by the biotin protein ligase, BirA. The resulting CAPN2*, heterodimerized with truncated CAPNS1, was purified from E. coli, and biotinylated in vitro. Biotinylated calpain2* served as ‘bait’ for streptavidin affinity capture of calpain2 and its interacting proteins from lysates of bovine aortic (BAEC) and human umbilical vein (HUVEC) endothelial cells (ECs). Protein-calpain2 complexes were formed in the presence of calcium to allow EGTA elution of interacting proteins and LC-MS/MS analysis in the absence of an abundance of bait peptides. Capture of the well characterized calpain inhibitor protein calpastatin (CAST), and a known substrate, vimentin provide proof of concept and validates the conformational integrity of the bait calpain2*. Significant overlap between datasets (two from BAEC and one HUVEC) is also encouraging. Of numerous other proteins including several annexins, ANXA1 was confirmed as a substrate for calpain2. Findings are expected to contribute to continuing efforts in the field to better characterize calpain2’s selection of substrates and may reveal other important clues to calpain’s localization and regulation

Octonionic representations of Clifford algebras and triality

The theory of representations of Clifford algebras is extended to employ the division algebra of the octonions or Cayley numbers. In particular, questions that arise from the non-associativity and non-commutativity of this division algebra are answered. Octonionic representations for Clifford algebras lead to a notion of octonionic spinors and are used to give octonionic representations of the respective orthogonal groups. Finally, the triality automorphisms are shown to exhibit a manifest \perm_3 \times SO(8) structure in this framework.Comment: 33 page

Q methodology and a Delphi poll: a useful approach to researching a narrative approach to therapy

Q methodology and a Delphi poll combined qualitative and quantitative methods to explore definitions of White and Epston's (1990) narrative approach to therapy among a group of UK practitioners. A Delphi poll was used to generate statements about narrative therapy. The piloting of statements by the Delphi panel identified agreement about theoretical ideas underpinning narrative therapy and certain key practices. A wider group of practitioners ranked the statements in a Q sort and made qualitative comments about their sorting. Quantitative methods (principal components analysis) were used to extract eight accounts of narrative therapy, five of which are qualitatively analysed in this paper. Agreement and differences were identified across a range of issues, including the social construction of narratives, privileging a political stance or narrative techniques and the relationship with other therapies, specifically systemic psychotherapy. Q methodology, combined with the Delphi poll, was a unique and innovative feature of this study