Essays on Intitutional Governance

This thesis consists of three chapters on the choice of institutional governance. The first chapter provides empirical evidence on the effect of local norms on the contractual choice, using a comprehensive dataset on US agricultural leasing contracts. We focus on the choice between cash-rent and share-rent contracts and examine whether the prevalence of share-rent contracts has an effect on contractual choice. We use a generalized spatial two-stage least squares approach to address endogeneity issues. Our results show that there is a strong tendency for agents to choose the contractual form that conforms to local norms. Our study also suggests that share-rent contracts are more likely to be chosen when there is a higher likelihood or more severe consequence of opportunistic behavior by agents. This suggests that share contracts reduce transaction costs by helping to foster a productive governance atmosphere for the contracting parties. The second chapter explores whether the choice of institutions depends on the historical experience and the stock of knowledge of economic agents. We provide firm-level evidence on the choice of between legal and relational governance, in the context of the transition economy of Romania. Our results show that previously state-owned businesses are more likely to rely on legal governance than other firms. We also find evidence that the legal knowledge held by firm managers affects the choice of governance, which is consistent with the path-dependence theory of institutional development. The third chapter is based on a cross-country study of the link between public spending on health care, quality of institutional governance and child health outcomes. We show that both public spending on health care and the quality of governance matter for the reduction of child and infant mortality rates

PharmDock: A Pharmacophore-Based Docking Program

Background Protein-based pharmacophore models are enriched with the information of potential interactions between ligands and the protein target. We have shown in a previous study that protein-based pharmacophore models can be applied for ligand pose prediction and pose ranking. In this publication, we present a new pharmacophore-based docking program PharmDock that combines pose sampling and ranking based on optimized protein-based pharmacophore models with local optimization using an empirical scoring function. Results Tests of PharmDock on ligand pose prediction, binding affinity estimation, compound ranking and virtual screening yielded comparable or better performance to existing and widely used docking programs. The docking program comes with an easy-to-use GUI within PyMOL. Two features have been incorporated in the program suite that allow for user-defined guidance of the docking process based on previous experimental data. Docking with those features demonstrated superior performance compared to unbiased docking. Conclusion A protein pharmacophore-based docking program, PharmDock, has been made available with a PyMOL plugin. PharmDock and the PyMOL plugin are freely available fromhttp://people.pharmacy.purdue.edu/~mlill/software/pharmdock webcite

Industry convergence in rural tourism development: a China-featured term or a new initiative?

Industry convergence is a popular term that has been widely referenced in the context of rural tourism development in China. All levels of government (local, regional, national) in China have repeatedly addressed the significance of industry convergence in their tourism plans and related policies. Despite its popularity, limited studies at present have explored this concept in-depth. Using Huai’an as a case, this study applied a path analysis and reported the industry convergence process in a destination. The findings of this study can provide both theoretical and practical implications that are useful for tourism planners and policy makers

PL-PatchSurfer: A Novel Molecular Local Surface-Based Method for Exploring Protein-Ligand Interactions

Structure-based computational methods have been widely used in exploring protein-ligand interactions, including predicting the binding ligands of a given protein based on their structural complementarity. Compared to other protein and ligand representations, the advantages of a surface representation include reduced sensitivity to subtle changes in the pocket and ligand conformation and fast search speed. Here we developed a novel method named PL-PatchSurfer (Protein-Ligand PatchSurfer). PL-PatchSurfer represents the protein binding pocket and the ligand molecular surface as a combination of segmented surface patches. Each patch is characterized by its geometrical shape and the electrostatic potential, which are represented using the 3D Zernike descriptor (3DZD). We first tested PL-PatchSurfer on binding ligand prediction and found it outperformed the pocket-similarity based ligand prediction program. We then optimized the search algorithm of PL-PatchSurfer using the PDBbind dataset. Finally, we explored the utility of applying PL-PatchSurfer to a larger and more diverse dataset and showed that PL-PatchSurfer was able to provide a high early enrichment for most of the targets. To the best of our knowledge, PL-PatchSurfer is the first surface patch-based method that treats ligand complementarity at protein binding sites. We believe that using a surface patch approach to better understand protein-ligand interactions has the potential to significantly enhance the design of new ligands for a wide array of drug-targets

Analysis of factors affecting the effectiveness of oil spill clean-up: A bayesian entwork approach

Ship-related marine oil spills pose a significant threat to the environment, and while it may not be possible to prevent such incidents entirely, effective clean-up efforts can minimize their impact on the environment. The success of these clean-up efforts is influenced by various factors, including accident-related factors such as the type of accident, location, and environmental weather conditions, as well as emergency response-related factors such as available resources and response actions. To improve targeted and effective responses to oil spills resulting from ship accidents and enhance oil spill emergency response methods, it is essential to understand the factors that affect their effectiveness. In this study, a data-driven Bayesian network (TAN) analysis approach was used with data from the U.S. Coast Guard (USCG) to identify the key accident-related factors that impact oil spill clean-up performance. The analysis found that the amount of discharge, severity, and the location of the accident are the most critical factors affecting the clean-up ratio. These findings are significant for emergency management and planning oil spill clean-up efforts.Postprint (published version

Age- and time-of-day dependence of glymphatic function in the human brain measured via two diffusion MRI methods

Advanced age, accompanied by impaired glymphatic function, is a key risk factor for many neurodegenerative diseases. To study age-related differences in the human glymphatic system, we measured the influx and efflux activities of the glymphatic system via two non-invasive diffusion magnetic resonance imaging (MRI) methods, ultra-long echo time and low-b diffusion tensor imaging (DTIlow–b) measuring the subarachnoid space (SAS) flow along the middle cerebral artery and DTI analysis along the perivascular space (DTI-ALPS) along medullary veins in 22 healthy volunteers (aged 21–75 years). We first evaluated the circadian rhythm dependence of the glymphatic activity by repeating the MRI measurements at five time points from 8:00 to 23:00 and found no time-of-day dependence in the awake state under the current sensitivity of MRI measurements. Further test–retest analysis demonstrated high repeatability of both diffusion MRI measurements, suggesting their reliability. Additionally, the influx rate of the glymphatic system was significantly higher in participants aged >45 years than in participants aged 21–38, while the efflux rate was significantly lower in those aged >45 years. The mismatched influx and efflux activities in the glymphatic system might be due to age-related changes in arterial pulsation and aquaporin-4 polarization

A compendium of genetic regulatory effects across pig tissues

The Farm Animal Genotype-Tissue Expression (FarmGTEx) project has been established to develop a public resource of genetic regulatory variants in livestock, which is essential for linking genetic polymorphisms to variation in phenotypes, helping fundamental biological discovery and exploitation in animal breeding and human biomedicine. Here we show results from the pilot phase of PigGTEx by processing 5,457 RNA-sequencing and 1,602 whole-genome sequencing samples passing quality control from pigs. We build a pig genotype imputation panel and associate millions of genetic variants with five types of transcriptomic phenotypes in 34 tissues. We evaluate tissue specificity of regulatory effects and elucidate molecular mechanisms of their action using multi-omics data. Leveraging this resource, we decipher regulatory mechanisms underlying 207 pig complex phenotypes and demonstrate the similarity of pigs to humans in gene expression and the genetic regulation behind complex phenotypes, supporting the importance of pigs as a human biomedical model.</p

Functional annotation of the cattle genome through systematic discovery and characterization of chromatin states and butyrate-induced variations

The functional annotation of genomes, including chromatin accessibility and modifications, is important for understanding and effectively utilizing the increased amount of genome sequences reported. However, while such annotation has been well explored in a diverse set of tissues and cell types in human and model organisms, relatively little data are available for livestock genomes, hindering our understanding of complex trait variation, domestication, and adaptive evolution. Here, we present the first complete global landscape of regulatory elements in cattle and explore the dynamics of chromatin states in rumen epithelial cells induced by the rumen developmental regulator—butyrate.https://doi.org/10.1186/s12915-019-0687-

PL-PatchSurfer: A Novel Molecular Local Surface-Based Method for Exploring Protein-Ligand Interactions

Structure-based computational methods have been widely used in exploring protein-ligand interactions, including predicting the binding ligands of a given protein based on their structural complementarity. Compared to other protein and ligand representations, the advantages of a surface representation include reduced sensitivity to subtle changes in the pocket and ligand conformation and fast search speed. Here we developed a novel method named PL-PatchSurfer (Protein-Ligand PatchSurfer). PL-PatchSurfer represents the protein binding pocket and the ligand molecular surface as a combination of segmented surface patches. Each patch is characterized by its geometrical shape and the electrostatic potential, which are represented using the 3D Zernike descriptor (3DZD). We first tested PL-PatchSurfer on binding ligand prediction and found it outperformed the pocket-similarity based ligand prediction program. We then optimized the search algorithm of PL-PatchSurfer using the PDBbind dataset. Finally, we explored the utility of applying PL-PatchSurfer to a larger and more diverse dataset and showed that PL-PatchSurfer was able to provide a high early enrichment for most of the targets. To the best of our knowledge, PL-PatchSurfer is the first surface patch-based method that treats ligand complementarity at protein binding sites. We believe that using a surface patch approach to better understand protein-ligand interactions has the potential to significantly enhance the design of new ligands for a wide array of drug-targets