Matching Items (3)
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- All Subjects: Microbiomes
- All Subjects: Metal castings
- Creators: Hansford, Dianne
- Creators: Halcomb, Michael Jordan
- Resource Type: Text
Description
Is it possible to treat the mouth as a natural environment, and determine new methods to keep the microbiome in check? The need for biodiversity in health may suggest that every species carries out a specific function that is required to maintain equilibrium and homeostasis within the oral cavity. Furthermore, the relationship between the microbiome and its host is mutually beneficial because the host is providing microbes with an environment in which they can flourish and, in turn, keep their host healthy. Reviewing examples of larger scale environmental shifts could provide a window by which scientists can make hypotheses. Certain medications and healthcare treatments have been proven to cause xerostomia. This disorder is characterized by a dry mouth, and known to be associated with a change in the composition, and reduction, of saliva. Two case studies performed by Bardow et al, and Leal et al, tested and studied the relationships of certain medications and confirmed their side effects on the salivary glands [2,3]. Their results confirmed a relationship between specific medicines, and the correlating complaints of xerostomia. In addition, Vissink et al conducted case studies that helped to further identify how radiotherapy causes hyposalivation of the salivary glands [4]. Specifically patients that have been diagnosed with oral cancer, and are treated by radiotherapy, have been diagnosed with xerostomia. As stated prior, studies have shown that patients having an ecologically balanced and diverse microbiome tend to have healthier mouths. The oral cavity is like any biome, consisting of commensalism within itself and mutualism with its host. Due to the decreased salivary output, caused by xerostomia, increased parasitic bacteria build up within the oral cavity thus causing dental disease. Every human body contains a personalized microbiome that is essential to maintaining health but capable of eliciting disease. The Human Oral Microbiomics Database (HOMD) is a set of reference 16S rRNA gene sequences. These are then used to define individual human oral taxa. By conducting metagenomic experiments at the molecular and cellular level, scientists can identify and label micro species that inhabit the mouth during parasitic outbreaks or a shifting of the microbiome. Because the HOMD is incomplete, so is our ability to cure, or prevent, oral disease. The purpose of the thesis is to research what is known about xerostomia and its effects on the complex microbiome of the oral cavity. It is important that researchers determine whether this particular perspective is worth considering. In addition, the goal is to create novel experiments for treatment and prevention of dental diseases.
ContributorsHalcomb, Michael Jordan (Author) / Chen, Qiang (Thesis director) / Steele, Kelly (Committee member) / Barrett, The Honors College (Contributor) / College of Letters and Sciences (Contributor)
Created2015-05
Description
I, Christopher Negrich, am the sole author of this paper, but the tools described were designed in collaboration with Andrew Hoetker. ConstrictR (constrictor) and ConstrictPy are an R package and python tool designed together. ConstrictPy implements the functions and methods defined in ConstrictR and applies data handling, data parsing, input/output (I/O), and a user interface to increase usability. ConstrictR implements a variety of common data analysis methods used for statistical and subnetwork analysis. The majority of these methods are inspired by Lionel Guidi's 2016 paper, Plankton networks driving carbon export in the oligotrophic ocean. Additional methods were added to expand functionality, usability, and applicability to different areas of data science. Both ConstrictR and ConstrictPy are currently publicly available and usable, however, they are both ongoing projects. ConstrictR is available at github.com/cnegrich and ConstrictPy is available at github.com/ahoetker. Currently, ConstrictR has implemented functions for descriptive statistics, correlation, covariance, rank, sparsity, and weighted correlation network analysis with clustering, centrality, profiling, error handling, and data parsing methods to be released soon. ConstrictPy has fully implemented and integrated the features in ConstrictR as well as created functions for I/O and conversion between pandas and R data frames with a full feature user interface to be released soon. Both ConstrictR and ConstrictPy are designed to work with minimal dependencies and maximum available information on the algorithms implemented. As a result, ConstrictR is only dependent on base R (v3.4.4) functions with no libraries imported. ConstrictPy is dependent upon only pandas, Rpy2, and ConstrictR. This was done to increase longevity and independence of these tools. Additionally, all mathematical information is documented alongside the code, increasing the available information on how these tools function. Although neither tool is in its final version, this paper documents the code, mathematics, and instructions for use, in addition to plans for future work, for of the current versions of ConstrictR (v0.0.1) and ConstrictPy (v0.0.1).
ContributorsNegrich, Christopher Alec (Author) / Can, Huansheng (Thesis director) / Hansford, Dianne (Committee member) / School of Mathematical and Statistical Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2018-05
Description
Metal castings are selectively machined-based on dimensional control requirements. To ensure that all the finished surfaces are fully machined, each as-cast part needs to be measured and then adjusted optimally in its fixture. The topics of this thesis address two parts of this process: data translations and feature-fitting clouds of points measured on each cast part. For the first, a CAD model of the finished part is required to be communicated to the machine shop for performing various machining operations on the metal casting. The data flow must include GD&T specifications along with other special notes that may be required to communicate to the machinist. Current data exchange, among various digital applications, is limited to translation of only CAD geometry via STEP AP203. Therefore, an algorithm is developed in order to read, store and translate the data from a CAD file (for example SolidWorks, CREO) to a standard and machine readable format (ACIS format - *.sat). Second, the geometry of cast parts varies from piece to piece and hence fixture set-up parameters for each part must be adjusted individually. To predictively determine these adjustments, the datum surfaces, and to-be-machined surfaces are scanned individually and the point clouds reduced to feature fits. The scanned data are stored as separate point cloud files. The labels associated with the datum and to-be-machined (TBM) features are extracted from the *.sat file. These labels are further matched with the file name of the point cloud data to identify data for the respective features. The point cloud data and the CAD model are then used to fit the appropriate features (features at maximum material condition (MMC) for datums and features at least material condition (LMC) for TBM features) using the existing normative feature fitting (nFF) algorithm. Once the feature fitting is complete, a global datum reference frame (GDRF) is constructed based on the locating method that will be used to machine the part. The locating method is extracted from a fixture library that specifies the type of fixturing used to machine the part. All entities are transformed from its local coordinate system into the GDRF. The nominal geometry, fitted features, and the GD&T information are then stored in a neutral file format called the Constraint Tolerance Feature (CTF) Graph. The final outputs are then used to identify the locations of the critical features on each part and these are used to establish the adjustments for its setup prior to machining, in another module, not part of this thesis.
ContributorsRamnath, Satchit (Author) / Shah, Jami J. (Thesis advisor) / Davidson, Joseph (Committee member) / Hansford, Dianne (Committee member) / Arizona State University (Publisher)
Created2016