Towards Accessible, Usable Knowledge Frameworks in Engineering

A substantial amount of research has been done in the field of engineering knowledge management, where countless ontologies have been developed for various applications within the engineering community. However, despite the success shown in these research efforts, the techniques have not been adopted by industry. This research aims to uncover the reasons for the slow adoption of engineering knowledge frameworks, namely ontologies, in industry. There are two projects covered in this thesis. The first project is the development of a cross-domain ontology for the Biomesh Project, which spans the fields of mechanical engineering, biology, and anthropology. The biology community is known for its embrace of ontologies and has made their use quite popular with the creation of the Gene Ontology. This ontology spawned the establishment of the Open Biological and Biomedical Ontologies (OBO) Foundry, a consortium which approves and curates ontologies in the biology field. No such consortium exists in the field of engineering. This project demonstrates the usefulness of curated reference ontologies. Ontological knowledge bases in four different domains were imported and integrated together to connect previously disparate information. A case study with data from the Biomesh Project demonstrates cross-domain queries and inferences that were not possible before the creation of this ontology. In the second part of this thesis we investigate the usability of current ontology tools. Protégé, the most popular ontology editing tool, is compared to OntoWiki, a semantic wiki. This comparison is done using proven techniques from the field of Human-computer interaction to uncover usability problems and point out areas where each system excels. A field of 16 subjects completed a set of tasks in each system and gave feedback based on their experience. It is shown that while OntoWiki offers users a satisfying interface, it lacks in some areas that can be easily improved. Protégé provides users with adequate functionality, but it is not intended for a novice user

Network Effects in Blau Space: Imputing Social Context from Survey Data

We develop a method of imputing ego network characteristics for respondents in probability samples of individuals. This imputed network uses the homophily principle to estimate certain properties of a respondent’s core discussion network in the absence of actual network data. These properties measure the potential exposure of respondents to the attitudes, values, beliefs, etc. of their (likely) network alters. We use American National Election Survey data (2016 ANES) to demonstrate that the imputed network features show substantial effects on individual level measures, such as political attitudes and beliefs. In some cases, the imputed network variable substantially reduces the effects of standard socio-demographic variables like age and education. We argue that the imputed network variable captures many of the aspects of social context that have been at the core of sociological analysis for decades

Social networks are more demographically diverse than in the past, but the tendency for the alike to associate remains a strong force in society

In recent decades, the U.S. has undergone significant social and demographic change, and has become much more racially and religiously heterogeneous. But have these changes been reflected in who people now associate with for friendship and other relationships? In new research, which measures changes in ‘homophily’, or the tendency for people who are similar to be more likely to know each other, Jeffrey A. Smith, Miller McPherson and Lynn Smith-Lovin find thatmore people now know someone with a different racial/religious background, and that these changes have occurred in line with demographic shifts. They also find that homophily is decreasing along gender lines as men and women occupy increasingly similar roles in society, and that there is less interaction between people in different age groups

Biophysical and atomic force microscopy characterization of the RNA from satellite tobacco mosaic virus

Agarose gel electrophoresis, circular dichroism and differential scanning calorimetry showed that single-stranded RNA from satellite tobacco mosaic virus transforms from a conformationally ‘closed state’ at 4°C to a more conformationally ‘open state’ at 65°C. The transition is reversible and shows no hysteresis. Atomic force microscopy (AFM) allowed visualization of the two states and indicated that the conformationally ‘closed state’ probably corresponds to the native encapsidated conformation, and that the ‘open state’ represents a conformation, characterized as short, thick chains of domains, as a consequence of the loss of tertiary interactions. Heating from 75°C to 85°C in the presence of EDTA was necessary to further unravel the ‘open’ conformation RNA into extended chains of lengths >280 nm. Virus exposed to low concentrations of phenol at 65°C, extruded RNA as distinctive ‘pigtails’ in a synchronous fashion, and these ‘pigtails’ then elongated, as the RNA was further discharged by the particles. Moderate concentrations of phenol at 65°C produced complete disruption of virions and only remains of decomposed particles and disordered RNA were evident. AFM images of RNA emerging from disrupted virions appear most consistent with linear arrangements of structural domains

A Soluble Sulfogalactosyl Ceramide Mimic Promotes ΔF508 CFTR Escape from Endoplasmic Reticulum Associated Degradation

SummaryAdaSGC binds Hsc70s to inhibit ATPase activity. Using single-turnover assays, adaSGC, a soluble SGC mimic, preferentially inhibited Hsp40-activated Hsc70 ATP hydrolysis (Ki ∼ 10 μM) to reduce C-terminal Hsc70-peptide binding and, potentially, chaperone function. ERAD of misfolded ΔF508 CFTR requires Hsc70-Hsp40 chaperones. In transfected baby hamster kidney (BHK) cells, adaSGC increased ΔF508CFTR ERAD escape, and after low-temperature glycerol rescue, maturation, and iodide efflux. Inhibition of SGC biosynthesis reduced ΔF508CFTR but not wtCFTR expression, whereas depletion of other glycosphingolipids had no affect. WtCFTR transfected BHK cells showed increased SGC synthesis compared with ΔF508CFTR/mock-transfected cells. Partial rescue of ΔF508CFTR by low-temperature glycerol increased SGC synthesis. AdaSGC also increased cellular endogenous SGC levels. SGC in the lung, liver, and kidney was severely depleted in ΔF508CFTR compared with wtCFTR mice, suggesting a role for CFTR in SGC biosynthesis

Application of an antibiotic spectrum index in the neonatal intensive care unit

Antimicrobial stewardship programs typically use days of therapy to assess antimicrobial use. However, this metric does not account for the antimicrobial spectrum of activity. We applied an antibiotic spectrum index to a population of very-low-birth-weight infants to assess its utility to evaluate the impact of antimicrobial stewardship interventions

Fruit Quality And Consumption By Songbirds During Autumn Migration

Seasonal fruits are an important food resource for small songbirds during autumn migration in southern New England. Therefore, conservation and management of important stopover sites used by migrating birds requires knowledge about nutritional requirements of songbirds and nutritional composition of commonly consumed fruits. We measured nutrient composition and energy density of nine common fruits on Block Island, Rhode Island, and conducted a field experiment to estimate consumption rates of three of these fruits by birds during autumn migration. Most common fruits on Block Island contained primarily carbohydrates (41.3–91.2% dry weight), and little protein (2.6–8.6%) and fat (0.9–3.7%), although three contained more fat: Myrica pennsylvanica (50.3%), Viburnum dentatum (41.3%), and Parthenocissus quinquefolia (23.6%). Bird consumption of high-fat, high-energy V. dentatum fruit and high-carbohydrate, low-energy Phytolacca americana fruit was greater than consumption of Aronia melanocarpa, a high-carbohydrate, low-energy fruit. We estimated that migratory birds on Block Island must eat up to four times their body mass in fruit wet weight each day to satisfy their energy requirements when eating low-energy fruits such as P. americana, and they cannot satisfy their protein requirements when eating only certain high-energy fruits such as V. dentatum. Our results suggest that many migratory birds must eat both fruits and insects to meet their dietary needs. Thus, shrubland habitat at important migratory stopover sites such as Block Island should be managed so that it contains a variety of preferred fruit-bearing shrubs and an adequate abundance of insects

Review of Acanthocephala (Hemiptera: Heteroptera: Coreidae) of America north of Mexico with a key to species

A review of Acanthocephala of America north of Mexico is presented with an updated key to species. A. confraterna is considered a junior synonym of A. terminalis, thus reducing the number of known species in this region from five to four. New state and country records are presented

20th to 21st Century Relative Sea and Land Level Changes in Northern California: Tectonic Land Level Changes and their Contribution to Sea-Level Rise, Humboldt Bay Region, Northern California

Sea-level changes are modulated in coastal northern California by land-level changes due to the earthquake cycle along the Cascadia subduction zone, the San Andreas plate boundary fault system, and crustal faults. Sea-level rise (SLR) subjects ecological and anthropogenic infrastructure to increased vulnerability to changes in habitat and increased risk for physical damage. The degree to which each of these forcing factors drives this modulation is poorly resolved. We use NOAA tide gage data and ‘campaign’ tide gage deployments, Global Navigation Satellite System (GNSS) data, and National Geodetic Survey (NGS) first-order levelling data to calculate vertical land motion (VLM) rates in coastal northern California. Sea-level observations, highway level surveys, and GNSS data all confirm that land is subsiding in Humboldt Bay, in contrast to Crescent City where the land is rising. Subtracting absolute sea-level rate (~1.99 mm/year) from Crescent City (CC) and North Spit (NS) gage relative sea-level rates reveals that CC is uplifting at ~2.83 mm/year and NS is subsiding at ~3.21mm/year. GNSS vertical deformation reveals similar rates of ~2.60 mm/year of uplift at Crescent City. In coastal northern California, there is an E-W trending variation in vertical land motion that is primarily due to Cascadia megathrust fault seismogenic coupling. This interseismic subsidence also dominates the N-S variation in vertical land motion in most of the study region. There exists a second-order heterogeneous N-S trend in vertical land motion that we associate to crustal fault-related strain. There may be non-tectonic contributions to the observed VLM rates

Molecular Pathways Underlying Adaptive Repair of the Injured Kidney: Novel Donation After Cardiac Death and Acute Kidney Injury Platforms

International audienceObjective: To test the hypothesis that gene expression profiling in peripheral blood from patients who have undergone kidney transplantation (KT) will provide mechanistic insights regarding graft repair and regeneration.Background: Renal grafts obtained from living donors (LD) typically function immediately, whereas organs from donation after cardiac death (DCD) or acute kidney injury (AKI) donors may experience delayed function with eventual recovery. Thus, recipients of LD, DCD, and AKI kidneys were studied to provide a more complete understanding of the molecular basis for renal recovery.Methods: Peripheral blood was collected from LD and DCD/AKI recipients before transplant and throughout the first 30 days thereafter. Total RNA was isolated and assayed on whole genome microarrays.Results: Comparison of longitudinal gene expression between LD and AKI/DCD revealed 2 clusters, representing 141 differentially expressed transcripts. A subset of 11 transcripts was found to be differentially expressed in AKI/DCD versus LD. In all recipients, the most robust gene expression changes were observed in the first day after transplantation. After day 1, gene expression profiles differed depending upon the source of the graft. In patients receiving LD grafts, the expression of most genes did not remain markedly elevated beyond the first day post-KT. In the AKI/DCD groups, elevations in gene expression were maintained for at least 5 days post-KT. In all recipients, the pattern of coordinate gene overexpression subsided by 28 to 30 days.Conclusions: Gene expression in peripheral blood of AKI/DCD recipients offers a novel platform to understand the potential mechanisms and timing of kidney repair and regeneration after transplantation