Stereo-Aware Extension of HOSE Codes

The file attached to this record is the author's final peer reviewed version. The Publisher's final version can be found by following the DOI link.Descriptions of molecular environments have many applications in chemoinformatics, including chemical shift prediction. Hierarchically ordered spherical environment (HOSE) codes are the most popular such descriptions. We developed a method to extend these with stereochemistry information. It enables distinguishing atoms which would be considered identical in traditional HOSE codes. The use of our method is demonstrated by chemical shift predictions for molecules in the nmrshiftdb2 database. We give a full specification and an implementation

Eosinophilic bronchitis, eosinophilic granuloma, and eosinophilic bronchopneumopathy in 75 dogs (2006-2016).

BackgroundEosinophilic lung disease is a poorly understood inflammatory airway disease that results in substantial morbidity.ObjectiveTo describe clinical findings in dogs with eosinophilic lung disease defined on the basis of radiographic, bronchoscopic, and bronchoalveolar lavage fluid (BAL) analysis. Categories included eosinophilic bronchitis (EB), eosinophilic granuloma (EG), and eosinophilic bronchopneumopathy (EBP).AnimalsSeventy-five client owned dogs.MethodsMedical records were retrospectively reviewed for dogs with idiopathic BAL fluid eosinophilia. Information abstracted included duration and nature of clinical signs, bronchoscopic findings, and laboratory data. Thoracic radiographs were evaluated for the pattern of infiltrate, bronchiectasis, and lymphadenomegaly.ResultsThoracic radiographs were normal or demonstrated a bronchial pattern in 31 dogs assigned a diagnosis of EB. Nine dogs had intraluminal mass lesions and were bronchoscopically diagnosed with EG. The remaining 35 dogs were categorized as having EBP based on radiographic changes, yellow green mucus in the airways, mucosal changes, and airway collapse. Age and duration of cough did not differ among groups. Dogs with EB were less likely to have bronchiectasis or peripheral eosinophilia, had lower total nucleated cell count in BAL fluid, and lower percentage of eosinophils in BAL fluid compared to dogs in the other 2 groups. In contrast to previous reports, prolonged survival (>55 months) was documented in dogs with EG.Conclusions and clinical importanceDogs with eosinophilic lung disease can be categorized based on imaging, bronchoscopic and BAL fluid cytologic findings. Further studies are needed to establish response to treatment in these groups

Hidden Markov model speed heuristic and iterative HMM search procedure

BACKGROUND: Profile hidden Markov models (profile-HMMs) are sensitive tools for remote protein homology detection, but the main scoring algorithms, Viterbi or Forward, require considerable time to search large sequence databases. RESULTS: We have designed a series of database filtering steps, HMMERHEAD, that are applied prior to the scoring algorithms, as implemented in the HMMER package, in an effort to reduce search time. Using this heuristic, we obtain a 20-fold decrease in Forward and a 6-fold decrease in Viterbi search time with a minimal loss in sensitivity relative to the unfiltered approaches. We then implemented an iterative profile-HMM search method, JackHMMER, which employs the HMMERHEAD heuristic. Due to our search heuristic, we eliminated the subdatabase creation that is common in current iterative profile-HMM approaches. On our benchmark, JackHMMER detects 14% more remote protein homologs than SAM's iterative method T2K. CONCLUSIONS: Our search heuristic, HMMERHEAD, significantly reduces the time needed to score a profile-HMM against large sequence databases. This search heuristic allowed us to implement an iterative profile-HMM search method, JackHMMER, which detects significantly more remote protein homologs than SAM's T2K and NCBI's PSI-BLAST

hnRNP A1 and secondary structure coordinate alternative splicing of Mag

Myelin-associated glycoprotein (MAG) is a major component of myelin in the vertebrate central nervous system. MAG is present in the periaxonal region of the myelin structure, where it interacts with neuronal proteins to inhibit axon outgrowth and protect neurons from degeneration. Two alternatively spliced isoforms of Mag mRNA have been identified. The mRNA encoding the shorter isoform, known as S-MAG, contains a termination codon in exon 12, while the mRNA encoding the longer isoform, known as L-MAG, skips exon 12 and produces a protein with a longer C-terminal region. L-MAG is required in the central nervous system. How inclusion of Mag exon 12 is regulated is not clear. In a previous study, we showed that heteronuclear ribonucleoprotein A1 (hnRNP A1) contributes to Mag exon 12 skipping. Here, we show that hnRNP A1 interacts with an element that overlaps the 5\u27 splice site of Mag exon 12. The element has a reduced ability to interact with the U1 snRNP compared with a mutant that improves the splice site consensus. An evolutionarily conserved secondary structure is present surrounding the element. The structure modulates interaction with both hnRNP A1 and U1. Analysis of splice isoforms produced from a series of reporter constructs demonstrates that the hnRNP A1-binding site and the secondary structure both contribute to exclusion of Mag exon 12

Personal Utility Cart

This final design report will detail the entire engineering design process from conceptualization through manufacturing and testing. After introducing the topic and scope of the project this document presents all of the benchmarking and research performed in order to obtain as much information about similar current products and possible solutions. Next the objectives of the project are presented where the needs are transformed into engineering specifications that will guide the design of the product. Design developed is then presented with ideation, idea evaluation and selection, analysis, manufacturing considerations, and final design selection. The final design is then presented with each of its three subsystems, including supporting analysis, manufacturing and testing plans, bill of materials and cost as well as material selection, safety considerations, and maintenance plans. Following that is the management plan where team roles are outlines and project deadlines are presented. Product realization is next, which includes the manufacturing process that was taken for all components as well as description of changes between the planned and built design and recommendations for future manufacturing changes. Design verification follows with testing procedures and results and a final budget for the manufactured design. Next are conclusions that summarize what was done during the project and recommendations which outline what could have been done differently from a design or project standpoint to provide insight for future designs. References for all researched information are included in order cited throughout the document. Finally all appendices are included at the end of the document that were referenced throughout the report as well as other important information

Civic and Political Leadership Education

Unique in its demands as a system of governance, democracy requires active citizen leadership to be successful. Citizen leadership, in turn, requires engagement based on knowledge and action. Therefore, civic and political education is essential to the success of any democracy. This article discusses a model of applied political and civic leadership education that is based in theory, yet practical to the lives of young people. Surveys of past participants demonstrate that after the program, participants are more confident that they have the skills to become involved in politics and in community life

Magnetic field dependence of the internal quality factor and noise performance of lumped-element kinetic inductance detectors

We present a technique for increasing the internal quality factor of kinetic inductance detectors (KIDs) by nulling ambient magnetic fields with a properly applied magnetic field. The KIDs used in this study are made from thin-film aluminum, they are mounted inside a light-tight package made from bulk aluminum, and they are operated near $150 \, \mathrm{mK}$. Since the thin-film aluminum has a slightly elevated critical temperature ($T_\mathrm{c} = 1.4 \, \mathrm{K}$), it therefore transitions before the package ($T_\mathrm{c} = 1.2 \, \mathrm{K}$), which also serves as a magnetic shield. On cooldown, ambient magnetic fields as small as approximately $30 \, \mathrm{\mu T}$ can produce vortices in the thin-film aluminum as it transitions because the bulk aluminum package has not yet transitioned and therefore is not yet shielding. These vortices become trapped inside the aluminum package below $1.2 \, \mathrm{K}$ and ultimately produce low internal quality factors in the thin-film superconducting resonators. We show that by controlling the strength of the magnetic field present when the thin film transitions, we can control the internal quality factor of the resonators. We also compare the noise performance with and without vortices present, and find no evidence for excess noise beyond the increase in amplifier noise, which is expected with increasing loss.Comment: 5 pages, 4 figure