Epitope profiling via mixture modeling of ranked data

We propose the use of probability models for ranked data as a useful alternative to a quantitative data analysis to investigate the outcome of bioassay experiments, when the preliminary choice of an appropriate normalization method for the raw numerical responses is difficult or subject to criticism. We review standard distance-based and multistage ranking models and in this last context we propose an original generalization of the Plackett-Luce model to account for the order of the ranking elicitation process. The usefulness of the novel model is illustrated with its maximum likelihood estimation for a real data set. Specifically, we address the heterogeneous nature of experimental units via model-based clustering and detail the necessary steps for a successful likelihood maximization through a hybrid version of the Expectation-Maximization algorithm. The performance of the mixture model using the new distribution as mixture components is compared with those relative to alternative mixture models for random rankings. A discussion on the interpretation of the identified clusters and a comparison with more standard quantitative approaches are finally provided.Comment: (revised to properly include references

Hierarchical orbital decompositions and extended decomposable distributions

Elliptically contoured distributions can be considered to be the distributions for which the contours of the density functions are proportional ellipsoids. Kamiya, Takemura and Kuriki (2006) generalized the elliptically contoured distributions to star-shaped distributions, for which the contours are allowed to be arbitrary proportional star-shaped sets. This was achieved by considering the so-called orbital decomposition of the sample space in the general framework of group invariance. In the present paper, we extend their results by conducting the orbital decompositions in steps and obtaining a further, hierarchical decomposition of the sample space. This allows us to construct probability models and distributions with further independence structures. The general results are applied to the star-shaped distributions with a certain symmetric structure, the distributions related to the two-sample Wishart problem and the distributions of preference rankings

ASPECT: A Survey to Assess Student Perspective of Engagement in an Active-Learning Classroom

This paper describes the development and validation of a survey to measure students? self-reported engagement during a wide variety of in-class active-learning exercises. The survey provides researchers and instructors alike with a tool to rapidly evaluate different active-learning strategies from the perspective of the learner

Similarity-based virtual screening using 2D fingerprints

This paper summarises recent work at the University of Sheffield on virtual screening methods that use 2D fingerprint measures of structural similarity. A detailed comparison of a large number of similarity coefficients demonstrates that the well-known Tanimoto coefficient remains the method of choice for the computation of fingerprint-based similarity, despite possessing some inherent biases related to the sizes of the molecules that are being sought. Group fusion involves combining the results of similarity searches based on multiple reference structures and a single similarity measure. We demonstrate the effectiveness of this approach to screening, and also describe an approximate form of group fusion, turbo similarity searching, that can be used when just a single reference structure is available

2020-06-19/20/21 DAILY UNM GLOBAL HEALTH COVID-19 BRIEFING

Executive Summary: NM Highlights: Dr. Scrase on-line briefing. NM cases. Campgrounds closed through July 4th. Otero prison reports. Navajo nation’s first police dies. Santa Fe cancels 4th July fireworks. Face coverings donated. NM infection rate drops. US Highlights: AZ Governor issues Exec Order. Economics, Workforce, Supply Chain, PPE: Epidemiology Highlights: Reopening hospitals metric. Comparison of mask effectiveness. Private practices suffer. Healthcare Policy Recommendations: Maternal mortality. Practice Guidelines: Recommendations on hepatobiliary surgery and neonate management. Drugs, Vaccines, Therapies, Clinical Trials: Animal studies generate new vaccine candidates and vaccine platform. 16 new clinical trials registered. Other Science: Respiratory secretions detected by trained dogs. MRI findings show brain lesions in non-survivors. Healthy blood vessels may protect children. Meta-analysis on pneumonia severity. Smoking and COVID-19 severity meta-analysis

Probabilistic approaches for modeling text structure and their application to text-to-text generation

Since the early days of generation research, it has been acknowledged that modeling the global structure of a document is crucial for producing coherent, readable output. However, traditional knowledge-intensive approaches have been of limited utility in addressing this problem since they cannot be effectively scaled to operate in domain-independent, large-scale applications. Due to this difficulty, existing text-to-text generation systems rarely rely on such structural information when producing an output text. Consequently, texts generated by these methods do not match the quality of those written by humans – they are often fraught with severe coherence violations and disfluencies. In this chapter, I will present probabilistic models of document structure that can be effectively learned from raw document collections. This feature distinguishes these new models from traditional knowledge intensive approaches used in symbolic concept-to-text generation. Our results demonstrate that these probabilistic models can be directly applied to content organization, and suggest that these models can prove useful in an even broader range of text-to-text applications than we have considered here.National Science Foundation (U.S.) (CAREER grant IIS- 0448168)Microsoft Research. New Faculty Fellowshi

2020-06-15/16 DAILY UNM GLOBAL HEALTH COVID-19 BRIEFING

Executive Summary: NM Highlights: NM case updates. Tribal outreach campaign. Santa Fe firefighters support first responders. US Highlights: COVID-19 hospitalizations rise in Texas. US retail sales up in May. Projected COVID-19 deaths in US. International Highlights: COVID-19 prevention and control in Africa. COVID-19 response and challenge in Africa. Epidemiology Highlights: Herd immunity in Europe. Social distance measures effects. Modeling infections in India. Fecal analysis. Wastewater-based Epidemiology Consortium. Healthcare Policy Recommendations: Public health approach to lockdown debate. All of Us Program adds new COVID-19 initiatives. Practice Guidelines: Guidelines are reviewed on urology care. IBD endoscopy. Convalescent plasma use. Testing: Patient predictors of risk for positive COVID-19 test are reported and an online risk calculator is now available. Drugs, Vaccines, Therapies, Clinical Trials: Steroid dexamethasone reduces 28-day mortality by 1/3. Research links ‘inflamm-aging’ and cytokine storm in elderly. Cancer drug may reduce severe COVID-19. 48 new trials registered. Other Science: Postpone surgery. Proteins predict outcomes. Neurologic manifestations. Thromboembolic risk. Zoonotic transmission. Liver failure. Cardiac complications

2020-06-03/04 DAILY UNM GLOBAL HEALTH COVID-19 BRIEFING

Executive Summary: NM Highlights: Navajo Nation to end weekend curfew. NM case count. Navajo Nation case updates. Food distribution by PepsiCo. APS to get funding. US Highlights: 5 vaccine candidates. Arizona’s increased cases. Some states postpone primaries. Pork plant infections. Economics, Workforce, Supply Chain, PPE: Impact on global supply chains. Residency selection process disrupted. Facemask filtration efficiency. Resources for underserved countries. Epidemiology Highlights: Morbidity and mortality in Africa. Healthcare Policy Recommendations: Need for social distancing. Psychological support guide. Return to work guidelines. Practice Guidelines: Anesthesia recommendations for ECT. Extracorporeal membrane oxygenation outcomes. Testing: Roche Elecsys IL-6 test is authorized by FDA to identify severe inflammatory response. Drugs, Vaccines, Therapies, Clinical Trials: HCQ RCT does not show disease prevention. Lancet HCQ study retraction. Adjunctive convalescent plasma did not show clinical improvement. Mixed remdesivir results. Virtual drug screening. Heparin improved survival. Moderna phase 3. Skin science for vaccine development. ECMO therapy. 48 new clinical trials. Other Science: Androgens and poor male outcomes. Trust in science enhances prevention compliance. High VTE prevalence in critically ill

2020-06-29/30 DAILY UNM GLOBAL HEALTH COVID-19 BRIEFING

Executive Summary: NM Highlights: NM cases update. ABQ nursing home hit hard. UNM student family housing closure. White Sands National Park reopening. 52% of federal COVID-19 relief money for tribal communities. Bill signed to help NM taxpayers. US Highlights: Polarization of political elite response on Twitter. International Highlights: China’s military to use Ad5-nCoV vaccine in trials. Economics, Workforce, Supply Chain, PPE: Decontaminate N95 respirators using a microwave. Epidemiology Highlights: Mask-wearing prevents transmission. Face-masks associated with Italy’s declining epidemic. Healthcare Policy Recommendations: Social distancing reassessed? Lessons learned from previous pandemics. Digital tools against COVID-19. Investigating cultural and psychological factors to reduce spread. Practice Guidelines: Preserving couple relationships during COVID-19. Testing: No difference in viral load between symptomatic and asymptomatic individuals. A new fast point-of-care virus detection test. Few patient serum samples have virus RNA (at low viral load) and these are not associated with infectious disease. Symptoms and temperature reports are informative to screen health care workers. Drugs, Vaccines, Therapies, Clinical Trials: 37 new trials registered June 29-30. Other Science: Multisystem pediatric inflammatory syndrome. Hazardous postoperative outcomes. Childhood immunization in Africa. Citizen science and protein folding