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Introduction: Olmesartan medoxomil is an ester prodrug commonly prescribed to treat high blood pressure, heart failure, and diabetic kidney disease. Aim: To study the bioequivalence of Olvas tablets (containing olmesartan medoxomil 40mg) of Cadila Pharmaceuticals Ltd., India with Benicar® tablets (containing olmesartan medoxomil 40mg) of Daiichi Sankyo, Inc., Parsippany, New Jersey. Materials and Methods: Forty healthy, adult, male subjects were studied in a single-dose, open-label, two-treatment, two-period, two-sequence, two-way cross-over study. Detailed demographic data along with clinical examination, vital signs, medical history, laboratory tests including hematology, biochemistry, serology and urine analysis. ECG and chest X-ray were performed. Pharmacokinetic primary parameters like Cmax, AUC0-t, AUC0-? and secondary parameters like Tmax, t1/2, Kel, and AUC Extrapolation were calculated for both the drug formulations. Results: Demographic parameters were comparable for both the treatment arms. Olmesartan medoxomil 40mg of Cadila Pharmaceuticals Ltd was found to in the acceptance range for bioequivalence, 80.00-125.00% for the 90% confidence intervals for the difference of means of Ln-transformed parameters Cmax, AUC0-t and AUC0-?. Conclusion: Both Olmesartan Medoxomil tablets 40mg (containing olmesartan medoxomil 40mg) of Cadila Pharmaceuticals Ltd., India with Benicar® tablets 40mg (containing olmesartan medoxomil 40mg) of Daiichi Sankyo, Inc., Parsippany, New Jersey were found to be bioequivalent. Keywords: Olmesartan, Bioavailability, Bioequivalence, Pharmacokinetics.

The Model AI Assignments session seeks to gather and disseminate the best assignment designs of the Artificial Intelligence (AI) Education community. Recognizing that assignments form the core of student learning experience, we here present abstracts of nine AI assignments from the 2020 session that are easily adoptable, playfully engaging, and flexible for a variety of instructor needs. Assignment specifications and supporting resources may be found at http://modelai.gettysburg.edu.

High-throughput screening (HTS) using new approach methods is revolutionizing toxicology. Asexual freshwater planarians are a promising invertebrate model for neurotoxicity HTS because their diverse behaviors can be used as quantitative readouts of neuronal function. Currently, three planarian species are commonly used in toxicology research: Dugesia japonica, Schmidtea mediterranea, and Girardia tigrina. However, only D. japonica has been demonstrated to be suitable for HTS. Here, we assess the two other species for HTS suitability by direct comparison with D. japonica. Through quantitative assessments of morphology and multiple behaviors, we assayed the effects of 4 common solvents (DMSO, ethanol, methanol, ethyl acetate) and a negative control (sorbitol) on neurodevelopment. Each chemical was screened blind at 5 concentrations at two time points over a twelve-day period. We obtained two main results: First, G. tigrina and S. mediterranea planarians showed significantly reduced movement compared to D. japonica under HTS conditions, due to decreased health over time and lack of movement under red lighting, respectively. This made it difficult to obtain meaningful readouts from these species. Second, we observed species differences in sensitivity to the solvents, suggesting that care must be taken when extrapolating chemical effects across planarian species. Overall, our data show that D. japonica is best suited for behavioral HTS given the limitations of the other species. Standardizing which planarian species is used in neurotoxicity screening will facilitate data comparisons across research groups and accelerate the application of this promising invertebrate system for first-tier chemical HTS, helping streamline toxicology testing.

At ACM-BCB 2017, several contributions in the form of paper and poster presentations were given by undergraduate students. A solicitation then went out to the ACM-SIGBIO community to highlight undergraduate research in the ACM-SIBGIO newsletter. What follows below are four contributions that showcase computational biology and bioinformatics research performed by undergraduate students.

We propose a framework that leverages deep residual CNNs pretrained on large, non-biomedical image data sets. These pretrained networks learn cross-domain features that improve low-level interpretation of images. We evaluate our model on brain imaging data and show that pretraining and the use of deep residual networks are crucial to seeing large improvements in Alzheimer's Disease diagnosis from brain MRIs.

We consider the task of KBP slot filling – extracting relation information from newswire documents for knowledge base construction. We present our pipeline, which employs Relational Dependency Networks (RDNs) to learn linguistic patterns for relation extraction. Additionally, we demonstrate how several components such as weak supervision, word2vec features, joint learning and the use of human advice, can be incorporated in this relational framework. We evaluate the different components in the benchmark KBP 2015 task and show that RDNs effectively model a diverse set of features and perform competitively with current state-of-the-art relation extraction methods.

Parkinson's, a progressive neural disorder, is difficult to identify due to the hidden nature of the symptoms associated. We present a machine learning approach that uses a definite set of features obtained from the Parkinsons Progression Markers Initiative(PPMI) study as input and classifies them into one of two classes: PD(Parkinson's disease) and HC(Healthy Control). As far as we know this is the first work in applying machine learning algorithms for classifying patients with Parkinson's disease with the involvement of domain expert during the feature selection process. We evaluate our approach on 1194 patients acquired from Parkinsons Progression Markers Initiative and show that it achieves a state-of-the-art performance with minimal feature engineering.

Uch37 is a de-ubiquitylating enzyme that is functionally linked with the 26S proteasome via Rpn13, and is essential for metazoan development. Here, we report the X-ray crystal structure of full-length human Uch37 at 2.95 A resolution. Uch37's catalytic domain is similar to those of all UCH enzymes characterized to date. The C-terminal extension is elongated, predominantly helical and contains coiled coil interactions. Additionally, we provide an initial characterization of Uch37's oligomeric state and identify a systematic error in previous analyses of Uch37 activity. Taken together, these data provide a strong foundation for further analysis of Uch37's several functions.

Improvements in medical imaging techniques have provided clinicians the ability to obtain detailed brain images of patients at lower costs. This increased availability of rich data opens up new avenues of research that promise better understanding of common brain ailments such as Alzheimer’s Disease and dementia. Improved data mining techniques, however, are required to leverage these new data sets to identify intermediate disease states (e.g., mild cognitive impairment) and perform early diagnosis. We propose a graphical model framework based on conditional random fields (CRFs) to mine MRI brain images. As a proof-of-concept, we apply CRFs to the problem of brain tissue segmentation. Experimental results show robust and accurate performance on tissue segmentation comparable to other state-of-the-art segmentation methods. In addition, results show that our algorithm generalizes well across data sets and is less susceptible to outliers. Our method relies on minimal prior knowledge unlike atlas-based techniques, which assume images map to a normal template. Our results show that CRFs are a promising model for tissue segmentation, as well as other MRI data mining problems such as anatomical segmentation and disease diagnosis where atlas assumptions are unreliable in abnormal brain images.

In line with institutions across the United States, the Computer Science Department at Swarthmore College has faced the challenge of maintaining a demographic composition of students that matches the student body as a whole. To combat this trend, our department has made a concerted effort to revamp our introductory course sequence to both attract and retain more women and minority students. The focus of this paper is the changes instituted in our Introduction to Computer Science course (i.e., CS1) intended for both majors and non-majors. In addition to changing the content of the course, we introduced a new student mentoring program that is managed by a full-time coordinator and consists of undergraduate students who have recently completed the course. This paper describes these efforts in detail, including the extension of these changes to our CS2 course and the associated costs required to maintain these efforts. We measure the impact of these changes by tracking student enrollment and performance over 13 academic years. We show that, unlike national trends, enrollment from underrepresented groups has increased dramatically over this time period. Additionally, we show that the student mentoring program has increased both performance and retention of students, particularly from underrepresented groups, at statistically significant levels.

A major bottleneck in high-throughput protein crystallography is producing protein-structure models from an electron-density map. In previous work, we developed Acmi, a probabilistic framework for sampling all-atom protein-structure models. Acmi uses a fully connected, pairwise Markov random field to model the 3D location of each non-hydrogen atom in a protein. Since exact inference in this model is intractable, Acmi uses loopy belief propagation (BP) to calculate marginal probability distributions. In cases of approximation, BP's message-passing protocol becomes a crucial design decision. Previously, Acmi took a naive, round-robin protocol to sequentially process messages. Others have proposed informed methods for message scheduling by ranking messages based on the amount of new information they contain. These information-theoretic measures, however, fail in the highly connected, large output space domain of protein-structure inference. In this work, we develop a framework for using domain knowledge as a criterion for prioritizing messages in BP. Specifically, we show that using predictions of protein-disorder regions effectively guides BP in our task. Our results show that guiding BP using protein-disorder prediction improves the accuracy of marginal probability distributions and also produces more accurate, complete protein-structure models.

An important problem in high-throughput protein crystallography is constructing a protein model from an electron-density map. Previous work by some of this paper's authors [1] describes an automated approach to this otherwise time-consuming process. An important step in the previous method requires searching the density map for many small template protein-fragments. This previous approach uses Fourier convolution to quickly match some rotation of the template to the entire density map. This paper proposes an alternate approach that makes use of the spherical-harmonic decomposition of the template and of some region in the density map. This new framework allows us to mask specific regions of the map, enabling a first-pass filter to eliminate a majority of the density map without requiring an expensive rotational search. We show our new template matching method improves accuracy and reduces running time, compared to our previous approach. Protein models constructed using this matching also show significant accuracy improvement.

Motivation: One bottleneck in high-throughput protein crystallography is interpreting an electron-density map, that is, fitting a molecular model to the 3D picture crystallography produces. Previously, we developed Acmi (Automatic Crystallographic Map Interpreter), an algorithm that uses a probabilistic model to infer an accurate protein backbone layout. Here, we use a sampling method known as particle filtering to produce a set of all-atom protein models. We use the output of Acmi to guide the particle filter's sampling, producing an accurate, physically feasible set of structures.Results: We test our algorithm on 10 poor-quality experimental density maps. We show that particle filtering produces accurate all-atom models, resulting in fewer chains, lower sidechain RMS error and reduced R factor, compared to simply placing the best-matching sidechains on Acmi's trace. We show that our approach produces a more accurate model than three leading methods—Textal, Resolve and ARP/WARP—in terms of main chain completeness, sidechain identification and crystallographic R factor.Availability: Source code and experimental density maps available at http://ftp.cs.wisc.edu/machine-learning/shavlik-group/programs/acmi/Contact: dimaio@cs.wisc.edu

An important problem in high-throughput protein crystallography is constructing a protein model from an electron-density map. DiMaio et al. (2006) describe an automated approach to this otherwise time-consuming process. One important step involves searching the density map for many small protein fragments, or templates. The previous approach uses Fourier convolution to quickly compare some rotation of the template to the entire density map. We propose to instead use the spherical-harmonic decomposition of the template and of some region in the density map. In this new framework, we are able to eliminate areas of the map from the search process if they are unlikely to match to any templates. We design several “first-pass filters” for this elimination task, including one filter which uses a set of rotation-invariant descriptors (derived from the spherical-harmonic decomposition) of a sphere of density to train an accurate classifier. We show our new template-matching method improves accuracy and reduces running time, compared to our previous approach. Protein models constructed using this matching also show significant accuracy improvement. We extend our method to produce a structural-homology detection algorithm that, due to its use of electron-density maps, is more sensitive than sequence-only methods.