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Common names of species are important for communicating with the general public. In principle, these names should provide an accessible way to engage with and identify species. The common names of species have historically been labile without standard guidelines, even within a language. Currently, there is no systematic assessment of how often common names communicate identifiable and biologically relevant characteristics about species. This is a salient issue in ornithology, where common names are used more often than scientific names for species of birds in written and spoken English, even by professional researchers. To gain a better understanding of the types of terminology used in the English-language common names of bird species, a group of 85 professional ornithologists and non-professional contributors classified unique descriptors in the common names of all recognized species of birds. In the AvianLexiconAtlas database produced by this work, each species’ common name is assigned to one of ten categories associated with aspects of avian biology, ecology, or human culture. Across 10,906 species of birds, 89% have names describing the biology of the species, while the remaining 11% of species have names derived from human cultural references, human names, or local non-English languages. Species with common names based on features of avian biology are more likely to be related to each other or be from the same geographic region. The crowdsourced data collection also revealed that many common names contain specialized or historic terminology unknown to many of the data collectors, and we include these terms in a glossary and gazetteer alongside the dataset. The AvianLexiconAtlas can be used as a quantitative resource to assess the state of terminology in English-language common names of birds. Future research using the database can shed light on historical approaches to nomenclature and how people engage with species through their names.

The serine protease thrombin plays an essential regulatory role in blood clotting. Prothrombin is converted to the active α-thrombin in response to tissue damage, allowing the enzyme to cleave procoagulative substrates such as fibrinogen and PAR, enabling the formation of the clot. On the other hand, when thrombin binds its protein cofactor thrombomodulin (TM), the enzyme loses substrate specificity for procoagulative substrates, and engages the anticoagulative pathway by selectively targeting the substrate protein C for proteolytic activation. Despite decades of study, the mechanism by which TM enables thrombin to cleave protein C has yet to be fully characterized, indicating a need for further investigation. Crystallographic evidence shows no notable difference between the thrombin and thrombin-TM structures, suggesting the influence of TM is dynamic in nature. The work presented in this thesis uses two biophysical techniques, hydrogen-deuterium exchange mass spectrometry (HDXMS) and nuclear magnetic resonance spectrometry (NMR) to report the effects of TM on thrombin dynamics.In Chapter II, HDXMS and NMR were used to evaluate the regions of thrombin effected by the presence of TM. The results show two paths of communication between the active site and TM binding site of thrombin, as well as large scale conformational changes throughout all of thrombin. From these data we generated a model of the dynamic influence of TM on thrombin that describes the global protein dynamics necessary for the execution of the serine protease catalytic mechanism. Chapter III presents a study of the dynamics of the W215A thrombin mutant using HDXMS. Previous studies have shown that mutations at Trp 215 impart dramatic changes to the substrate specificity of thrombin, and the W215A mutation appeared to favor protein C activation over procoagulative substrate activation. We found that alterations to the hydrophobic environment at and around Trp 215 increased the dynamics of the surrounding thrombin loops, as well as the N-terminus of the thrombin heavy chain over 10 Å away from the sites of mutation.In Chapter IV, the dynamics of the W215A/E217A mutant was investigated in the presence and absence of TM through HDXMS. The W215A/E217A mutant heavily prefers protein C over procoagulative thrombin substrates, causing us to ask whether TM binding recovers the destabilizing effects of these mutations. We found that TM was capable of stabilizing parts of the W21A/E217A thrombin mutant, but could not recover the increased dynamics of the primary substrate recognition pocket. These results suggest that the primary cause of the decreased activity of the W215A/E217A mutant towards procoagulative substrates results from the mutation of Trp 215, which is not important recognition element for protein C binding but is so for procoagulative substrates.

Common names of species are important for communicating with the general public. In principle, these names should provide an accessible way to engage with and identify species. The common names of species have historically been labile without standard guidelines, even within a language. Currently, there is no systematic assessment of how often common names communicate identifiable and biologically relevant characteristics about species. This is a particular issue in ornithology, where common names are used more often than scientific names for species of birds in written and spoken English, even by professional researchers. To gain a better understanding of the types of terminology used in the common names of bird species and their frequency of use, we used a crowdsourcing approach and recruited 85 professional ornithologists and non-professional participants to classify unique descriptors in the English-language common names of all recognized bird species from around the world. Each species' common name was assigned to one of ten categories associated with aspects of avian biology, ecology, or human culture. Across 10,906 species of birds, 89% have names describing the biology of the species, while the remaining 11% of species have names derived from human cultural references or local non-English languages. Species with common names based on features of avian biology are more likely to be related to each other or be from the same geographic region. The crowdsourced data collection also revealed that many common names contained specialized or historic terminology unknown to many of the data collectors, and this was documented in a glossary and gazetteer alongside the dataset. As the first comprehensive assessment of the state of terminology in English-language common names of birds, the AvianLexiconAtlas database sheds light on historical approaches to nomenclature and provides insight into how the general public currently engages with species through their names.Competing Interest StatementThe authors have declared no competing interest.Footnotes* The title, abstract, introduction, and conclusion have been updated to present the new dataset, glossary, and gazetteer produced during this research as a research database, now called the AvianLexiconAtlas. Researchers from across academic fields can use the resources in this database to study the history of English-language bird names from a quantitative perspective. In the text we clarify the utility of this database as a resource, but have not changed any of the methods, analyses, figures, or supplemental files.* https://github.com/ajshultz/AvianLexiconAtlas

Previously, catalytic cerium oxide nanoparticles (CNPs, nanoceria, CeO2-x NPs) have been widely utilized for chemical mechanical planarization in the semiconductor industry and for reducing harmful emissions and improving fuel combustion efficiency in the automobile industry. Researchers are now harnessing the catalytic repertoire of CNPs to develop potential new treatment modalities for both oxidative- and nitrosative-stress induced disorders and diseases. In order to reach the point where our experimental understanding of the antioxidant activity of CNPs can be translated into useful therapeutics in the clinic, it is necessary to evaluate the most current evidence that supports CNP antioxidant activity in biological systems. Accordingly, the aims of this review are three-fold: (1) To describe the putative reaction mechanisms and physicochemical surface properties that enable CNPs to both scavenge reactive oxygen species (ROS) and to act as antioxidant enzyme-like mimetics in solution; (2) To provide an overview, with commentary, regarding the most robust design and synthesis pathways for preparing CNPs with catalytic antioxidant activity; (3) To provide the reader with the most up-to-date in vitro and in vivo experimental evidence supporting the ROS-scavenging potential of CNPs in biology and medicine.

Modern experimental technologies can assay large numbers of biological sequences, but engineered protein libraries rarely exceed the sequence diversity of natural protein families. Machine learning (ML) models trained directly on experimental data without biophysical modeling provide one route to accessing the full potential diversity of engineered proteins. Here we apply deep learning to design highly diverse adeno-associated virus 2 (AAV2) capsid protein variants that remain viable for packaging of a DNA payload. Focusing on a 28-amino acid segment, we generated 201,426 variants of the AAV2 wild-type (WT) sequence yielding 110,689 viable engineered capsids, 57,348 of which surpass the average diversity of natural AAV serotype sequences, with 12–29 mutations across this region. Even when trained on limited data, deep neural network models accurately predict capsid viability across diverse variants. This approach unlocks vast areas of functional but previously unreachable sequence space, with many potential applications for the generation of improved viral vectors and protein therapeutics. Viable AAV capsids are designed with a machine learning approach.

ObjectiveStudies of dermatomyositis (DM) are frequently limited to single-centre cohorts. We used two large nationally representative US cohorts to conduct a descriptive epidemiological study of the characteristics, treatments and outcomes of patients with incident DM.MethodsThis retrospective study identified two DM inception cohorts using (1) commercial claims and (2) electronic health record (EHR) data from the Excellence Network in Rheumatology to Innovate Care and High-impact research (ENRICH), a community rheumatology practice-based research network. Patient characteristics, treatments and healthcare utilisation were assessed using the 18 months before and 12 months after diagnosis in claims and the 12 months before and after diagnosis in EHR data.ResultsWe identified 2475 patients (claims) and 1196 patients (EHR) with incident DM. Among 998 patients in the EHR cohort with available laboratory data, 472 had available myositis panel results, with 165 (35.0%) having a positive myositis-specific antibody. Glucocorticoid use was common, 68.7% and 73.8% in the two cohorts, respectively, with initial doses most often >20 mg/day; among glucocorticoid users, mean cumulative dose was 1407 mg in the claims cohort. Hydroxychloroquine, methotrexate and mycophenolate were the most commonly used immunomodulatory therapies. During follow-up in the claims data cohort, incidence per 1000 person-years was 92.2, 15.3, 6.4, 2.9 and 2.1 for all-cause hospitalisation, malignancy, interstitial lung disease, gastrostomy tube placement and myocarditis, respectively.ConclusionAdministrative claims and EHR data can be leveraged to assess treatment patterns and longitudinal outcomes/disease manifestations in incident dermatomyositis cohorts. This study highlights a high burden of glucocorticoid exposure, significant heterogeneity in treatment and high healthcare utilisation in this population.

Background: Perturbation-based balance training (PBT) is a promising fall risk reduction method that involves inducing unexpected perturbations to balance to train participants reactive balance control. Due to the unpredictable nature of PBT, its acceptability to older adults could present a barrier to the implementation of PBT in the community. Aim/Purpose: The purpose of this study was to assess the perceived acceptability of a community-based PBT program to both older adults and healthcare professionals (HCPs). Methods: Nineteen older adults (aged 69.6 ± 6.6 years, 17 women, 2 men) and three HCPs participated in the qualitative study. Participants completed four PBT sessions facilitated in conjunction with HCPs. Interviews, based on the theoretical framework of acceptability, were conducted before and after PBT and analyzed using template analysis. Results: PBT was perceived as effective by older adults and HCPs. However, HCPs perceived the equipment cost as a substantial barrier to feasibility in the community.

Analytical skills are in high demand across business sectors and various positions. Therefore, it is pivotal for marketing students to have exposure and practice leveraging analytical methods and tools before graduation and entering the job market. However, qualitative techniques to gather marketing analytics and insights are rarely taught as an approach. As a result, the authors created the Social Listening Stoplight Activity to teach students how to qualitatively gather marketing analytics insights for actionable recommendations that can be used to adjust social media strategies for increased engagement. By leveraging data from the Social Listening Stoplight Activity, the authors qualitatively analyze undergraduate and graduate student assignment submissions to assess the activity as a method to teach students qualitative social listening, a growing industry skill. This research finds that students exhibit more difficulty with qualitative versus quantitative strategic social media marketing analysis skills, further justifying the need for an activity like this in marketing analytics and social media courses. Students must not only be able to assess numerical data, but they also must be able to interpret and communicate recommendations to truly contribute to organizations.