Using Persistent Homology for Topological Analysis of Protein Interaction Network of Candida Antarctica Lipase B Molecular Dynamic Simulation Model

In this work, we aim to examine the activity of one of the most efficient and commonly used lipases, Candida Antarctica Lipase B (CalB), from the perspective of multiple computational techniques. To this end, we first conduct a series of Molecular Dynam- ics Simulations on CalB in different conditions to analyze the conformational changes of the protein and probe its unusual high-temperature activity. Next, we build the protein interaction network of amino acids for CalB to study pairwise interactions between amino acids (nodes) and probe the protein in terms of statistical features of links’ distribution. Finally, we employ an algebraic topology-based method to study the protein interaction network from a broader perspective. The ”Persistent Homol- ogy (PH) method” is then presented as a way to exceed pairwise interactions and examine protein networks in terms of patterns of interaction between the nodes. Per- sistent Homology studies the evolution of the protein interaction network’s topologi- cal features (homology groups) in different states. Employing topological analysis, we compare the active form of CalB at high temperatures to its inactive states to account for possible topological contributions to the protein functionality. By discovering a prominent 1-dimensional hole in the active form of the protein, we highlight the role of higher-order interaction patterns in the network. Moreover, using the evolution of topological features, we study topological changes in protein networks and show the decline in the total number of 1-dimensional features as the protein loses activity and compactness over time. Accordingly, we propose that the protein’s general conforma- tional changes and three-dimensional structure are not the only facets contributing to its active state. Instead, we suggest examining the topology of the protein inter- action network, referred to as different dimensional holes of the networks, as a higher dimensional analysis should be used to account for protein functionality. Hence, in this work, we desire to present that one needs to consider topological features acting as patterns of interaction between the components to study, examine or predict the folding of polypeptide chains into active structures

Assessment of Policies and Programs That Apply Adverse Childhood Experiences (ACE) Study Research

Introduction: Adverse Childhood Experiences (ACE) are common among the population. Based on the reported data and studies, the prevalence of ACEs related health issues is significantly high throughout the U.S. While policies and programs exist to address ACEs, more information is needed to understand the number of states that have legislation and the specific initiatives that fall under the legislation. Method: To preliminarily answer this question, several online search engines were utilized: Google, PubMed, ACEs Connection Website, ACE Too High, CDC Website, state health department website, and ASTHO. From these sources, documented state legislations on ACEs were identified using the search terms policies, programs, state legislation, ACEs, toxic stress, childhood trauma, and childhood adversity. Information was organized within Excel Spreadsheets by sector, initiative, for each state. Result: Based on the CDC website, only 12 states and the District of Columbia utilized the Optional ACE module from 2009 to 2012. Throughout the US, only half of the states have ACE-related legislations within four main sectors identified as education, healthcare, child welfare and juvenile justice. The information on Puerto Rico and U.S. territories for ACEs legislation was not evident. Among the 24 states that have legislation to address ACEs, California and Vermont have 7 specific initiatives, Washington state has 6, Massachusetts has 5, and Oregon and Tennessee have 4. House and Senate Bills were identified for four states including Massachusetts, Tennessee, Virginia, and Washington state. Most legislation are associated with child welfare and education sectors. Juvenile justice sector had the greatest gaps. Conclusion: From the present assessment it appears that there is a lack of data on the prevalence of ACEs among adults across states. Furthermore, most of the initiatives around ACEs are focused on child welfare and education sectors. However, to have a strong impact on ACEs prevention, legislation should exist that cover multiple sectors. The role of monitoring the population through data collection is needed to inform policies set for the prevention and treatment of ACEs

Banking instability: causes and remedies

This thesis was submitted for the award of Doctor of Philosophy and was awarded by Brunel University LondonThe recent U.S. subprime mortgage crisis rapidly spread throughout the world and put the global financial system under extraordinary pressure. The main implication of the recent crisis is that complex banking regulations failed to adequately identify and limit riskiness of banking systems at both domestic and international levels. In spite of a large empirical literature on the causes and remedies of the recent crisis, there remains substantial uncertainty on (i) how risk measuring models performed during crisis, (ii) how systematic factors such as house prices affected the financial system, and (iii) how effectively government policy responses resolved the financial crisis. This thesis seeks to narrow this gap in the literature by offering three empirical essays. The first essay investigates the performance of alternative parametric VaR models in forecasting riskiness of international equity portfolios. Notably, alternative univariate VaR models are compared to multivariate conditional volatility models with special focus given to conditional correlation models. Conditional correlation models include the constant conditional correlation (CCC), dynamic conditional correlation (DCC), and asymmetric DCC (ADCC) models. Various criteria are then applied for backtesting VaR models and to evaluate their one-day-ahead forecasting ability in a wide range of countries and during different global financial conditions. It is found that most VaR models have satisfactory performance with small number of violations during pre-crisis period. However, the number of violations, mean deviation of violations, and maximum deviation of violations dramatically increase during crisis period. Furthermore, portfolio models incur lower number of violations compared to univariate models while DCC and ADCC models perform better than CCC models during crisis period. From risk management perspective, most single index models fail to pass Basel criteria for internal VaR models during crisis period, whereas empirical evidence on the choice between CCC, DCC, and ADCC models is mixed. The recent crisis also raised serious concerns about factors that can systematically destabilise the whole banking system. In particular, the collapse of house prices in the United States triggered the recent subprime mortgage crisis, which was associated with a sharp increase in the number of nonperforming loans and bank failures. This in turn demonstrates the key role that house prices play in systematically undermining the whole banking system. The second essay investigates the determinants of nonperforming loans (NPL) with a special focus on house price fluctuations as a key systematic factor. Using a panel of U.S. banking institutions from 1999 to 2012, the analysis is carried out across different loan categories, different types of banks, and different bank size. It is found that house price fluctuations have a significant impact on the evolution of nonperforming loans, while the magnitude of their impact varies across loan categories, institution types, and between large and small banks. Also, the impact of house price fluctuations on nonperforming loans is more pronounced during crisis period. The last essay of this thesis investigates the effectiveness of the U.S. government strategy to combat the crisis. As a comprehensive response to the recent financial crisis, the US government created the Troubled Asset Relief Program (TARP). The Capital Purchase Program (CPP) was launched as an initial program under the TARP. The CPP was designed to purchase preferred stocks or equity warrants from viable financial institutions. Using a large panel of the U.S. commercial banks over the period 2007Q1 to 2012Q4, survival analysis is used to investigate the impact of TARP funds on the likelihood of survival in the recipient banks. It is found that larger recipient banks are more likely to avoid regulatory closure, while receiving capital assistance does not effectively help banks to avoid technical failure. This implies that governmental capital assistance serves larger banks much better than their smaller counterparts. In addition, TARP recipients are more likely to be acquired, regardless of their size and financial health. In summary, the empirical findings reveal that capital infusions do not enhance the survival likelihood of the recipient banking institutions

Effect of carboxymethyl cellulose-based coatings incorporated with Zataria multiflora Boiss. essential oil and grape seed extract on the shelf life of rainbow trout fillets

To prolong the shelf life of seafood products, lipid oxidation and growth of microorganisms should be retarded. The objective of the current study was evaluating the potential application of carboxymethyl cellulose (CMC) coatings incorporated with Zataria multiflora Boiss. essential oil (ZMEO) and grape seed extract (GSE) on chemical (thiobarbituric acid reactive substances (TBARS) and total volatile basic nitrogen (TVB-N)), microbial (total viable count, lactic acid bacteria and Pseudomonas spp.) and organoleptic attributes of rainbow trout fillets during refrigerated storage for twenty days. GCeMS analysis showed that ZMEO is rich in monoterpene phenols such as thymol and carvacrol. The following results were obtained after 20 days of storage: The minimum level of TVB-N was measured in the fillets coated with CMC + 2 v/v ZMEO + 0.5 v/v GSE. The minimum number of total viable bacteria, lactic acid bacteria and Pseudomonas spp. were determined in the fillets coated with CMC + 2 v/v ZMEO + 1 v/v GSE. The fillets coated with CMC + 1 v/v ZMEO + 1 v/v GSE showed the best organoleptic properties. Our results revealed that CMC-based coatings incorporated with ZMEO and GSE could improve chemical, microbial and sensorial characteristics of rainbow trout fillets during cold storage. © 2015 Elsevier Ltd

Change agents’ orientations to change

This study explores five field education officers’ (FEOs) understanding of their dual roles as educational reformers and community developers in the rural, mountainous district of Chitral, Pakistan. In particular, it examines their specific actions and methods (strategies) and their underlying assumptions and core values (orientations) of change. These FEOs work as change agents in schools and in the local communities where schools have been established by the Aga Khan Education Service, Pakistan (AKES,P). The study’s findings derive from empirical data collected through qualitative research methods, such as semi-structured interviews (individual and focus-group), non-participant observations, post-observation discussions, informal conversations and analysis of relevant documents. The findings capture three realms of the FEOs’ world: a) The FEOs’ role as external change agents; (b) their daily practices of change, and (c) their conceptual underpinnings of change. In the first realm, the study finds that the FEOs play a unique role, that of educational reformer and community developer, stimulating change in both schools and in local communities. These FEOs are authorized by AKESP’s district management; therefore, it is mandatory for AKESP schools and schools’ communities to accept their interventions. In the second realm, analysis of the FEOs’ specific actions and key methods for change reveals four distinct strategies the FEOs adopt for school change —Teacher-Centred, Moral Persuasion, Pragmatic, and Leadership— and three main strategies for community development —Participatory, Training, and Power-Laden. All seven strategies illuminate the FEOs’ understanding of change at the level of practice. In the third realm, this study explores the FEOs’ underlying assumptions, core values, and key concepts of change; it reconstructs three broad change orientations —Political, Technical, and Spiritual— into which each FEO’s theoretical understandings and conceptual frameworks of change are categorized. Examining the interrelatedness of the FEOs’ roles, strategies, and change orientations reveals that each FEO’s change orientation serves as a lens through which that FEO views and approaches change, defines his role, and shapes his strategies for change. Despite their distinct orientations, unique role, and particular strategies, all five FEOs operate within a common broader framework of socioeducational change or more, specifically, community-based school change

Role of civil society institutions in promoting diversity and pluralism in Chitral District of Khyber Pakhtunkhwa, Pakistan

Pakistan is a country with a fast growing population of nearly 190 million people divided into a large number of ethnic, cultural, linguistic, political and religious groups. The basic ideology behind the creation of Pakistan was Islam and it was considered to be the unique force which could bind together the religiously, ethnically, linguistically, and culturally diverse society. An overwhelming majority of Pakistan’s population is Muslim with Sunni and Shia as the two major schools of thoughts but there are many other smaller sects within Muslim and non-Muslim population. Ethnically, Pakistani society is divided into major groups such as Punjabis, Sindhis, Pukhtuns, Balochis, Saraikis, Kashmiris, Hazaad, Shina and Baltis, and Chitralis etc. with numerous smaller ethnic groups

Improving Breastfeeding in New American Communities of Burlington, VT

Community Health Centers of Burlington (CHCB), a Federally Qualified Health Center (FQHC), provides healthcare services including social work and financial assistance to these New American communities. The flagship site, Riverside, provides a specialized OB clinic where many of these community women obtain prenatal and postnatal care. Continuing to understand the barriers these communities and families face in providing the recommended healthcare to their newborns allows mission-driven CHCB to most effectively communicate, support, and effectively direct resources to these barriers. Barriers and challenges to breastfeeding were identified during this rotation through confidential interactions with patients, shared with the staff and providers at CHCB.https://scholarworks.uvm.edu/fmclerk/1451/thumbnail.jp