How to retrieve the normal modes using the POD

International audienceProper orthogonal decomposition (POD) is an increasingly popular way to analyze data, and to obtain either a low- dimensional approximated description of a high-dimensional process, or useful information for damage assessment. In the case of a dynamic system with n degrees of freedom, the purpose of POD is to retrieve the modal properties from the measured response. Until now, POD has been used for systems with a diagonal mass matrix. The aim of this presentation is double: first, to demonstrate that POD can also be used for a non-diagonal symmetric mass matrix; and second, to present sufficient conditions on the response sampling, in order to retrieve the modal characteristics with a prescribed accuracy. The conditions to obtain this approximation with a given accuracy are first explicitly given for the case without damping. Then the case of proportional damping is addressed and similar conditions are shown. The critical case of two modal frequencies close together is also studied, given that it requires particular conditions. The obtained conditions show that the expected accuracy is explicitly limited by the damping ratio. Some numerical tests illustrate the accuracy evolution of the approximated normal modes obtained by this method, with respect to the variation of the observation time and the damping ratio. This careful analysis can be useful for finding the cause of poor approximation properties in more complex cases, such as analysis of variation in nonlinear normal modes

Developing a Single-Cycle Infectious System to Study an ERV-K Retroviral Envelope

Thesis advisor: Welkin JohnsonEndogenous Retroviruses (ERVs) are “fossilized” retroviruses of a once exogenous retrovirus located in the genome of extant vertebrates. Retroviral infection results in a provirus integration into the host genome. An infection of a germline cell could lead to the provirus potentially being inherited by the offspring of the infected individual. Once in the genome, the provirus becomes subject to evolutionary processes and can become either lost or fixed in a population, remaining as “fossils” long after the exogenous retrovirus has gone extinct23. Notably, 8% of the human genome consists of ERVs30. Human Endogenous Retrovirus Type K (HERV-K)(HML-2) family is of particular interest. HERV-K integrations are as old as 30-35 million years, endogenizing before the separation of humans and Old World Monkeys. However, there are human specific insertions, some as young as 150,000 – 250,000 years, making them the youngest insertion in the human genome. There are over 90 insertions in the human genome; the bulk is shared by all humans44,47. Transcripts of HERV-K genes are upregulated in multiple cancer and tumor cell lines 14,39,46, as well as in HIV-1 infected patients 7,11,29. Just as there are human specific insertions of ERV-K, there are also Old World Monkey specific insertions44. I have identified an intact endogenous retroviral envelope open reading frame on chromosome 12 of the rhesus macaque genome. This viral envelope-encoding sequence, which I refer to as rhERV-K env, retains all the canonical features of a retroviral Env protein. An alignment between rhERV-K env and a consensus sequence of HERV-K, HERV-Kcon env, shows a 70% amino acid sequence identity. For experimental purposes, reconstructed HERV-K envelopes have been incorporated into virions of Human Immunodeficiency virus (HIV-1)19,26,49, Murine Leukemia Virus (MLV)12, and Vesicular stomatitis Virus (VSV)26,41,49. While these approaches have illuminated some aspects of HERV-K Env-mediated entry, to date a cell-surface receptor has not been identified for any ERV-K Env. This could be due to its low infectivity levels12,26,49, its seemingly broad cell tropism limiting identification of null cell lines26,49, or possibly the HERV-K consensus reconstructions are not an accurate representation of the progenitor HERV-K virus. I am interested in understanding how the ERV-K retrovirus accessed the human germline (some 150,000 – 250,000 years ago). To do this, I focused specifically on the envelope proteins of HERV-K and rhERV-K, with the goal of analyzing the ERV-K entry process. The identification and inclusion of rhERV-K Env in this study is meant to circumvent the possibility that the previously described consensus reconstructions of human HERV-K Env are not representative, and may also provide a means to compare the endogenization process in the human/ape and old-world monkey lineages. I focused on developing two systems for single-cycle infection, one based on Mason-Pfizer Monkey Virus (MPMV) (which has not been done before), and a second based on MLV, which has previously been reported on. MPMV, like HERV-K, is a betaretrovirus, and I reasoned that possibly using a betaretrovirus would overcome some of the low-infectivity issues associated with prior attempts using HIV and MLV. To develop a system for examining function of the ERV-K Env proteins, I addressed 3 issues: 1. Are the HERV-K Env and rhERV-K Env proteins expressed and properly processed? 2. Can they be incorporated into virions of a heterologous virus? 3. Are ERV-K pseudotyped virions infectious? I have answered these questions in the following thesis.Thesis (MS) — Boston College, 2017.Submitted to: Boston College. Graduate School of Arts and Sciences.Discipline: Biology

Optimizing TILLING and Ecotilling techniques for potato (Solanum tuberosum L)

<p>Abstract</p> <p>Background</p> <p>The TILLING and Ecotilling techniques for the discovery of nucleotide polymorphisms were applied to three potato (<it>Solanum tuberosum</it>) cultivars treated with gamma irradiation. The three mutant cultivars tested were previously shown to exhibit salinity tolerance, an important trait in countries like Syria where increasing soil salinity is affecting agricultural production.</p> <p>Findings</p> <p>Three gene-specific primer pairs were designed from BAC sequence to amplify ~1 to 1.5 kb of gene target. One of the three primer pairs amplified a single gene target. We used this primer pair to optimize enzymatic mismatch cleavage and fluorescence DNA detection for polymorphism discovery. We identified 15 putative nucleotide polymorphisms per kilobase. Nine discovered polymorphisms were unique to one of the three tetraploid cultivars tested.</p> <p>Conclusion</p> <p>This work shows the utility of enzymatic mismatch cleavage for TILLING and Ecotilling in different varieties of potato. The method allows for rapid germplasm characterization without the cost and high informatics load of DNA sequencing. It is also suitable for mutation discovery in high-throughput reverse genetic screens.</p

Improving Transgender Policy for a More Equitable Workplace

Sex and gender categories have become more fluid in recent years. With evolving understandings of sexual orientation and gender identity, public administrators are confronted with questions of how to craft policy and make decisions based on new conceptions of sex and gender for transgender employees. Policy and practice is especially challenging in the workplace where sex and gender encompass both personal and professional dimensions. Within the public sector, the federal government is recognized as a leader on these issues, and this work examines federal transgender policy to answer the following questions: 1) how are federal agencies addressing transgender issues in the workplace through formal policy? and 2) what can be done to improve future transgender policy? To gain a better understanding of what constitutes an effective transgender workplace policy, we conducted a qualitative content analysis of nine transgender plans from the following federal agencies: Consumer Financial Protection Bureau, Equal Employment Opportunity Commission, Internal Revenue Service, National Aeronautics and Space Administration, United States Office of Special Counsel, United States Department of Interior, United States Department of Labor, United States Environmental Protection Agency, and United States Office of Personnel Management. Our analysis includes the identification of major themes within the nine policy documents. From this analysis, we propose best practices and future policy directions, as well as suggest ways of expanding the limited scholarship on transgender issues in the public sector

Determination of Uranium Concentration in Sheep Organs for Some Iraqi&#1765;s Cities

The aim of this research is to determine the uranium concentration and its distribution in many sheep organs that live in different region of Iraq. The uranium concentration in tissue samples is measured by using fission tracks registration in CR-39 detector that caused by the bombardment of U235 with thermal neutrons from (241Am-Be) neutron source of thermal flux (5x 103 n.cm-2. s-1). The results show that the maximum uranium concentration in bronchiole tissues of the animals was found in Karbala city (3.706ppm) while the minimum concentration (0.127 ppm) was found in Al-Faluja city, also the same result in lung tissue the maximum value was found in Karbala city (2.313ppm) and the minimum concentration in Al Fluja (0.082). Otherwise, the maximum concentration in liver tissue was found in AdDiwaniyah city (1.156ppm) while the minimum concentration in Al Fluja city (0.153ppm). The uranium concentrations in heart tissues were found various than the previous results. The results of average uranium concentration in each animal were ranged from 0.149 to 1.675 ppm, the maximum values were found in the cities in south region of Iraq

Experience with Renal Autotransplantation: Typical and Atypical Indications

Introduction and Objectives. Renal autotransplantation is a kidney-saving surgical procedure used in selected patients. The purpose of this report is to review nine typical and atypical indications for kidney autotransplantation and evaluate its effectiveness in maintaining kidney function and avoiding cancer recurrence. Materials and Methods. From 1999 till 2014, nine renal autotransplantations were performed in our center. A retrospective case review was done. Four of nine patients had a solitary functioning kidney. Typical indications for autotransplantation included extended ureteric disease in 5 patients, intrasinusal tumor on a solitary kidney in 1 patient, and renal artery aneurysm in 1 patient. Atypical indications consisted in bilateral urothelial tumors in 1 patient and interrupted live kidney transplantation in 1 patient. Mean cold ischemia time was 209 minutes. Demographic factors, indications, renal function before and after surgery, and in the long term, cancer recurrence and disease-free survival were evaluated. Results. Renal function was maintained in 8 patients during the early follow-up. No serious complications occurred in the postoperative period. Median duration of follow-up was 50 months. In 4 patients with a normal contralateral kidney, mean preoperative and at discharge creatinine clearance were 105.45 ml/min and 121.02 ml/min, respectively. Although values showed an improvement in the kidney function, the difference was not significant (p value 0.3). In the other 4 patients with a solitary kidney, mean discharge creatinine clearance was 99.24 ml/min surprisingly higher than the preoperative value 96.92 ml/min. At the last follow-up, kidney function was preserved for the two groups (normal contralateral kidney/solitary kidney) with relatively stable creatinine clearance values: 108.45 ml/min and 85.9 ml/min, respectively. No patients required secondary dialysis. Conclusion. Renal autotransplantation is a rare, safe, and effective surgical procedure for the treatment of complex urologic conditions. In some instances, it may be of great utility for kidney salvage in some carefully selected patients

Natural Language Processing in Electronic Health Records in Relation to Healthcare Decision-making: A Systematic Review

Background: Natural Language Processing (NLP) is widely used to extract clinical insights from Electronic Health Records (EHRs). However, the lack of annotated data, automated tools, and other challenges hinder the full utilisation of NLP for EHRs. Various Machine Learning (ML), Deep Learning (DL) and NLP techniques are studied and compared to understand the limitations and opportunities in this space comprehensively. Methodology: After screening 261 articles from 11 databases, we included 127 papers for full-text review covering seven categories of articles: 1) medical note classification, 2) clinical entity recognition, 3) text summarisation, 4) deep learning (DL) and transfer learning architecture, 5) information extraction, 6) Medical language translation and 7) other NLP applications. This study follows the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. Result and Discussion: EHR was the most commonly used data type among the selected articles, and the datasets were primarily unstructured. Various ML and DL methods were used, with prediction or classification being the most common application of ML or DL. The most common use cases were: the International Classification of Diseases, Ninth Revision (ICD-9) classification, clinical note analysis, and named entity recognition (NER) for clinical descriptions and research on psychiatric disorders. Conclusion: We find that the adopted ML models were not adequately assessed. In addition, the data imbalance problem is quite important, yet we must find techniques to address this underlining problem. Future studies should address key limitations in studies, primarily identifying Lupus Nephritis, Suicide Attempts, perinatal self-harmed and ICD-9 classification

Improving Transgender Policy for a More Equitable Workplace

Sex and gender categories have become more fluid in recent years. With evolving understandings of sexual orientation and gender identity, public administrators are confronted with questions of how to craft policy and make decisions based on new conceptions of sex and gender for transgender employees. Policy and practice is especially challenging in the workplace where sex and gender encompass both personal and professional dimensions. Within the public sector, the federal government is recognized as a leader on these issues, and this work examines federal transgender policy to answer the following questions: 1) how are federal agencies addressing transgender issues in the workplace through formal policy? and 2) what can be done to improve future transgender policy? To gain a better understanding of what constitutes an effective transgender workplace policy, we conducted a qualitative content analysis of nine transgender plans from the following federal agencies: Consumer Financial Protection Bureau, Equal Employment Opportunity Commission, Internal Revenue Service, National Aeronautics and Space Administration, United States Office of Special Counsel, United States Department of Interior, United States Department of Labor, United States Environmental Protection Agency, and United States Office of Personnel Management. Our analysis includes the identification of major themes within the nine policy documents. From this analysis, we propose best practices and future policy directions, as well as suggest ways of expanding the limited scholarship on transgender issues in the public sector