Miracle-dz/UniFAR-FTUs huggingface dataset:
ChemPer: An Open Source Tool for Automatically Generating SMIRKS Patterns

Force fields are used in a variety of research fields including computer-aided drug design, biomaterials, and polymer chemistry. However, force fields also continue to limit the accuracy of predictions of physical properties. Current parameterization of these force fields involves a huge amount of human effort -- often years of work -- and depends heavily on the chemical intuition of those involved. The Open Force Field Initiative is working to replace this tedious process with an automated machinery to learn parameters and chemical perception. Our new SMIRKS-based force field format, SMIRNOFF, allows all parameter types to be defined independently. This allows for easier extension compared to the traditional atom type-based force fields where the chemical perception of all parameter types is intertwined. We will need to be capable of programmatically learning SMIRKS patterns in order to fully automate force field parameterization. In this work, we present ChemPer -- a new tool for generating SMIRKS patterns based on clustered fragments (i.e. bonds, angles, or torsions) which should be assigned the same force field parameter. We demonstrate the utility of ChemPer by clustering fragments based on a reference force field, and then regenerating those parameters starting with a simple set of alkanes, ethers, and alcohols. Next, we create SMIRKS patterns for a protein SMIRNOFF which match the parameters from AMBER99. We conclude with a discussion of other potential applications and expansions to ChemPer.
Quantitative flaw characterization with ultrasonic phased arrays

Ultrasonic nondestructive evaluation (NDE) is a critical diagnostic tool in many industries. It is used to characterize potentially dangerous flaws in critical components for aerospace, automotive, and energy applications. The use of phased array transducers allows for the extension of traditional techniques and the introduction of new methods for quantitative flaw characterization. An equivalent flaw sizing technique for use in time-of-flight diffraction setups is presented that provides an estimate of the size and orientation of isolated cracks, surfacebreaking cracks, and volumetric flaws such as voids and inclusions. Experimental validation is provided for the isolated crack case. A quantitative imaging algorithm is developed that corrects for system effects and wave propagation, making the images formed directly related to the properties of the scatterer present. Simulated data is used to form images of cylindrical and spherical inclusions. The contributions of different signals to the image formation process are discussed and examples of the quantitative nature of the images are shown.
Risk Management: How to Assess, Transfer and Communicate Critical Risks

Preface. - Part I Reference Theories. - Chapter 1 From Social and Natural Science Comes a Historical Overview on the Concepts of Uncertainty and Risk. - Chapter 2 Governance and Risk Management. - Chapter 3 Risk Management Perspectives. - Part II Risk Assessment: Approaches, Techniques and Good Practices. - Chapter 4 The Need for an Enterprise-Wide Approach to Risk Management. - Chapter 5 Risk Identification. - Chapter 6 Risk Analysis. - Part III Risk Treatment: Approaches, Techniques and Good Practices. - Chapter 7 Risk Treatment. - Part IV Supply Chain Risk Management and Business Continuity. - Chapter 8 Operational Risk and Supply Chain Risk Management.
The Phonology-syntax connection

This work deals with the insolvency both of companies and of individuals. Its publication coincides with the coming into force of the radical amendments to insolvency law contained within the Enterprise Bill 2002. The book should be suitable for those studying insolvency at undergraduate or postgraduate level, and for those studying for professional examinations and practising in the area.
A method to evaluate corn stover biomass for fermentability to ethanol and the characterization of maize (Zea mays) brown midrib mutants

iv CHAPTER 1. GENERAL INTRODUCTION . 1 RATIONALE . 1 THESIS ORGANIZATION . 2 AUTHOR’S ROLE.3 Role in Research Articles.3 Role in and Contribution to other efforts . 4 LITERATURE REVIEW . 5 Introduction . 5 Section 1. Using Biomass for Energy.6 Section 2. Cell Wall Structure and Synthesis . 13 Section 3. The Phenylpropanoid Pathway and its Mutants.19 Section 4. GFP Discovery and Properties . 23 Section 5. History of Breeding for Ruminant Digestibility . 25 Section 6. High-throughput Screening in Breeding Programs . 29 REFERENCES.32 CHAPTER 2. DEVELOPMENT OF A REAL-TIME SUGAR-CONSUMING BIOSENSOR AND ITS APPLICATION TO A CORN STOVER HYDROLYSIS BIOASSAY.40 ABSTRACT . 40 INTRODUCTION . 41 MATERIALS AND METHODS.44 Site-Directed Mutagenesis and Transformation . 44 Preparation of Corn Stover Samples . 44 Hydrolysis measured by glucose assay . 44 Growth of liquid cultures for growth characterization experiments.45 Characterization of the Biosensor . 46 Application of the Biosensor . 49 RESULTS.50 Feedback inhibition of a preparation of cellulases and hemicellulases . 50 Characterization of the Biosensor . 51 Application of the Biosensor . 54 DISCUSSION.56 Feedback inhibition of a preparation of cellulases and hemicellulases . 56 Characterization of the Biosensor . 57 Application of the Biosensor . 59 ACKNOWLEDGEMENTS . 60 REFERENCES.61 FIGURES AND TABLES . 65 CHAPTER 3. QUALITY CONTROL OF SIMULTANEOUS SACCHARIFICATION AND CATABOLISM.73 ABSTRACT . 73 INTRODUCTION . 74 MATERIALS AND METHODS.75 Preparation of Corn Stover Samples . 75 Simultaneous Saccharification and Catabolism Procedures . 76 Statistical Analyses . 78 RESULTS AND DISCUSSION . 80
What's the time Mr Wolf?

"What's the time Mr Wolf? " is an imagistic documentary about living with epilepsy which is the most common, serious neurological condition in the UK. A group of people at an acting workshop have something in common, not just that a seizure could strike at any moment, but they also have the courage to open up to us. "A seizure is like a wolf creeping up on you, ready to pounce. " "As the wolf comes within eyesight, there is that fear and I slow down. "
The use of agile systems development methodologies in the telecommunication industry in South Africa

Over the last decade, systems development professionals have recognised the need to use agile systems development methodologies (ASDMs) in the telecommunication industry. This is partly due to the barriers identified by Mansurov (2000) which suggest that the use of agile methodologies in the telecommunication industry would reduce the ratio of time-to-market. In the South African context, the industry has cemented its position as a major driving force of the economy as a whole. The in~ustry' s level of competitiveness is in part informed by the information technology practices that it follows, and hence systems development is deemed to be a crucial and value-adding component ofthe environment This research therefore aims to investigate the systems development practices currently being used in the telecommunication industry of South Africa, as well as the perceived sentiments towards the use of ASDMs. The investigation into the level of applicability of ASDMs in the industry is largely informed by literature from agile proponents which suggest that ASDMs are highly suitable to projects where the user requirements continuously change. In order to identify the current SD practices followed and the sentiments towards ASDMs in the telecommunication industry, the interpretive paradigm was used. Three prominent organisations were identified and case studies were conducted at each of these companies. The data collection method used was a combination of semi-structured interviews and questionnaires, and the data analysis tools were ATLAS.ti for the semi-structured interviews and SPSS for the questionnaires. Thereafter, the data collected was analysed by using the cross-case analysis method. The results indicated that the incumbent companies in the telecommunication industry used an SDM that followed the waterfall approach, and the use of ASDMs was informed by a multitude offactors.
Webbasierte Selbsthilfe zur Stimmungsverbesserung in der Wartezeit auf ambulante Psychotherapie – Eine qualitative Erhebung der Teilnehmerperspektive

Zusammenfassung Ziel der Studie Patienten warten in Deutschland durchschnittlich 5 Monate auf den Beginn einer ambulanten Psychotherapie. Begleitete webbasierte Selbsthilfeinterventionen können depressive Symptome in der Wartezeit reduzieren. Ziel der Studie ist zu untersuchen, wie Betroffene die Teilnahme an einer webbasierten Intervention zur Stimmungsverbesserung erleben. Methodik Patienten auf den Wartelisten kooperierender Hochschulambulanzen wurden dazu eingeladen, im Rahmen einer Studie eine webbasierte Intervention zur Stimmungsverbesserung zu nutzen. Elf Teilnehmende der Intervention wurden in einem qualitativen Telefoninterview zu ihren Erfahrungen mit der Maßnahme befragt. Die Daten wurden entsprechend den Prinzipien der Grounded Theory analysiert. Ergebnisse Aus den Daten konnten 3 Kategorien extrahiert werden, welche das Erleben der Teilnehmenden hinsichtlich ihrer Erwartungen, ihrer Erfahrungen sowie ihrer Adhärenz beschreiben. Die webbasierte Intervention wurde sehr unterschiedlich erlebt und sowohl mit positiven als auch negativen Erfahrungen verbunden. Die Teilnehmenden ließen sich anhand der beschriebenen Kategorien in 3 Nutzertypen gruppieren: Den selbstständigen Typus, den überforderten Typus und den anspruchsvollen Typus. Diskussion Nicht alle Patienten machen gleichermaßen gute Erfahrungen mit der Intervention und einige scheitern an der Umsetzung. Um Patienten bestmöglich auf die Nutzung der Intervention vorzubereiten, sollten sie vorab noch ausführlicher über die Handhabung und Ziele der Intervention aufgeklärt werden. Interventionen sollten individuell entsprechend des Unterstützungsbedarfs von Patienten implementiert werden, um positive Erfahrungen zu ermöglichen und adhärenzfördernd zu wirken.
Medición de la calidad de productos de software en un ambiente académico usando la norma iso/iec 9126

Quality is one of the attributes expected in the products we buy, software should not be an exception. Through this study, students of software engineering courses at the Escuela Superior Politecnica del Litoral were exposed to the use of ISO/ IEC 9126 to assess the quality of their software products. All software products were developed for ecuadorian organizations located in Guayaquil. During two semesters, a total of 41 students participated in the study using 5 standard features: functionality, reliability, usability, efficiency and maintainability. It was found that functionality was a predominant feature compared to the others. In addition, the time taken for developing new software products was considerable less than the one taken for developing new versions of existing products that needed to be integrated to the rest of the systems. Lessons learned and recommendations are provided at the end of this article.
Measuring the marginal cost of road use

The Swedish National Road and Transport Research Institute (VTI) has carried out this survey, which is expected to generate results of use for implementation of marginal cost based pricing of transport in terms of the principles laid down in the white paper on a common transport policy presented by the EU Commission in September 2001. The purpose of the survey is to review alternative methods that may be used for estimating marginal infrastructure costs. The survey identifies four different approaches to the measurement of the marginal cost of road use and evaluates empirical studies based on these approaches. One approach is referred to as the econometric approach. There are few examples of this approach, which is explained by the fact that it is difficult to generate the required data. The value of the approach is also limited by that it relies on historical data. Two of the other methods are based on similar assumptions. It is argued that both what is called the indirect approach and the full cost allocation approach basically rely on the properties of Newbery's 'fundamental theorem'. A fourth approach identified in the Survey is to use the pavement management systems (PMS) used by road authorities in the planning of road works. The idea is not new, but has rarely been applied. It is demonstrated in the survey how the approach may be employed for a specific road by way of the HDM 4 model, developed by the World Bank. There are several advantages of using a PMS, including that marginal costs will be derived with the same methodology that is used to rank investments, determine maintenance priorities and to prepare a road authority's budget. (A) This report is also available electronically via Internet at http://www.vti. se/pdf/reports/M963AGS.pdf
The Significance of Strategic Control on the Growth of Churches in Harare, Zimbabwe

The research aimed to assess the effect of strategic control on the growth of churches in Harare, Zimbabwe. The research looked at the influence of strategic control on the growth on both Mainline and Pentecostal churches. The study followed a positivism philosophy, where an explanatory research design was applied. A multi-stage stratified random sampling was used to select the study participants who were adult congregants and church leaders from two strata, one stratum being made up of mainline churches and the other one by Pentecostal churches. Multi-stage stratified random sampling was deemed appropriate for the research as it ensured that there was representativeness within and across the strata. Data was collected from systematically selected congregants and church leaders in selected churches through interviewer-administered questionnaires using Open Datakit, a mobile data collection platform. Data analysis revealed that there was evidence of implementation of strategic control (mean score of 4) as part of strategic management practices in both Mainline and Pentecostal churches. Additionally, the findings show that strategic control influences the growth of churches (p-value <0.001). These findings showed that churches like any other organizations can be affected by the change in the socio-economic environment and thus they should implement appropriate strategies to remain viable and relevant. Strategic control plays a crucial role in ensuring that those strategies are effectively implemented. An effective Strategic Management Framework should be formulated and guide how churches can continuously control the implementation of their strategies to remain viable and achieve their mandate.
Commande d'une machine asynchrone dédiée à la traction des chariots de manutention électriques

Ce travail propose un systeme de traction AC pour les chariots de manutention electriques. Ce systeme embarque est compose d'une machine asynchrone basse tension, fort courant alimentee par un onduleur de tension MLI et une batterie. Le controle vectoriel direct a orientation du flux rotorique est propose pour piloter l'ensemble. Cette strategie permet d'obtenir des performances dynamiques et statiques du chariot qui repondent au cahier des charges desire. Pour developper un systeme a bas prix, une reduction du nombre de capteur est faite. Un observateur deterministe d'ordre complet du flux rotorique est mis en place, en association avec la reconstruction des courants statorique au moyen de la mesure du courant de bus de l'onduleur. Le capteur de vitesse de rotation est remplace par un observateur adaptatif de vitesse. L'architecture du systeme de traction propose est validee en simulation avec le logiciel Saber. Un banc d'essai est realise pour obtenir une validation experimentale.
MPBond: efficient network-level collaboration among personal mobile devices

We demo MPBond, a novel multipath transport system allowing multiple personal mobile devices to collaboratively fetch content from the Internet. Inspired by the success of MPTCP, MPBond applies the concept of distributed multipath transport where multiple subflows can traverse different devices. Other key design aspects of MPBond include a device/connection management scheme, a buffering strategy, a packet scheduling algorithm, and a policy framework tailored to MPBond's architecture. We install MPBond on commodity mobile devices and show how easy it is to configure the usage of MPBond for unmodified apps. We visualize the runtime behavior of MPBond to further illustrate its design. We also demonstrate the download time and energy reduction of file download, as well as the video streaming QoE improvement with MPBond.
Geometric Modeling of Sheet Deformation within a Virtual Environment

In this paper we present a real-time, computationally inexpensive environment for on-screen, accurate simulations of thermoplastic sheet materials on a conventional Personal Computer. A pseudoimmersive virtual environment is constructed to handle the implementation of a real-time aesthetically accurate deformation algorithm called MaSSE: Mass-Spring Simulation Engine. The motion of the sheet is controlled by gravity and by using a mouse-pointing device to manipulate the sheet within the environment. An application for the environment is centered on, although not restricted to, mechanical engineering-based real-time simulations of heat-sensitive sheet materials.
Ultra-wideband communications: fundamentals and applications

The Easy-to-Understand, Up-to-the-Minute Guide to UWB Technologies, Applications, and MarketsUltra-wideband's exceptional capacity and power characteristics make it one of this generation's most exciting technologies. From wireless communications to entertainment, and from the automotive industry to homeland security, UWB is poised to revolutionize an extraordinary array of applications. Now, one of the field's leading experts presents the most accessible and up-to-date UWB guidebook ever written.Dr. Faranak Nekoogar explains UWB principles and technologies simply and clearly, addressing key issues such as pulse generation, modulation, multiple access techniques, and interference. In addition, she presents a complete market analysis--identifying the most promising applications, initial and future markets, and regulatory trends.Ultra-Wideband Communications: Fundamentals and Applications will be indispensable for everyone interested in UWB technology, regardless of their radio frequency experience: engineers, managers, marketers, analysts, purchasing agents, business strategists, journalists, and students alike.Inside you will find An introduction to UWB: history, background, advantages, and challenges How UWB compares to narrowband and spread-spectrum wideband systems Fundamentals of UWB short-pulse generation and propagation Competing single-band and multiband approaches UWB antenna concepts and their implications for systems and networks Popular modulation/demodulation schemes and multiple-access techniques Coexistence with today's WLAN, GPS, and cellular phone systems Current and evolving FCC and worldwide regulation of UWB technology In-depth coverage of UWB applications and markets, with adoption timelines and forecasts through 2010 A comprehensive, easy-to-understand glossary and extensive references for further reading
Animating and sustaining niche social networks

Within the communicative space online Social Network Sites (SNS) afford, Niche Social Networks Sites (NSNS) have emerged around particular geographic, demographic or topic-based communities to provide what broader SNS do not: specified and targeted content for an engaged and interested community. Drawing on a research project developed at the Queensland University of Technology in conjunction with the Australian Smart Services Cooperative Research Centre that produced an NSNS based around Adventure Travel, this paper outlines the main drivers for community creation and sustainability within NSNS. The paper asks what factors motivate users to join and stay with these sites and what, if any, common patterns can be noted in their formation. It also outlines the main barriers to online participation and content creation in NSNS, and the similarities and differences in SNS and NSNS business models. Having built a community of 100 registered members, the staywild.com. au project was a living laboratory, enabling us to document the steps taken in producing a NSNS and cultivating and retaining active contributors. The paper incorporates observational analysis of user-generated content (UGC) and user profile submissions, statistical analysis of site usage, and findings from a survey of our membership pool in noting areas of success and of failure. In drawing on our project in this way we provide a template for future iterations of NSNS initiation and development across various other social settings: not only niche communities, but also the media and advertising with which they engage and interact. Positioned within the context of online user participation and UGC research, our paper concludes with a discussion of the ways in which the tools afforded by NSNS extend earlier understandings of online ‘communities of interest’. It also outlines the relevance of our research to larger questions about the diversity of the social media ecology.
Advanced glycation and type 1 diabetes

This dissertation studies the connection between the glycation of proteins and type 1 diabetes-related complications, among which cardiovascular diseases. Several determinants of the glycation of proteins were related to cardiovascular diseases in type 1 diabetes. The main conclusion is that the glycation of proteins is a mechanism that can lead to complications in type 1 diabetes. With the observed connections the research creates perspectives for prevention or treatment of type 1 diabetes-related complications.
Cross-layer design of all-optical networks incorporating crosstalk effects

The performance of current optical networks is inherently limited by the speed of electronic components, and especially the electronic switches; a new generation of optical networks, referred to as all-optical networks, overcome this limitation by switching data entirely optically using all-optical crossconnects (OXCs). However, all-optical networks are prone to phenomena that are unknown to current optical networks. For instance, OXCs are subject to optical leaks, resulting in unwanted components called node crosstalk being added to transmitted signals. Node crosstalk is propagated over long paths without any signal regeneration. We study the interplay between nonlinear fiber and node crosstalk signals over long distance as a source of Quality of Service (QoS) degradation, measured in terms of bit-error rate (BER). We present a crosstalk model for all-optical networks and give exact expressions for the performance degradation resulting from the joint propagation of a signal and node crosstalk in large networks. Realizing that crosstalk can be a serious impairment for proper network operation, we propose to mitigate physical layer impact (including node crosstalk) at call admission time using specifically designed QoS-aware Routing and Wavelength Assignment (RWA) algorithms (a network-layer technique). Our new RWA algorithms choose a route and a wavelength for incoming calls in all-optical networks (viewed as circuit-switched networks) depending on the physical-layer state, making RWA algorithms and all-optical networks design a cross-layer issue. We show that our new RWA algorithms outperform traditional RWA algorithms while exhibiting additional interesting properties, such as enhancing the fairness among the users in the network. Our RWA algorithms are evaluated with simulations on realistic large-scale metropolitan and regional network topologies. To decrease the time to evaluate QoS-aware RWA algorithms, we also present an analytical technique to evaluate the performance of a class of RWA algorithms incorporating multiple physical layer impairments including node crosstalk. Our analytical technique is shown by simulation on various network topologies to model accurately all-optical network behavior.