Miracle-dz/UniFAR-FTUs huggingface dataset:
Structure-function analyses of plant glycan-degrading enzymes

ii Lay Summary . iv Preface . v List of Tables . xiv List of Figures . xv List of Abbreviations . xix Acknowledgements . xxiii Dedication . xxv Chapter 1: Introduction . 1 1.1 Complex Carbohydrate-Enzyme Interactions in the Biosphere . 1 1.1.1 The Plant Cell Wall . 1 1.1.1.1 Xyloglucans . 2 1.1.1.2 Mixed-Linkage Glucans . 3 1.1.1.3 β-Mannans . 4 1.1.1.4 Xylans. 5 1.1.1.5 Pectins . 5 1.1.2 Enzyme Specificities in the Breakdown of Plant Polysaccharides . 6 1.1.2.1 Glycoside Hydrolases . 6 1.1.2.2 Polysaccharide Lyases. 8 1.1.2.3 Glycosyltransferases. 9 1.1.2.4 Carbohydrate Esterases . 9 1.1.2.5 Auxiliary Activities . 9 1.1.2.6 Carbohydrate-Binding Modules . 10 1.2 Carbohydrate-Active Enzyme Discovery . 10 1.2.1 CAZymes in Plants . 11 1.2.2 Fungal CAZymes . 12 1.2.3 Bacterial and Archaeal CAZymes . 13 1.2.4 Polysaccharide Utilisation Loci in Gut Bacteroidetes . 14 1.2.4.1 Surface Glycan-Binding Proteins . 15 viii 1.2.4.2 TonB-Dependent Transporters . 16 1.2.4.3 Carbohydrate-Degrading Enzymes . 16 1.2.4.4 Sensor/Regulators. 17 1.3 Quantifying CAZyme Activities . 18 1.3.1 Quantifying Glycoside Hydrolysis . 18 1.3.1.1 Reducing End Quantitation . 18 1.3.1.2 Enzyme-Linked Assays . 19 1.3.1.3 HPLC Assays . 19 1.3.1.4 Chromogenic Substrates for Glycoside Hydrolases . 20 1.3.2 Quantifying Carbohydrate Esterase Activity . 21 1.3.2.1 Chromogenic Substrates . 21 1.3.2.2 Enzyme-Linked Assays . 21 1.3. 3 Measuring CAZyme-Substrate Interactions through Kinetic Analysis . 22 1.3. 3.1 Models of Enzyme Kinetics . 22 1.3. 3.2 Relating Kinetic Parameters to Molecular Interactions . 25 1.4 Determining Enzyme Specificity through Product Analysis . 26 1.4.1 Chemical Transformations for Carbohydrate Structure Determination. 26 1.4.2 Chromatographic Analysis of Carbohydrate Mixtures . 27 1.4.3 Identification of Carbohydrates using Mass Spectrometry . 28 1.4.4 Nuclear Magnetic Resonance Spectroscopy of Carbohydrates . 30 1.5 Relating Enzyme Function to Structure using X-ray Crystallography . 31 1.5. 1 Glycoside Hydrolase Active-Site Structure . 32 1.5. 2 Active Site Probes for Enzyme Active Site Labelling . 35 1.6 Aims of this Thesis . 35 Chapter 2: Crystallographic Insight into the Evolutionary Origins of Xyloglucan EndoTransglycosylases and Endo-Hydrolases . 37 2.
Humpback whale encounters: encouraging pro-environmental behaviours

ABSTRACT The aim of this study was to investigate the impact of whale encounters on tourists’ pro-environmental intentions, and possible influences of individual characteristics. Data were collected from whale watching/swim-with-whale experiences within Australia and the Kingdom of Tonga. Comparison of pre and post trip survey data (N = 267) indicated that engaging and reflecting during the experience was positively associated with pro-environmental intentions following the encounter. However, tourists who reportedly lacked mutualistic values, displayed a low awareness of consequences, or adopted non-nature-based tourism motivations were less likely to engage and reflect. Therefore, tour operators should aim to facilitate cognitive and affective processing during wildlife encounters, especially for groups that are less likely to engage as this could both increase experience satisfaction and the potential for attitude and behaviour change. Further exploration of these complex relationships and their application are recommended to maximize environmental protection efforts while minimizing the ecological impacts of wildlife tourism.
A first-approximation simple dynamic growth model for forest teak plantations in Gujarat state of India

Tectona grandis (teak) is one of the most important tropical timber species occurring naturally in India. In India, teak is the single most important commercial timber species. Scientifically sound growth models, based on advanced modelling techniques, are often not available, although they are necessary for the successful management of teak stands in the country. Long-term forest planning requires mathematical models. In this paper, an attempt is made to develop a dynamic growth model based on the limited data, consisting of three annual measurements, collected from 15 teak sample plots in Gujarat state of India. A biologically consistent whole-stand growth model is presented, which uses the state-space approach for modelling rates of change of dominant height, stand density and stand basal area. A simple model containing few free parameters performed well and is particularly well suited to situations where available data are scarce.
Determinant Factors Influencing Thai Tourists’ Intentions to Use Social Media for Travel Planning

Currently, information technology plays an important role in the tourism industry. Tourists like to use social media more widely for their travel planning, which affects the high competition between entrepreneurs while facing the challenge of improving the quality of data services provided through social media. This study developed a model of the relationships between structure factors that affect intentions to use social media for travel planning. The said model integrates the technology acceptance model (TAM) theory, the theory of planned behavior (TPB), and trust and satisfaction factors. In reference to a survey of 1333 samples from domestic tourists who used social media through their smartphone, it was found that satisfaction, attitudes, subjective norms, and perception can be used to control behavior, with a positively direct effect on intentions of use. In addition, we examined the indirect effect on intentions of use. Perceived ease of use, perceived usefulness, and subjective norms had a positively significant indirect effect on intentions of use. These research results allow tourism entrepreneurs to precisely understand the stimulating factors of tourists’ intentions to use social media for travel-planning decisions, which will help lead to the development of tourism-marketing strategies and the support of sustainable competition.
IFRS 9 transition effect on equity in a post bank recovery environment: the case of Slovenia

Abstract On January 1, 2018, IFRS 9 became effective in the EU. It introduced the expected credit loss model to allow for timely recognition of credit losses, estimated not only on the actual credit loss experience but also on forward looking information related to current loan portfolio. Although the transition to IFRS 9 should lead to increased impairments and decrease in banks’ equity, this effect is ambiguous in the settings characterised by combined effects of optimistic macroeconomic outlook and strong regulatory intervention related to extensive loan portfolio restructuring. This paper investigates day-one transition effect of IFRS 9 on level of loan impairments and total equity of banks in Slovenia, Eurozone country, which barely averted international bailout in 2013 by extensive state assisted bank restructuring. The comparative analysis is done on banks that transferred deteriorated loan portfolio to the state’s Bank Assets Management Company and all other banks. In line with expectations we find that banks without extensive asset portfolio improvements recognised additional loan impairments on transition to IFRS 9, whereas the opposite effect is observed for banks which performed state-assisted loan portfolio restructuring. Our study provides additional insight on the effect of institutional and regulatory setting on IFRS 9 implementation effects.
Tropical Expansion Driven by Poleward Advancing Midlatitude Meridional Temperature Gradients

An abundance of evidence indicates that the tropics are expanding. Despite many attempts to decipher the cause, the underlying dynamical mechanism driving tropical expansion is still not entirely clear. Here, based on observations, multimodel simulations from the Coupled Model Intercomparison Project phase 5 (CMIP5) and purposefully designed numerical experiments, the variations and trends of the tropical width are explored from a regional perspective. We find that the width of the tropics closely follows the displacement of oceanic midlatitude meridional temperature gradients (MMTG). Under global warming, as a first‐order response, the subtropical ocean experiences more surface warming because of the mean Ekman convergence of anomalously warm water. The enhanced subtropical warming, which is partially independent of natural climate oscillations, such as the Pacific Decadal Oscillation, leads to poleward advance of the MMTG and drives the tropical expansion. Our results, supported by both observations and model simulations, imply that global warming may have already significantly contributed to the ongoing tropical expansion, especially over the ocean‐dominant Southern Hemisphere.
Historical connections between early marine science research and dissemination: the case study of aquarium Vasco Da Gama (Portugal) from late 19th century to mid-20th century

In the late 19th century, there was a bloom of public aquariums throughout Europe. Some of them were built for entertainment purposes, whereas others were connected to marine science stations. This article explores the origins and development of the aquarium/marine research station Vasco da Gama (Portugal) as an example of this duality. Initially, the aquarium was created in 1898 by the Portuguese Society of Geography, in a political context of national affirmation. In the first years, a deficient establishment, lack of financial resources, and scarce technical knowledge contributed for its degradation. Therefore, the Navy took over the aquarium in the early 1900s, delivering its management some years later to the Portuguese Society of Natural Sciences. After improvements and modifications, it became one of the first marine biological stations in 1919. This was important for the development of national marine science research at a time of scarce resources. Despite many years of a symbiotic relation between science research and dissemination, the demolition of part of the aquarium/marine station due to a road construction in 1940 brought issues of disequilibrium between both functions. This eventually led to the separation of aquarium and marine station in 1950. Other themes such as connections to national and international institutions are also discussed.
Assessment of Level of Patient Satisfaction after Prostatectomy for Benign Prostatic Hyperplasia in Referral Hospitals in Addis Ababa

Background Benign Prostatic hyperplasia is a very common problem in aging men. TURP comprises 95% of all surgical procedures and is the treatment of choice for prostates sized between 30ml and 80–100ml. Open surgery is the treatment of choice for large glands (bigger than 80–100ml) and for those with associated complications that have indication for open surgery. Many literatures show that the overall patient satisfaction rate and clinical outcome of TURP for BPH are very good. The objective of this study was ‘assessing the level of patient satisfaction after undergoing TURP and TVP for BPH. Methods In this research, convenient sampling technique was used. The study design was prospective cohort study. Standardized questioner was prepared in English and later translated into Amharic. Information about demographic characteristics, preoperative data, intraoperative data, and immediate postoperative data were taken while the patient was in the hospital. At the first and the third months after the prostatectomy, patients were inquired on their level of satisfaction about their disease specific satisfaction on the urinary function and their sexual function. We used HCAHPS Measure of Patient Satisfaction Tool, to collect data and analyzed using SPSS version 18. Results A total of 89 patients were enrolled in the study among which 65.2% had undergone TURP. The rate of major perioperative complication was found to be low. Over half of the patients had postoperative hospital stay of three or less days. Majority of the patients were satisfied with the care given by the nurses (68.2%) and doctors (84.3%) with relatively higher physicians' care satisfaction level. More than 60% of the patients were highly satisfied with their urinary surgical outcome. With regard to hospital environment, around 60% of the patients reported that they were very satisfied with cleanliness of the rooms, bath rooms and the quietness of the rooms at night. Conclusions Both TURP and TVP have high level of patient satisfaction associated with low perioperative major complications. Therefore both can be recommended for patients with clear indications for prostatectomy.
Bacille Calmette-Guérin Vaccination in Infancy Does Not Protect Against Coronavirus Disease 2019 (COVID-19): Evidence From a Natural Experiment in Sweden

BACKGROUND: The Bacille Calmette-Guérin (BCG) tuberculosis vaccine has immunity benefits against respiratory infections. Accordingly, it has been hypothesized to have a protective effect against COVID-19. Recent research found that countries with universal BCG childhood vaccination policies tend to be less affected by the COVID-19 pandemic. However, such ecological studies are biased by numerous confounders. Instead, this paper takes advantage of a rare nationwide natural experiment that took place in Sweden in 1975, where discontinuation of newborns BCG vaccination led to a dramatic fall of the BCG coverage rate, thus allowing us to estimate the BCG's effect without the biases associated with cross-country comparisons. METHODS: Numbers of COVID-19 cases and hospitalizations were recorded for birth cohorts born just before and just after 1975, representing 1,026,304 and 1,018,544 individuals, respectively. We used regression discontinuity to assess the effect of BCG vaccination on Covid-19 related outcomes. This method used on such a large population allows for a high precision that would be hard to achieve using a randomized controlled trial. RESULTS: The odds ratio for Covid-19 cases and Covid-19 related hospitalizations were 1·0005 (CI95: [0·8130-1·1881]) and 1·2046 (CI95: [0·7532-1·6560]), allowing us to reject fairly modest effects of universal BCG vaccination. We can reject with 95% confidence that universal BCG vaccination reduces the number of cases by 19% and the number of hospitalizations by 25%. CONCLUSIONS: While the effect of a recent vaccination must be evaluated, we provide strong evidence that receiving the BCG vaccine at birth does not have a protective effect against COVID-19 among middle-aged individuals.
Setting the Tone for the Team: A Multi‐Level Analysis of Managerial Control, Peer Control, and their Consequences for Job Satisfaction and Team Performance

In this study, we develop a multi-level theoretical framework linking antecedents and outcomes of peer control, defined as team members at the same hierarchical level noticing and responding to their peers’ behaviour or performance. Analysing multi-level data from 356 volunteers and 58 regional teams in a non-profit organization, we examine top-down managerial controls as antecedents of lateral peer control, both directly (i.e., monitoring and responding directly to peers) and indirectly (i.e., gossiping about and avoiding underperforming peers), and peer control’s effects on individualand team-level outcomes. In line with our predictions, we find formal managerial control and clan control to be antecedents of peer control, albeit with differential effects on direct and indirect peer control. We also find a significant association between peer control and both individual-level job satisfaction and team-level performance, but again, with crucial differences between the two types of peer controls and the two outcomes. Our study contributes to the development of a better theoretical understanding of peer control, sheds light on inconsistent findings across prior studies, provides novel insights into how team leaders can influence team members’ individual satisfaction and team-level performance via peer control, and reveals important trade-offs with regards to peer control’s influence on individualand team-level outcomes.
Comparison of confirmatory factor analysis estimation methods on binary data

This Monte Carlo simulation study aimed to investigate confirmatory factor analysis (CFA) estimation methods under different conditions, such as sample size, distribution of indicators, test length, average factor loading, and factor structure. Binary data were generated to compare the performance of maximum likelihood (ML), mean and variance adjusted unweighted least squares (ULSMV), mean and variance adjusted weighted least squares (WLSMV), and Bayesian estimators. As a result of the study, it was revealed that increased average factor loading and sample size had a positive effect on the performance of the estimation methods. According to the research findings, it can be said that the methods are sufficient to estimate average factor loading and interfactor correlations, regardless of the estimation methods, in most of the conditions where the average factor loading is 0.7. In small sample sizes particularly, the interfactor correlation was underestimated for skewed indicator conditions. According to the findings of the study, although there is not the most accurate method in all conditions, it can be recommended to use ULSMV method because it performs adequately in more conditions.
Till kinematics in the Stargard drumlin field, NW Poland constrained by microstructural proxies

Deciphering the relationships between streamlined subglacial landforms and deposits therein helps to constrain the dynamics of past ice sheets. Here we present microstructural analyses of till from the largest drumlin field in the North European Lowland generated by a major palaeo‐ice stream of the Scandinavian Ice Sheet. Data derived from thin sections and X‐ray microtomography (μCT) reveal multiple microstructures including microshears, circular structures, grain stacks and crushed grains. Long axes of micro‐clasts measured in thin sections are directionally clustered and have low, down‐ice‐oriented dip angles. Some samples reveal subordinate clustering oriented at high angles to the main direction. The μCT data show low clustering strengths of clasts and no systematic fabric pattern in the entire set of samples. There is no correspondence between the clast orientations and the directions of drumlin long axes, suggesting that the till is antecedent in relation to the drumlin‐shaping process. The observations indicate spatially and temporally variable, shallow‐seated brittle and ductile deformation controlled by porewater pressure fluctuations and generated time‐transgressively parallel to till accretion. Consistently with previous studies, the data suggest that the Stargard drumlins are erosional remnants of a pre‐existing terrain shaped by material removal from the inter‐drumlin areas.
A prospective post-partum evaluation of renal function in preeclampsia

It is a multisystem disease and several organs are affected at different stages of disease. Haematological changes associated most commonly is thrombocytopenia, haemolysis and intravascular coagulation. Commonly affected systems are renal system (manifested by reduced GFR, proteinuria, hyperuricemia and occasionally oliguria), liver (manifested by elevated transaminases with or without epigastric and right upper quadrant pain), and the brain (manifested by headaches, transient visual disturbances due to occipital lobe ischaemia and rarely convulsions, i.e. eclampsia). All this leads to increased maternal morbidity. Major maternal complications include HELLP syndrome, DIC, acute renal failure, placental abruption, pulmonary oedema, cardiac arrest and cerebral haemorrhage. The most common cause of ABSTRACT
Polysaccharide Content and Growth Rate of Lessonia Variegata J. Agardh: Investigating its Potential as a Commercial Species

The endemic brown alga Lessonia variegata has recently been shown to be four separate lineages. To determine differences between the four morphologically similar lineages, the economically valuable polysaccharides alginate and fucoidan were extracted and yields from each of the lineages were compared. In order to determine seasonal patterns in the yield of alginate and fucoidan, and the growth rate within L.variegata, polysaccharides were extracted and the growth rate measured on a monthly basis from March 2010 until February 2011 on plants from the Wellington lineage. The alginate and fucoidan yields were obtained via stepwise extraction with dilute acid and sodium carbonate as per the previously published methods of Usov et al. (1985). The growth rate of L. variegata from the Wellington lineage was assayed using the hole punch technique first described by Parke (1948). The yield of alginate within the Wellington lineage of L. variegata fluctuated seasonally with the highest percent occurring in spring and summer 2010. The yield of fucoidan in the Wellington lineage was at its highest in mid-autumn and late spring 2010. Two different growth rates were detected for the Wellington lineage of L. variegata. There was a period of significantly high growth from late winter 2010 until late summer 2011.The Wellington lineage had the lowest yield of alginate and the highest yield of fucoidan compared to the Northern lineage, the Kaikoura lineage and the Southern lineage. Based on the findings of this study, an appropriate harvest period for the Wellington lineage of L. variegata would be in early to mid-summer when polysaccharide yields and growth rates are high and the alga is vegetative.
Trichoderma spp. and a carob (Ceratonia siliqua) galactomannan to control the root-knot nematode Meloidogyne incognita on tomato plants

Abstract Restrictions about the use of chemicals have limited the availability of control measures against plant-parasitic nematodes. The search for more sustainable approaches has focused the attention on biological control agents, such as Trichoderma species. In recent years, there has been a growing interest in the use of biopolymers for a wide range of applications. These polysaccharide-based compounds may be 20 good carriers of microbial agents or act as barriers against pathogens or pests for their ability to form coating films. In this study, we evaluated the combination of a biopolymer obtained from the leguminous plant Ceratonia siliqua and T. harzianum M10, T. atroviride P1 or T. longibrachiatum MK1, as root protector or adjuvant agents, for the management of the root-knot nematode Meloidogyne incognita. Coating tomato roots with the carob galactomannan biopolymer followed by soil application of selected Trichoderma strains reduced the root galling index caused by M. incognita and soil nematode population in comparison to untreated control under greenhouse conditions. 25 Scanning electron microscopy revealed that coated tomato roots were embedded within a polymeric material. The sedimentation test showed that the addition of this biopolymer retarded the tendency of Trichoderma spores to settle in the bottom of aqueous suspension. In conclusion, beneficial fungi combined or formulated with a biopolymer could represent a promising strategy to increase their activity in plant protection and enhance their proliferation or distribution into rhizosphere.