Automated Annotation-Based Bio-Ontology Alignment with Structural Validation

We outline the structure of an automated process to both align multiple bio-ontologies in terms of their genomic co-annotations, and then to measure the structural quality of that alignment. We illustrate the method with a genomic analysis of 70 genes implicated in lung disease against the Gene Ontology

Eddy Covariance flux errors due to random and systematic timing errors during data acquisition

Modern eddy covariance (EC) systems collect high-frequency data (10–20 Hz) via digital outputs of instru ments. This is an important evolution with respect to the tra ditional and widely used mixed analog/digital systems, as fully digital systems help overcome the traditional limita tions of transmission reliability, data quality, and complete ness of the datasets

Eddy covariance flux errors due to random and systematic timing errors during data acquisition

Modern eddy covariance (EC) systems collect high-frequency data (10–20 Hz) via digital outputs of instruments. This is an important evolution with respect to the traditional and widely used mixed analog/digital systems, as fully digital systems help overcome the traditional limitations of transmission reliability, data quality, and completeness of the datasets. However, fully digital acquisition introduces a new problem for guaranteeing data synchronicity when the clocks of the involved devices themselves cannot be synchronized, which is often the case with instruments providing data via serial or Ethernet connectivity in a streaming mode. In this paper, we suggest that, when assembling EC systems “inhouse”, aspects related to timing issues need to be carefully considered to avoid significant flux biases. By means of a simulation study, we found that, in most cases, random timing errors can safely be neglected, as they do not impact fluxes significantly. At the same time, systematic timing errors potentially arising in asynchronous systems can effectively act as filters leading to significant flux underestimations, as large as 10 %, by means of attenuation of high-frequency flux contributions. We characterized the transfer function of such “filters” as a function of the error magnitude and found cutoff frequencies as low as 1 Hz, implying that synchronization errors can dominate high-frequency attenuations in open- and enclosed-path EC systems. In most cases, such timing errors neither be detected nor characterized a posteriori. Therefore, it is important to test the ability of traditional and prospective EC data logging systems to assure the required synchronicity and propose a procedure to implement such a test relying on readily available equipment

Evaluation of renal perfusion in hyperthyroid cats before and after radioiodine treatment

Background: Hyperthyroidism and chronic kidney disease (CKD) are common in elderly cats. Consequently, both diseases often occur concurrently. Furthermore, renal function is affected by thyroid status. Because changes in renal perfusion play an important role in functional renal changes in hyperthyroid cats, investigation of renal perfusion may provide novel insights. Objectives: To evaluate renal perfusion in hyperthyroid cats with contrast-enhanced ultrasound (CEUS). Animals: A total of 42 hyperthyroid cats was included and evaluated before and 1 month after radioiodine treatment. Methods: Prospective intrasubject clinical trial of contrast-enhanced ultrasound using a commercial contrast agent (SonoVue) to evaluate renal perfusion. Time-intensity curves were created, and perfusion parameters were calculated by off-line software. A linear mixed model was used to examine differences between pre-and post-treatment perfusion parameters. Results: An increase in several time-related perfusion parameters was observed after radioiodine treatment, indicating a decreased blood velocity upon resolution of the hyperthyroid state. Furthermore, a small post-treatment decrease in peak enhancement was present in the renal medulla, suggesting a lower medullary blood volume. Conclusions and Clinical Importance: Contrast-enhanced ultrasound indicated a higher cortical and medullary blood velocity and higher medullary blood volume in hyperthyroid cats before radioactive treatment in comparison with 1-month post-treatment control

Monitoring a Small Northwestern Iowa Stream Undergoing Watershed Changes

Stream ecosystems are influenced by their watersheds. Intact watersheds support high water quality and habitat heterogeneity, while providing native allochthonous input. In Iowa, watershed degradation associated with agricultural activities and expanding residential development negatively impacts streams by increasing sedimentation, pesticide exposure, and eutrophication. Our study continued a monitoring program of a low order stream in Sioux County, Iowa. As the surrounding watershed shifts from agricultural to residential use, we are recording changes in stream biodiversity and water quality. At three study sites, we documented the stream’s physical and chemical characteristics and collected macroinvertebrate samples. We also introduced various substrata (gravel, maple leaves, and pavers) to the stream to observe macroinvertebrate colonization. As expected, we found the stream dominated by taxa tolerant of poor water quality. Our results indicate that substrate type significantly affected colonization, with gravel supporting the lowest richness and abundance of macroinvertebrates. Overall, location and colonization month (September vs. October) only affected a subset of our samples. These results differ markedly from those of a similar 2018 study. We anticipate that the results of this study will be compared to future work, enabling researchers to monitor how the stream responds to changes in the watershed and hydrological events

Feedforward control of thermal history in laser powder bed fusion: Toward physics-based optimization of processing parameters

We developed and applied a model-driven feedforward control approach to mitigate thermal-induced flaw formation in laser powder bed fusion (LPBF) additive manufacturing process. The key idea was to avert heat buildup in a LPBF part before it is printed by adapting process parameters layer-by-layer based on insights from a physics-based thermal simulation model. The motivation being to replace cumbersome empirical build-and-test parameter optimization with a physics-guided strategy. The approach consisted of three steps: prediction, analysis, and correction. First, the temperature distribution of a part was predicted rapidly using a graph theory-based computational thermal model. Second, the model-derived thermal trends were analyzed to isolate layers of potential heat buildup. Third, heat buildup in affected layers was corrected before printing by adjusting process parameters optimized through iterative simulations. The effectiveness of the approach was demonstrated experimentally on two separate build plates. In the first build plate, termed fixed processing, ten different nickel alloy 718 parts were produced under constant processing conditions. On a second identical build plate, called controlled processing, the laser power and dwell time for each part was adjusted before printing based on thermal simulations to avoid heat buildup. To validate the thermal model predictions, the surface temperature of each part was tracked with a calibrated infrared thermal camera. Post-process the parts were examined with non-destructive and destructive materials characterization techniques. Compared to fixed processing, parts produced under controlled processing showed superior geometric accuracy and resolution, finer grain size, increased microhardness, and reduced surface roughness

Stormbreaker8 and A3Wally Bacteriophage Genome Annotations

Stormbreaker8 and A3Wally are two novel bacteriophages isolated and purified on Microbacterium foliorum NRRL B-24224 by students in the Fall 2020 Discovery course. Stormbreaker8, an EA1 cluster lytic phage, was isolated from soil collected in Orange City, IA. Its circular permuted genome contains 41,751 base-pairs with 63.4% GC content. A3Wally, a GD cluster phage, was isolated from soil collected in Sioux Center, IA. Its genome is 60.1% GC, contains 194,724 base-pairs, and its ends are direct terminal repeats. Spring 2021 Genetics students annotated the genomes using bioinformatics software

Eddy covariance flux errors due to random and systematic timing errors during data acquisition

Modern eddy covariance (EC) systems collect high-frequency data (10–20&thinsp;Hz) via digital outputs of instruments. This is an important evolution with respect to the traditional and widely used mixed analog/digital systems, as fully digital systems help overcome the traditional limitations of transmission reliability, data quality, and completeness of the datasets.However, fully digital acquisition introduces a new problem for guaranteeing data synchronicity when the clocks of the involved devices themselves cannot be synchronized, which is often the case with instruments providing data via serial or Ethernet connectivity in a streaming mode. In this paper, we suggest that, when assembling EC systems in-house, aspects related to timing issues need to be carefully considered to avoid significant flux biases.By means of a simulation study, we found that, in most cases, random timing errors can safely be neglected, as they do not impact fluxes significantly. At the same time, systematic timing errors potentially arising in asynchronous systems can effectively act as filters leading to significant flux underestimations, as large as 10&thinsp;%, by means of attenuation of high-frequency flux contributions. We characterized the transfer function of such filters as a function of the error magnitude and found cutoff frequencies as low as 1&thinsp;Hz, implying that synchronization errors can dominate high-frequency attenuations in open- and enclosed-path EC systems. In most cases, such timing errors neither be detected nor characterized a posteriori. Therefore, it is important to test the ability of traditional and prospective EC data logging systems to assure the required synchronicity and propose a procedure to implement such a test relying on readily available equipment.</p

Serum Cystatin C Concentrations in Cats with Hyperthyroidism and Chronic Kidney Disease.

BACKGROUND: Currently, no test can accurately predict the development of azotemia after treatment of hyperthyroidism. Serum cystatin C concentrations (sCysC) might be less influenced by changes in body muscle mass and so better indicate the presence of concurrent chronic kidney disease (CKD) in hyperthyroidism. HYPOTHESES: sCysC will be higher in hyperthyroid cats that develop azotemia compared with hyperthyroid cats that remain nonazotemic after treatment; sCysC will be higher in nonhyperthyroid cats with azotemic CKD than healthy older cats and, sCysC will decrease after treatment of hyperthyroidism. ANIMALS: Ninety-one cats treated in first opinion practice. METHODS: Case-control study. sCysC were compared between hyperthyroid cats which developed azotemia within 4 months of successful treatment of hyperthyroidism (pre-azotemic group) and hyperthyroid cats which remained nonazotemic after treatment (nonazotemic group), and between nonhyperthyroid cats with azotemic CKD and healthy older cats. sCysC were also compared between hyperthyroid cats before treatment and at time of establishment of euthyroidism. Data are presented as median [25th, 75th percentile]. RESULTS: Baseline sCysC were not different between the pre-azotemic and nonazotemic groups (1.9 [1.4, 2.3] mg/L versus 1.5 [1.1, 2.2] mg/L, respectively; P = .22). sCysC in nonhyperthyroid cats with azotemic CKD and healthy older cats were not significantly different (1.5 [1.0, 1.9] mg/L versus 1.2 [0.8, 1.4] mg/L, respectively; P = .16). sCysC did not change significantly after treatment of hyperthyroidism (pretreatment 1.8 [1.2, 2.3] mg/L, after treatment 1.6 [1.1, 2.4] mg/L; P = .82). CONCLUSIONS AND CLINICAL IMPORTANCE: sCysC do not appear to be a reliable marker of renal function in hyperthyroid cats.This is the final version of the article. It first appeared from Wiley via https://doi.org/10.1111/jvim.1395