Miracle-dz/UniFAR-FTUs huggingface dataset:
Factors causing a higher level of liver abscesses in organic compared with conventional dairy herds

A data analysis based on the Danish Cattle Data Base shows that organic Holstein-Friesian cows have significantly higher frequencies of liver abscesses (LA) than conventional Holstein-Friesian cows (8% versus 5%). Based on a questionnaire among 91 organic dairy herds, a statistical analysis was made in order to identify which feeding and management factors that were related to the level of LA in the herds. Compared with conventional herds, the feed ration in organic herds had a lower energy and fatty acid level and a higher starch level. During summer season the organic herds had a lower level of digestible cell walls in the ration. Organic herds with a higher grazing level had a higher level of LA (P=0.012). Increasing levels of grain also tended to increase the level of LA. A herd-based analysis (644 herds) showed that lower minimum fat percentage and a higher variation in both fat and protein percentage corresponded with higher levels of LA. Organic herds generally had a 0.1 unit lower fat percentage. The results indicate that organic dairy cows, compared with conventional dairy cows, are more exposed to rumen acidosis and liver abscesses due to higher starch levels and unbalanced feeding strategies in particular during grazing.
Molecular analysis of candidate probiotic effector molecules of Lactobacillus plantarum

Probiotics are health-promoting microorganisms that exert their beneficial effects in several ways. While it is known that probiotic bacteria interact with cells of the host gastrointestinal tractand modulate cell-signaling responses by which they might promote health, the underlying molecular mechanism and probiotic “effector” molecules that are responsible for these effects remain largely unexplored. In this thesis, effector molecules of the lactic acid bacterium Lactobacillus plantarum were discovered that interact with diverse host cell types and manipulate cell-associated signaling pathways. This work represents crucial steps to better understand the exact mode of probiotic action, which is a prerequisite for their controlled, safe, purpose-directed, and person-specific applications in the context of health improvement and disease prevention.
CEO Health and Corporate Governance

Boards hire and fire CEOs based on imperfect information. Using comprehensive data on 28 cohorts in Sweden, we analyze the role of a potentially important attribute—CEO health—in corporate governance. Boards hire CEOs who are healthier than other high-skill professionals, in particular in mental health. After hiring, CEOs’ health develops similarly to a control group of executives. Health predicts turnover, measured at appointment and during tenure. These results are consistent with boards appointing CEOs with health robust enough to withstand the pressures of the job, correcting mismatches occurring at the time of appointment, and responding expediently to health shocks.
Combined 3D-QSAR Modeling and Molecular Docking Study on metronidazole-triazole-styryl hybrids as antiamoebic activity

A series of twenty-two metronidazole-triazole-styryl hybrids as antiamoebic agents were studied based on the combination of 3D-QSAR and surflex-docking. The CoMFA and CoMSIA models were carried out using eighteen compounds in the training set and four compounds in the test set gives Q 2 values of 0.684 and 0.664 respectively, and R 2 values of 0.882 and 0.894 respectively. The adapted alignment method with the suitable parameters resulted in reliable models. Based on contour maps produced by the CoMFA and CoMSIA, we suggested new compounds with high predicted activities, Surflex-docking revealed the important interactions between the ligand and receptor. Therefore, it confirmed the stability of predicted molecules in the receptor with PDB: 4CCQ.
Spatial Pattern and Effects of Urban Coordinated Development in China’s Urbanization

Regional urbanization in China has made formidable progress in, among other things, economic growth and urban sprawl, but local development is undergoing severe stress with irreversible impacts for urban ecological environment. Furthermore, spatial interactions are proved to be related to urban coordinated development. However, this spatial effect cannot usually be found in the literature. Based on the concept of coordinated development, the interaction among the economic, social and ecological systems of cities at prefecture level and above in China can be modeled by a coupling coordination model, and then analyzed using spatial analysis methods and spatial econometrics models, which can explain the patterns in spatial variation and its evolutionary trends. The results show that urban coordinated development has an apparent spatial heterogeneity, and East China develops better than West China. Moreover, urban coordinated development has an increasing global trend, which mainly results from East China, while the other regions cannot provide a definite boost. Lastly, there is an evident spatial dependence in urban coordinated development, which is positively influenced by an area’s own previous condition and its neighboring cities. Furthermore, population size, local GDP and green land, etc. have spatial spillover effects on urban coordinated development in China.
Noncentrosymmetric Orthophosphate YM3(PO4)3 (M = Sr, Ba) Crystals: Single Crystal Growth, Structure, and Properties

Two noncentrosymmetric orthophosphate crystals, YSr3(PO4)3 and YBa3(PO4)3, with melting points over 1800 oC have been grown by using the Czochralski technique. The YSr3(PO4)3 and YBa3(PO4)3 crystal.
Implementation of WRF-Hydro at two drainage basins in the region of Attica, Greece

Abstract. An integrated modeling approach for simulating flood events is presented in the current study. An advanced flood forecasting model, which is based on the coupling of hydrological and atmospheric components, was used for a twofold objective: first to investigate the potential of a coupled hydrometeorological model to be used for flood forecasting at two drainage basins in the area of Attica (Greece) and second to investigate the influence of the use of the coupled hydrometeorological model on the improvement of the precipitation forecast skill. For this reason, we used precipitation and hydrometric in-situ data for 7 events at two selected drainage regions of Attica. The simulations were carried out with WRF-Hydro model, which is an enhanced version of the Weather Research and Forecasting (WRF) model complemented with the feedback of terrestrial hydrology on the atmosphere, where surface and subsurface runoff were computed at a fine resolution grid of 95 m. Results showed that WRF-Hydro is capable to produce the observed discharge after the adequate calibration method at the studied basins. Besides, the WRF-Hydro has the tendency to slightly improve the simulated precipitation in comparison to the simulated precipitation produced the atmospheric only version of the model. These outcomes provide confidence that the model configuration is robust and, thus, can be used for flood research and operational forecasting purposes in the area of Attica.
Regulation of Experimental Autoimmune Encephalomyelitis in the C57BL/6J Mouse by NK1.1+, DX5+, αβ+ T Cells1

C57BL/6 (B6) mice with targeted mutations of immune function genes were used to investigate the mechanism of recovery from experimental autoimmune encephalomyelitis (EAE). The acute phase of passive EAE in the B6 mouse is normally resolved by partial recovery followed by mild sporadic relapses. B6 TCR β-chain knockout (KO) recipients of a myelin oligodendrocyte glycoprotein p35–55 encephalitogenic T cell line failed to recover from the acute phase of passive EAE. In comparison with wild-type mice, active disease was more severe in β2-microglobulin KO mice. Reconstitution of TCR β-chain KO mice with wild-type spleen cells halted progression of disease and favored recovery. Spleen cells from T cell-deficient mice, IL-7R KO mice, or IFN-γ KO mice were ineffective in this regard. Irradiation or treatment of wild-type spleen cell population with anti-NK1.1 mAb before transfer abrogated the protective effect. Removal of DX5+ cells from wild-type spleen cells by anti-DX5 Ab-coated magnetic beads before reconstitution abrogated the suppressive properties of the spleen cells. TCR-deficient recipients of the enriched DX5+ cell population recovered normally from passively induced acute disease. DX5+ cells were sorted by FACS into DX5+ αβTCR+ and DX5+ αβTCR− populations. Only recipients of the former recovered normally from clinical disease. These results indicate that recovery from acute EAE is an active process that requires NK1.1+, DX5+ αβ+ TCR spleen cells and IFN-γ.
Patient Satisfaction and Clinical Efficacy of an Advanced Practice Provider Stone Prevention Clinic.

INTRODUCTION The benefits of a multidisciplinary stone prevention clinic are well established. However, the outcomes of advanced practice provider integration into this model have not been reported. Our goal was to assess the feasibility of an advanced practice provider managed stone prevention clinic. METHODS High risk kidney stone patients were evaluated by an advanced practice provider and registered dietitian. Medical and dietary interventions were formulated based on medical and dietary history, labs and imaging. Post-intake surveys assessed patient satisfaction and educational impact. Survey results, stone risk parameters and acute stone events were retrospectively reviewed. Paired samples t-tests were used to assess changes in 24-hour urine parameters. RESULTS We followed 77 patients over an average of 4.34 visits (750±464 days). Of the 63 surveys completed 100% found their visit helpful and 98.4% would recommend the clinic. Of the 65 patients with multiple 24-hour urine studies significant reductions were seen in stone supersaturation profiles for uric acid (54.2%, p <0.01) and calcium phosphate (31.8%, p=0.04). Supersaturation profiles for uric acid, calcium phosphate and calcium oxalate decreased with each followup visit. Number of registered dietician appointments was associated with reduced supersaturation of calcium oxalate (-2.29, p=0.04). Number of advanced practice provider appointments was associated with reduced supersaturation of uric acid (-0.34, p=0.02). In all, 15 patients experienced an acute stone event and 8 patients had 1 or more emergency room visit. CONCLUSIONS The implementation of an advanced practice provider managed stone prevention clinic is feasible in the community setting. This is supported by positive feedback, educational impact and reductions in stone risk parameters.
Allosteric regulation of MDM2 protein

iv Aims . v Abbreviations . vi Table of Contents . xi List of figures . xiii Chapter 1 . 1 Introduction . 1 1.1 Carcinogenesis . 2 1.2 Tumour suppressors and oncogenes . 3 1.3 The p53 tumour suppressor protein . 4 1.4 MDM2 MOUSE DOUBLE MINUTE 2 HOMOLOG . 10 1.5 Targeting the MDM2-p53 interaction for cancer therapy. 45 Chapter 2 . 52 Materials and Methods. 52 2.1 General Reagents . 54 2.2 General Lab Equipment . 54 2.3 Cell Culture . 54 2.4 Microbiological Techniques . 57 2.5 Molecular Biology Methods . 60 2.6 Clonning and Site Directed Mutagenesis (SDM) . 68 2.7 Protein Purification . 75 2.8 Assays . 76 Chapter 3 . 89 Structure-function analysis of the MDM2 RING finger . 89 3.1 Introduction . 90 3.2 Experimental Results . 92 3.3 Discussion . 110 3.4 Figures. 114 Chapter 4 . 138 RING – dependent allosteric regulation of the MDM2 hydrophobic pocket. 138
Oomycete Genetics and Genomics: Diversity, Interactions and Research Tools

FOREWORD. PREFACE. CONTRIBUTORS. Chapter 1 The Evolutionary Phylogeny of Oomycetes-Insights Gained from Studies of Holocarpic Parasites of Algae and Invertebrates ( Gordon W. Beakes and Satoshi Sekimoto ). Chapter 2 Ecology of Lower Oomycetes ( Martina Strittmatter, Claire M.M. Gachon, and Frithjof C. Kupper ). Chapter 3 Taxonomy and Phylogeny of the Downy Mildews (Peronosporaceae) ( Marco Thines, Hermann Voglmayr, and Markus Goker ). Chapter 4 An Introduction to the White Blister Rusts (Albuginales) ( Marco Thines and Hermann Voglmayr ). Chapter 5 The Asexual Life Cycle ( Adrienne R. Hardham ). Chapter 6 Sexual Reproduction in Oomycetes: Biology, Diversity, and Contributions to Fitness ( Howard S. Judelson ). Chapter 7 Population Genetics and Population Diversity of Phytophthora infestans ( William E. Fry, Niklaus J. Grunwald, David E.L. Cooke, Adele McLeod, Gregory A. Forbes, and Keqiang Cao ). Chapter 8 Phytophthora capsici: Sex, Selection, and the Wealth of Variation ( Kurt Lamour ). Chapter 9 Evolution and Genetics of the Invasive Sudden Oak Death Pathogen Phytophthora ramorum ( Niklaus J. Grunwald and Erica M. Goss ). Chapter 10 Phytophthora sojae: Diversity Among and Within Populations ( Anne Dorrance and Niklaus J. Grunwald ). Chapter 11 Pythium Genetics ( Frank Martin ). Chapter 12 Bremia lactucae and Lettuce Downy Mildew ( Richard Michelmore, Oswaldo Ochoa, and Joan Wong ). Chapter 13 Downy Mildew of Arabidopsis Caused by Hyaloperonospora arabidopsidis (Formerly Hyaloperonospora parasitica) ( Nikolaus L. Schlaich and Alan Slusarenko ). Chapter 14 Interactions Between Phytophthora infestans and Solanum ( Mireille van Damme, Sebastian Schornack, Liliana M. Cano, Edgar Huitema, and Sophien Kamoun ). Chapter 15 Phytophthora sojae and Soybean ( Mark Gijzen and Dinah Qutob ). Chapter 16 Phytophthora brassicae As a Pathogen of Arabidopsis ( Felix Mauch, Samuel Torche, Klaus Schlappi, Lorelise Branciard, Khaoula Belhaj, Vincent Parisy, and Azeddine Si-Ammour ). Chapter 17 Aphanomyces euteiches and Legumes ( Elodie Gaulin, Arnaud Bottin, Christophe Jacquet, and Bernard Dumas ). Chapter 18 Effectors ( Brett M. Tyler ). Chapter 19 Pythium insidiosum and Mammalian Hosts ( Leonel Mendoza ). Chapter 20 Saprolegnia-Fish Interactions ( Emma J. Robertson, Victoria L. Anderson, Andrew J. Phillips, Chris J. Secombes, Javier Dieguez-Uribeondo, and Pieter van West ). Chapter 21 Aphanomyces astaci and Crustaceans ( Lage Cerenius, M. Gunnar Andersson, and Kenneth Soderhall ). Chapter 22 Progress and Challenges in Oomycete Transformation ( Howard S. Judelson and Audrey M.V. Ah-Fong ). Chapter 23 In Planta Expression Systems ( Vivianne G.A.A. Vleeshouwers and Hendrik Rietman ). Chapter 24 Gene Expression Profiling ( Paul R.J. Birch and Anna O. Avrova ). Chapter 25 Mechanisms and Application of Gene Silencing in Oomycetes ( Stephen C. Whisson, Anna O. Avrova, Laura J. Grenville Briggs, and Pieter van West ). Chapter 26 Global Proteomics and Phytophthora ( Alon Savidor ). Chapter 27 Strategy and tactics for genome sequencing ( Michael C. Zody and Chad Nusbaum ). INDEX.
Parallel or Intersecting Lines? Intelligent Bibliometrics for Investigating the Involvement of Data Science in Policy Analysis

Efforts to involve data science in policy analysis can be traced back decades but transforming analytic findings into decisions is still far from straightforward task. Data-driven decision-making requires understanding approaches, practices, and research results from many disciplines, which makes it interesting to investigate whether data science and policy analysis are moving in parallel or whether their pathways have intersected. Our investigation, from a bibliometric perspective, is driven by a comprehensive set of research questions, and we have designed an intelligent bibliometric framework that includes a series of traditional bibliometric approaches and a novel method of charting the evolutionary pathways of scientific innovation, which is used to identify predecessor–descendant relationships in technological topics. Our investigation reveals that data science and policy analysis have intersecting lines, and it can foresee that a cross-disciplinary direction in which policy analysis interacting with data science has become an emergent area in both communities. However, equipped with advanced data analytic techniques, data scientists are moving faster and further than policy analysts. The empirical insights derived from our research should be beneficial to academic researchers and journal editors in related research communities, as well as policy-makers in research institutions and funding agencies.
Sensing and Responding to Stress Stimuli in Caenorhabditis elegans: Implications for Aging and Immunity

Author(s): Twumasi-Boateng, Kwame | Advisor(s): Shapira, Michael | Abstract: Animals have evolved sophisticated mechanisms to perceive stress or even anticipate it before it has caused damage. Ideally, stress responses are controlled to ensure that they are specific and not excessive lest they cause collateral damage to the host. Here I describe my work in Caenorhabditis elegans examining the initiation and consequences of stress responses. In chapters 2 and 3, I examine the mechanisms of initiation of C.elegans immune responses to Pseudomonas aeruginosa, focusing on pathogen recognition. In chapters 4 and 5 I describe a project that was initiated within the realm of host-pathogen interactions, but evolved to focus on age as a context determining the outcome of both biotic and abiotic stress responses. Despite extensive knowledge of conserved signaling pathways in the C.elegans immune response, a question that has remained elusive is whether C.elegans can directly recognize pathogens, or if alternatively, they detect cellular damage caused by infection. I have shown that the immune response to P. aeruginosa can be dissociated from colonization and that potential damage from secreted molecules cannot induce a marker of the early immune response; in contrast, a non-pathogenic Pseudomonad can. This suggests that the response can be initiated at least in part by structural features of the bacteria. Furthermore, I have identified a family of genes in C.elegans encoding LysM domain proteins which are known to participate in recognition of microbial envelope components. Genetic and functional analyses suggest a potential role for family members in pathogen recognition in C. elegans. In the second half of this dissertation, I show that while the C.elegans JNK homolog KGB-1 is stress-protective during development, its activation in adults compromises stress resistance as well as general lifespan. I go on to show that this phenomenon is mediated in part by KGB-1's age-dependent antagonistic modulation of the conserved FOXO transcription factor, DAF-16. Genome-wide analysis of the KGB-1 transcriptome revealed that KGB-1 regulates several genes in an age-specific manner, and pointed to another conserved transcription factor, FOS-1 as a mediator of KGB-1's effects. Interestingly, the phenomenon of the same protein having opposite effects dependent on age is reminiscent of the Antagonistic Pleiotropy theory for the evolution of aging. Our results shed light on molecular mechanisms underlying this long-standing theory.
Heme-dependent Tryptophan Oxidation: Mechanistic Studies on Tryptophan 2,3-Dioxygenase and MauG

Hemoenzymes are prevalent in nature and participate in a wide range of biological activities. Frequently, high-valence iron intermediates are involved in the catalytic events of these enzymes, especially when the activation of peroxide or dioxygen is involved. Building on the fundamental framework of iron-oxygen chemistry, the mechanistic understandings of these enzymes and their reactive intermediates constantly attract attention from the enzymology community. This dissertation work focused on the mechanistic studies on two hemoenzymes, tryptophan 2,3-dioxygenase (TDO) and MauG, both of which catalyze unique chemical transformations, i.e., tryptophan oxidation. TDO and MauG are structurally distinct from each other; they catalyze different types of oxidization reactions on tryptophan via diverse strategies. TDO catalyzes the ring-cleavage dioxygenation reaction of free L-tryptophan, incorporating both oxygen atoms from dioxygen into the substrate. MauG uses hydrogen peroxide as the oxidant to catalyze a complex posttranslational-modification reaction on two tryptophan residues from a protein substrate. It utilizes radical chemistry to perform a 40-Å long-range catalytic event. Despite the differences in their catalytic behavior, both enzymes are suggested to employ highvalence iron intermediates in their reactions. A collection of biochemical and spectroscopic approaches was employed to obtain detailed insight into the electronic and structural contributions to the formation and stabilization of high-valence iron intermediates, and into the heme-dependent tryptophan-oxidation mechanisms. In the study of TDO, we solved the long-standing mystery of how the active Fe(II) enzyme is generated from the resting Fe(III) form by hydrogen peroxide. A peroxide-driven reactivation mechanism was established based on the identification of a compound ES-type ferryl intermediate. Additional efforts were dedicated to clarify the controversy in the literature regarding the catalytic roles of a distal histidine residue. Chemical-rescue approaches were used to specify the catalytic contributions of the target residue. In the study of MauG, we discovered an unprecedented tryptophan-mediated charge-resonance phenomenon in the bis-Fe(IV) redox state. This discovery provides the molecular basis for the chemical reactivity of the catalytically competent bis-Fe(IV) intermediate. Together with our collaborators, we also outlined the mechanism of the MauG-mediated long-range catalysis by identifying the catalytic functions of several important residues along the reaction pathway. INDEX WORDS: High-valence iron, Chemical rescue, Electron paramagnetic resonance, Posttranslational modification, Radical enzymology, Electron transfer, Electron hopping, Charge resonance, Long-range catalysis HEME-DEPENDENT TRYPTOPHAN OXIDATION: MECHANISTIC STUDIES ON TRYPTOPHAN 2,3-DIOXYGENASE AND MAUG
Prediction of Aerosolized Fungal Spores by Determining Respiratory Intensity of the Growing Colony

ABSTRACT Aerosolization of fungal spores from moldy surfaces can cause adverse health effects. The spores of an older colony are more easily detached than those of a younger colony. When the growth age of a colony is known, the aerosolization of spores can be more accurately predicted. This study proposed the adoption of respiratory intensity as an indicator of the growth age of Aspergillus niger colonies. Respiratory intensity is the mass of carbon dioxide produced by the respiration of a colony per unit quantity of spores within a certain time. Two types of colonies, with homogeneous and heterogeneous age distributions, were aerosolized in a wind tunnel to determine the spore release proportion and validate the method. The results revealed that the respiratory intensity of the homogeneous colony is closely correlated with the growth age when the age of the colony is less than 14 days under standard growth conditions. The spore release proportion increases with the growth age and the blowing speed. The predicted spore release proportion for a heterogeneous colony is more precise when the colony is divided into multiple sub-colonies to characterize the growth age for each individual spore release proportion. The relative errors of the predicted spore release proportions as compared with the test values were less than 10%.