Microfluidic platforms for the characterization of in meso membrane protein crystallization

Membrane proteins, which reside in the membranes of cells, play a critical role in many important biological processes including cellular signaling, immune response, and material and energy transduction. Because of their key role in maintaining the environment within cells and facilitating intercellular interactions, understanding the function of these proteins is of tremendous medical and biochemical significance. Indeed, the malfunction of membrane proteins has been linked to numerous diseases including diabetes, cirrhosis of the liver, cystic fibrosis, cancer, Alzheimer's disease, hypertension, epilepsy, cataracts, tubulopathy, leukodystrophy, Leigh syndrome, anemia, sensorineural deafness, and hypertrophic cardiomyopathy.1-3 However, the structure of many of these proteins and the changes in their structure that lead to disease-related malfunctions are not well understood. Additionally, at least 60% of the pharmaceuticals currently available are thought to target membrane proteins, despite the fact that their exact mode of operation is not known.4-6 Developing a detailed understanding of the function of a protein is achieved by coupling biochemical experiments with knowledge of the structure of the protein. Currently the most common method for obtaining three-dimensional structure information is X-ray crystallography. However, no a priori methods are currently available to predict crystallization conditions for a given protein.7-14 This limitation is currently overcome by screening a large number of possible combinations of precipitants, buffer, salt, and pH conditions to identify conditions that are conducive to crystal nucleation and growth.7,9,11,15-24 Unfortunately, these screening efforts are often limited by difficulties associated with quantity and purity of available protein samples. While the two most significant bottlenecks for protein structure determination in general are the (i) obtaining sufficient quantities of high quality protein samples and (ii) growing high quality protein crystals that are suitable for X-ray structure determination,7,20,21,23,25-47 membrane proteins present additional challenges. For crystallization it is necessary to extract the membrane proteins from the cellular membrane. However, this process often leads to denaturation. In fact, membrane proteins have proven to be so difficult to crystallize that of the more than 66,000 structures deposited in the Protein Data Bank,48 less than 1% are for membrane proteins, with even fewer present at high resolution (< 2Å)4,6,49 and only a handful are human membrane proteins.49 A variety of strategies including detergent solubilization50-53 and the use of artificial membrane-like environments have been developed to circumvent this challenge.43,53-55 In recent years, the use of a lipidic mesophase as a medium for crystallizing membrane proteins has been demonstrated to increase success for a wide range of membrane proteins, including human receptor proteins.54,56-62 This in meso method for membrane protein crystallization, however, is still by no means routine due to challenges related to sample preparation at sub-microliter volumes and to crystal harvesting and X-ray data collection. This dissertation presents various aspects of the development of a microfluidic platform to enable high throughput in meso membrane protein crystallization at a level beyond the capabilities of current technologies. Microfluidic platforms for protein crystallization and other lab-on-a-chip applications have been well demonstrated.9,63-66 These integrated chips provide fine control over transport phenomena and the ability to perform high throughput analyses via highly integrated fluid networks. However, the development of microfluidic platforms for in meso protein crystallization required the development of strategies to cope with extremely viscous and non-Newtonian fluids. A theoretical treatment of highly viscous fluids in microfluidic devices is presented in Chapter 3, followed by the application of these strategies for the development of a microfluidic mixer capable of preparing a mesophase sample for in meso crystallization at a scale of less than 20 nL in Chapter 4. This approach was validated with the successful on chip in meso crystallization of the membrane protein bacteriorhodopsin. In summary, this is the first report of a microfluidic platform capable of performing in meso crystallization on-chip, representing a 1000x reduction in the scale at which mesophase trials can be prepared. Once protein crystals have formed, they are typically harvested from the droplet they were grown in and mounted for crystallographic analysis. Despite the high throughput automation present in nearly all other aspects of protein structure determination, the harvesting and mounting of crystals is still largely a manual process. Furthermore, during mounting the fragile protein crystals can potentially be damaged, both from physical and environmental shock. To circumvent these challenges an X-ray transparent microfluidic device architecture was developed to couple the benefits of scale, integration, and precise fluid control with the ability to perform in situ X-ray analysis (Chapter 5). This approach was validated successfully by crystallization and subsequent on-chip analysis of the soluble proteins lysozyme, thaumatin, and ribonuclease A and will be extended to microfluidic platforms for in meso membrane protein crystallization. The ability to perform in situ X-ray analysis was shown to provide extremely high quality diffraction data, in part as a result of not being affected by damage due to physical handling of the crystals. As part of the work described in this thesis, a variety of data collection strategies for in situ data analysis were also tested, including merging of small slices of data from a large number of crystals grown on a single chip, to allow for diffraction analysis at biologically relevant temperatures. While such strategies have been applied previously,57,59,61,67 they are potentially challenging when applied via traditional methods due to the need to grow and then mount a large number of crystals with minimal crystal-to-crystal variability. The integrated nature of microfluidic platforms easily enables the generation of a large number of reproducible crystallization trials. This, coupled with in situ analysis capabilities has the potential of being able to acquire high resolution structural data of proteins at biologically relevant conditions for which only small crystals, or crystals which are adversely affected by standard cryocooling techniques, could be obtained (Chapters 5 and 6). While the main focus of protein crystallography is to obtain three-dimensional protein structures, the results of typical experiments provide only a static picture of the protein. The use of polychromatic or Laue X-ray diffraction methods enables the collection of time resolved structural information. These experiments are very sensitive to crystal quality, however, and often suffer from severe radiation damage due to the intense polychromatic X-ray beams. Here, as before, the ability to perform in situ X-ray analysis on many small protein crystals within a microfluidic crystallization platform has the potential to overcome these challenges. An automated method for collecting a "single-shot" of data from a large number of crystals was developed in collaboration with the BioCARS team at the Advanced Photon Source at Argonne National Laboratory (Chapter 6). The work described in this thesis shows that, even more so than for traditional structure determination efforts, the ability to grow and analyze a large number of high quality crystals is critical to enable time resolved structural studies of novel proteins. In addition to enabling X-ray crystallography experiments, the development of X-ray transparent microfluidic platforms also has tremendous potential to answer other scientific questions, such as unraveling the mechanism of in meso crystallization. For instance, the lipidic mesophases utilized during in meso membrane protein crystallization can be characterized by small angle X-ray diffraction analysis. Coupling in situ analysis with microfluidic platforms capable of preparing these difficult mesophase samples at very small volumes has tremendous potential to enable the high throughput analysis of these systems on a scale that is not reasonably achievable using conventional sample preparation strategies (Chapter 7). In collaboration with the LS-CAT team at the Advanced Photon Source, an experimental station for small angle X-ray analysis coupled with the high quality visualization capabilities needed to target specific microfluidic samples on a highly integrated chip is under development. Characterizing the phase behavior of these mesophase systems and the effects of various additives present in crystallization trials is key for developing an understanding of how in meso crystallization occurs. A long term goal of these studies is to enable the rational design of in meso crystallization experiments so as to avoid or limit the need for high throughput screening efforts. In summary, this thesis describes the development of microfluidic platforms for protein crystallization with in situ analysis capabilities. Coupling the ability to perform in situ analysis with the small scale, fine control, and the high throughput nature of microfluidic platforms has tremendous potential to enable a new generation of crystallographic studies and facilitate the structure determination of important biological targets. The development of platforms for in meso membrane protein crystallization is particularly significant because they enable the preparation of highly viscous mixtures at a previously unachievable scale. Work in these areas is ongoing and has tremendous potential to improve not only current the methods of protein crystallization and crystallography, but also to enhance our knowledge of the structure and function of proteins which could have a significant scientific and medical impact on society as a whole. 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THE RELATIVE SIGNIFICANCE OF SYNTACTIC KNOWLEDGE AND VOCABULARY KNOWLEDGE IN SECOND LANGUAGE LISTENING COMPREHENSION

The main purpose of the current study was to examine the role of vocabulary knowledge (VK) and syntactic knowledge (SK) in L2 listening comprehension, as well as their relative significance. Unlike previous studies, the current project employed assessment tasks to measure aural and proceduralized VK and SK. In terms of VK, to avoid under-representing the construct, measures of both breadth (VB) and depth (VD) were included. Additionally, the current study examined the role of VK and SK by accounting for individual differences in two important cognitive factors in L2 listening: metacognitive knowledge (MK) and working memory (WM). Also, to explore the role of VK and SK more fully, the current study accounted for the negative impact of anxiety on WM and L2 listening. The study was carried out in an English as a Foreign Language (EFL) context, and participants were 263 Iranian learners at a wide range of English proficiency from lower-intermediate to advanced. Participants took a battery of ten linguistic, cognitive and affective measures. Then, the collected data were subjected to several preliminary analyses, but structural equation modeling (SEM) was then used as the primary analysis method to answer the study research questions. Results of the preliminary analyses revealed that MK and WM were significant predictors of L2 listening ability; thus, they were kept in the main SEM analyses. The significant role of WM was only observed when the negative effect of anxiety on WM was accounted for. Preliminary analyses also showed that VB and VD were not distinct measures of VK. However, the results also showed that if VB and VD were considered separate, VD was a better predictor of L2 listening success. The main analyses of the current study revealed a significant role for both VK and SK in explaining success in L2 listening comprehension, which differs from findings from previous empirical studies. However, SEM analysis did not reveal a statistically significant difference in terms of the predictive power of the two linguistic factors. Descriptive results of the SEM analysis, along with results from regression analysis, indicated to a more significant role for VK.

Elucidating the interactions between the adhesive and transcriptioanl functions of beta-catenin in normal and cancerous cells

Wnt signalling is involved in a wide range of physiological and pathological processes. The presence of an extracellular Wnt stimulus induces cytoplasmic stabilisation and nuclear translocation of beta-catenin, a protein that also plays an essential role in cadherin-mediated adhesion. Two main hypotheses have been proposed concerning the balance between beta-catenin's adhesive and transcriptional functions: either beta-catenin's fate is determined by competition between its binding partners, or Wnt induces folding of beta-catenin into a conformation allocated preferentially to transcription. The experimental data supporting each hypotheses remain inconclusive. In this paper we present a new mathematical model of the Wnt pathway that incorporates beta-catenin's dual function. We use this model to carry out a series of in silico experiments and compare the behaviour of systems governed by each hypothesis. Our analytical results and model simulations provide further insight into the current understanding of Wnt signalling and, in particular, reveal differences in the response of the two modes of interaction between adhesion and signalling in certain in silico settings. We also exploit our model to investigate the impact of the mutations most commonly observed in human colorectal cancer. Simulations show that the amount of functional APC required to maintain a normal phenotype increases with increasing strength of the Wnt signal, a result which illustrates that the environment can substantially influence both tumour initiation and phenotype.

Modele niepełnosprawności jako determinanty przeobrażeń struktury podażowej rynku turystycznego dostępnego dla osób niepełnosprawnych

The research aims to answer a fundamental question: which of the disability models currently in use is optimal for creating “accessible tourism-oriented” amenities, as well as more detailed problems: (1) what is disability and what determines different disability models? (2) what types of tourism market supply available for the disabled do the different disability models suggest? (3) are the disability models complementary or mutually exclusive? (4) is the idea of social integration and inclusion of people with disabilities (PWD) while on tourist trips supported of the society? Data sources comprise selected literature and results of a survey conducted using the face-to-face method and the SurveyMonkey website from May 2013 to July 2014. The surveyed group included 619 people (82% were Polish, the other 18% were foreigners from: Russia, Germany, Portugal, Slovakia, Canada, Tunisia and the United Kingdom). The research showed that the different disability models – medical, social, geographical and economic – are useful when creating the tourism supply for the PWD. Using the research results, the authors suggested a model of “diversification of tourism market supply structure available for the disabled”, which includes different types of supply – from specialist to universal. This model has practical usage and can help entrepreneurs with the segmentation of tourism offers addressed to the PWD. The work is innovative, both in its theoretical approach (the review of disability models and their practical application in creating tourism supply) and empirical values – it provides current data for the social attitude towards the development of PWD tourism. Especially the presentation of a wide range of perception of disability as well as the simple classification of tourism supply that meets the varied needs of PWD, is a particular novelty of this chapter.

Objectives for management of socio-ecological systems in the Great Barrier Reef region, Australia

A wide range of goals and objectives have to be taken into account in natural resources management. Defining these objectives in operational terms, including dimensions such as sustainability, productivity, and equity, is by no means easy, especially if they must capture the diversity of community and stakeholder values. This is especially true in the coastal zone where land activities affect regional marine ecosystems. In this study, the aim was firstly to identify and hierarchically organise the goals and objectives for coastal systems, as defined by local stakeholders. Two case study areas are used within the Great Barrier Reef region being Mackay and Bowen–Burdekin. Secondly, the aim was to identify similarities between the case study results and thus develop a generic set of goals to be used as a starting point in other coastal communities. Results show that overarching high-level goals have nested sub-goals that contain a set of more detailed regional objectives. The similarities in high-level environmental, governance, and socio-economic goals suggest that regionally specific objectives can be developed based on a generic set of goals. The prominence of governance objectives reflects local stakeholder perceptions that current coastal zone management is not achieving the outcomes they feel important and that there is a need for increased community engagement and co-management. More importantly, it raises the question of how to make issues relevant for the local community and entice participation in the local management of public resources to achieve sustainable environmental, social, and economic management outcomes. © 2015 Springer-Verlag Berlin Heidelberg

Slot Film Cooling: A Comprehensive Experimental Characterization

When components of a propulsion system are exposed to elevated flow temperatures there is a risk for catastrophic failure if the components are not properly protected from the thermal loads. Among several strategies, slot film cooling is one of the most commonly used, yet poorly understood active cooling techniques. Tangential injection of a relatively cool fluid layer protects the surface(s) in question, but the turbulent mixing between the hot mainstream and cooler film along with the presence of the wall presents an inherently complex problem where kinematics, thermal transport and multimodal heat transfer are coupled. Furthermore, new propulsion designs rely heavily on CFD analysis to verify their viability. These CFD models require validation of their results, and the current literature does not provide a comprehensive data set for film cooling that meets all the demands for proper validation, namely a comprehensive (kinematic, thermal and boundary condition data) data set obtained over a wide range of conditions. This body of work aims at solving the fundamental issue of validation by providing high quality comprehensive film cooling data (kinematics, thermal mixing, heat transfer). 3 distinct velocity ratios (VR=uc/u∞) are examined corresponding to wall-wake (VR~0.5), min-shear (VR ~ 1.0), and wall-jet (VR~2.0) type flows at injection, while the temperature ratio TR= T∞/Tc is approximately 1.5 for all cases. Turbulence intensities at injection are 2-4% for the mainstream (urms/u∞, vrms/u∞,), and on the order of 8-10% for the coolant (urms/uc, vrms/uc,). A special emphasis is placed on inlet characterization, since inlet data in the literature is often incomplete or is of relatively low quality for CFD development. The data reveals that min-shear injection provides the best performance, followed by the wall-jet. The wall-wake case is comparably poor in performance. The comprehensive data suggests that this relative performance is due to the mixing strength of each case, as well as the location of regions of strong mixing with respect to the wall. Kinematic and thermal data show that strong mixing occurs in the wall-jet away from the wall (y/s>1), while strong mixing in the wall-wake occurs much closer to the wall (y/s<1). Min-shear cases exhibit noticeably weaker mixing confined to about y/s=1. Additionally to these general observations, the experimental data obtained in this work is analyzed to reveal scaling laws for the inlets, near-wall scaling, detecting and characterizing coherent structures in the flow as well as to provide data reduction strategies for comparison to CFD models (RANS and LES).

Study of led lamps technologies impact on the utility

With the growing interest in the issue of reducing powerconsumption in electricity applications, energy-saving devises and the problem of their operation gains more attention. The increase in the utilization of energy-saving lamps, especially LED lamps, leads to the wide interest in their influence on the power system. The impact of discussed devices on the voltage and current in the grid must be thoroughly studied before launching devices into the market. The studies undertaken on the LED lamps present in a wide range the issue of harmonic emission from lamps and their influence on power quality. Due to many anufacturing technologies, different LED devices can have various effects on the utility. It is significant to carry out researches concerning the adverse effects of energy-saving lamps in order to utilize devices that meet certain requirements which are set by the international commissions.

Africans in Scotland: heterogeneity and sensitivities to HIV

Aim: To investigate how diversity within the African migrant population in Scotland affects their understandings of HIV and uptake of HIV testing and treatment, in order to improve HIV-related outcomes. Background: In the UK, Africans have the worst outcomes for HIV infection, primarily due to late diagnosis. Improvement requires better understanding of the barriers to healthcare engagement. This PhD study investigates how diversity among first generation African migrants in Scotland could affect engagement with general healthcare and HIV related interventions and services. Methods: I conducted qualitative research, involving participant observation at two sites (an African religious group and an asylum seeker/refugee drop-in centre) and interviews with African migrants attending these and three additional sites (two advocacy charities and a student association). Data were collected in two cities (Glasgow and Edinburgh) and two smaller towns (Paisley and Kirkcaldy). I interviewed 27 Africans, including economic migrants (n=8), students (n=9) and asylum seeker/refugees (n=10) and 14 representatives from organisations with high levels of African attendees (e.g., country associations, community organisations, advocacy groups, commercial establishments and religious based organisations). Thematic data analysis was carried out. Results: Diversity of the population and related issues of identity: Participants were highly diverse and reported considerable heterogeneity in the African diaspora in Scotland. The identity of “African” was bound with various negative stereotypes and appeals to this identity did not necessarily have relevance for participants. Nature of African affiliated organisations in Scotland: There were a wide range of organisations that advertised their remit as catering for the African diaspora. They varied in consistency and sustainability and contributed towards healthcare engagement to different degrees. Engagement with healthcare: There were multiple experiences and understandings of the healthcare system within the sample as a whole, and to an extent by migrant type. Whilst the majority reported successful and satisfactory service use, distinct barriers emerged. These included: understandings of rights and access to care based on African models of healthcare; the interplay of religious based understandings with ideas about access to healthcare; and assumptions and anxiety about the connections between visa status and health status. Knowledge of HIV and engagement with HIV related services: Participants had good knowledge about HIV, with some notable exceptions, but there was no patterning by migrant type. They had diverse views about risk of HIV infection, most of which did not align with the HIV epidemiology that identifies African migrants as an at risk group. Most of the sample did not think targeting African migrants for HIV interventions would be successful and were hostile to the proposal for various reasons, especially because they believed it would perpetuate stigma and prejudice towards the African diaspora. There were mixed experiences of HIV related services, and prompts to test for HIV had elicited a range of reactions, the majority negative. Conclusion: Diversity within the African diaspora in Scotland should be taken into account to improve the salience and relevance of future HIV interventions. Attitudes towards current HIV testing promotion suggest that a more cooperative approach could be taken with African communities to build on existing relationships of trust and understandings of HIV.

Application of an online-biomass sensor in an optical multisensory platform prototype for growth monitoring of biotechnical relevant microorganism and cell lines in single-use shake flasks

In the context of this work we evaluated a multisensory, noninvasive prototype platform for shake flask cultivations by monitoring three basic parameters (pH, pO2 and biomass). The focus lies on the evaluation of the biomass sensor based on backward light scattering. The application spectrum was expanded to four new organisms in addition to E. coli K12 and S. cerevisiae [1]. It could be shown that the sensor is appropriate for a wide range of standard microorganisms, e.g., L. zeae, K. pastoris, A. niger and CHO-K1. The biomass sensor signal could successfully be correlated and calibrated with well-known measurement methods like OD600, cell dry weight (CDW) and cell concentration. Logarithmic and Bleasdale-Nelder derived functions were adequate for data fitting. Measurements at low cell concentrations proved to be critical in terms of a high signal to noise ratio, but the integration of a custom made light shade in the shake flask improved these measurements significantly. This sensor based measurement method has a high potential to initiate a new generation of online bioprocess monitoring. Metabolic studies will particularly benefit from the multisensory data acquisition. The sensor is already used in labscale experiments for shake flask cultivations.

Trabalho temporário e qualidade dos serviços prestados: reflexão sobre a evolução recente na região de Setúbal

Os conceitos de qualidade e capital humano são amplamente conhecidos e a sua importância aceite por todos. A aplicação destes pressupostos à realidade do trabalho temporário, tomou-se um imperativo face ao contexto económico actual, repleto de rápidas mudanças organizacionais, caracterizado por colaboradores detentores de um novo leque de competências e flexibilidade profissional. Ao longo deste trabalho. procurou-se analisar a possível integração do trabalho temporário num novo modelo de relações laborais, na tentativa de distanciamento da corrente associação do trabalho temporário a uma "forma atípica de trabalho'', estabelecendo ainda uma breve evolução do trabalho temporário na Península de Setúbal. baseada na apreciação de trabalhos análogos. Em resultado da aplicação de questionário. definiu-se uma hierarquia de características individuais e organizacionais, como critério válido para um futuro processo de recrutamento e selecção, permitindo averiguar, ao nível do individuo, um aumento de competências profissionais e técnicas, acompanhado pelo incremento de formação e experiência profissional. Concluindo ao nível organizacional que qualidades como flexibilidade e dinamismo, aliado à experiência profissional, são factores críticos no processo de recrutamento e selecção, sendo imprescindíveis na procura contínua da qualidade, facilitando o alcance da excelência individual e organizacional. ABSTRACT: Quality and Human Capital are widely know concepts and their importance is accepted by all. Therefore, it has become imperative to make use of them in the contex t of temporary work given the current economic situation for they are present wherever organizational change happens rapidly and stakeholders possess a wide range of professional competencies and flexibility. The aim of this work is to study the possible integration of temporary work into a new model for labour relations, in an effort to distance temporay work from the notion of "atypical form of work" with which it is presently associated. Moreover, it presents a brief evolution of temporary work in the Peninsula of Setúbal, based on the analiysis of similar works. The findings obtained from our surveys ena bled us to define a hierarchy of individual and organizational characteristics which can serve as valid criteria in future recruitment and selection processes. With these processes it is al so possible to assess any increase of professional and technical competencies regarding the individual as well improvement as regards training and professional experience. At the organizational level, qualities such as nexibility and dynamism, together with professional experience, turned out to be critical factors in the recruitment and selection process. Not only are they indispensable in the constant pursuit of quality, but they also make it easy to achieve individual and organizational excellence.

SEQUENTIAL DECISIONS AND PREDICTIONS IN NATURAL LANGUAGE PROCESSING

Natural language processing has achieved great success in a wide range of ap- plications, producing both commercial language services and open-source language tools. However, most methods take a static or batch approach, assuming that the model has all information it needs and makes a one-time prediction. In this disser- tation, we study dynamic problems where the input comes in a sequence instead of all at once, and the output must be produced while the input is arriving. In these problems, predictions are often made based only on partial information. We see this dynamic setting in many real-time, interactive applications. These problems usually involve a trade-off between the amount of input received (cost) and the quality of the output prediction (accuracy). Therefore, the evaluation considers both objectives (e.g., plotting a Pareto curve). Our goal is to develop a formal understanding of sequential prediction and decision-making problems in natural language processing and to propose efficient solutions. Toward this end, we present meta-algorithms that take an existent batch model and produce a dynamic model to handle sequential inputs and outputs. Webuild our framework upon theories of Markov Decision Process (MDP), which allows learning to trade off competing objectives in a principled way. The main machine learning techniques we use are from imitation learning and reinforcement learning, and we advance current techniques to tackle problems arising in our settings. We evaluate our algorithm on a variety of applications, including dependency parsing, machine translation, and question answering. We show that our approach achieves a better cost-accuracy trade-off than the batch approach and heuristic-based decision- making approaches. We first propose a general framework for cost-sensitive prediction, where dif- ferent parts of the input come at different costs. We formulate a decision-making process that selects pieces of the input sequentially, and the selection is adaptive to each instance. Our approach is evaluated on both standard classification tasks and a structured prediction task (dependency parsing). We show that it achieves similar prediction quality to methods that use all input, while inducing a much smaller cost. Next, we extend the framework to problems where the input is revealed incremen- tally in a fixed order. We study two applications: simultaneous machine translation and quiz bowl (incremental text classification). We discuss challenges in this set- ting and show that adding domain knowledge eases the decision-making problem. A central theme throughout the chapters is an MDP formulation of a challenging problem with sequential input/output and trade-off decisions, accompanied by a learning algorithm that solves the MDP.

Tecnología Nanopore para la secuenciación de DNA

Nanopore-based sequencer will open the path to the fourth-generation DNA sequencing technology. The main differences between this technique and the previous ones are: DNA molecule that will be sequenced does not need a previous amplification step, is not necessary any type of specific label both molecular adaptors, and it has been abolished enzymatic process in the nucleotide sequence identification event. These differences have as result a more economic method since don’t spend the necessary reagents for the previous techniques, furthermore it lets to sequence samples with a low DNA concentration. This technique is based in the use of a membrane with a biologic nanopore inserted in it whereby the molecule to analyze (analyte) it made to pass, this membrane is placed between two reservoirs containing ions, when an external volatage is applied in both sides this lead to an ion current through the nanopore. When an analyte cross the nanopore the ion current is modified, that modification in the amplitude and duration of ion current determine the physical and chemical properties of that analyte. By means of subsequent statistical analyzes it can be determined to what sequence own this ion current blockade patterns. More used nanopores are the biologic ones, although they are working to develop synthetic nanopores. The main biologic nanopores are: α-Hemolysin from Staphylococcus aureus (α-HL), Mycobacterium smegmatis porin A (MspA) and bacteriophage phi29 pore (phi29). Α-HL and MspA have in their narrowest point a diameter similar to nucleotide size, they are functional at high temperature both wide range of pH (2-12) but MspA is able to read four nucleotide at the same time while α- HL just can read one by one. Finally, phi29 present a bigger diameter what let to get information about DNA spatial conformation and their interaction with proteins (Feng et al., 2015). Nowaday Oxford Nanopore Technologies (ONT) is the only company which has developed Nanopore technology; they have two devices available to sequencing (PromethION and MinION). The MinION is a single-use DNA sequencing device with the size of a USB memory with a total of 3000 nanopores that can sequence until 200kb. The PrometheION is big size sequencer that own 48 different cells, what let to sequence different samples at the same time, with a total of 144.000 nanopores and reading of several megabases (https://www.nanoporetech.com/). The high processivity and low cost become this technique in a great option to massive- sequencing.

Thin films of Cu, In and Sb chalcogenides as photovoltaic absorbers

Many different photovoltaic technologies are being developed for large-scale solar energy conversion such as crystalline silicon solar cells, thin film solar cells based on a-Si:H, CIGS and CdTe. As the demand for photovoltaics rapidly increases, there is a pressing need for the identification of new visible light absorbing materials for thin-film solar cells. Nowadays there are a wide range of earth-abundant absorber materials that have been studied around the world by different research groups. The current thin film photovoltaic market is dominated by technologies based on the use of CdTe and CIGS, these solar cells have been made with laboratory efficiencies up to 19.6% and 20.8% respectively. However, the scarcity and high cost of In, Ga and Te can limit in the long-term the production in large scale of photovoltaic devices. On the other hand, quaternary CZTSSe which contain abundant and inexpensive elements like Cu, Zn, Sn, S and Se has been a potential candidate for PV technology having solar cell efficiency up to 12.6%, however, there are still some challenges that must be accomplished for this material. Therefore, it is evident the need to find the alternative inexpensive and earth abundant materials for thin film solar cells. One of these alternatives is copper antimony sulfide(CuSbS2) which contains abundant and non-toxic elements which has a direct optical band gap of 1.5 eV, the optimum value for an absorber material in solar cells, suggesting this material as one among the new photovoltaic materials. This thesis work focuses on the preparation and characterization of In6Se7, CuSbS2 and CuSb(S1-xSex)2 thin films for their application as absorber material in photovoltaic structures using two stage process by the combination of chemical bath deposition and thermal evaporation.

Evaluation of the conductor-like screening model for real solvents for the prediction of the water activity coefficient at infinite dilution in ionic liquids

Ionic liquids (ILs) have attracted great attention, from both industry and academia, as alternative fluids for very different types of applications. The large number of cations and anions allow a wide range of physical and chemical characteristics to be designed. However, the exhaustive measurement of all these systems is impractical, thus requiring the use of a predictive model for their study. In this work, the predictive capability of the conductor-like screening model for real solvents (COSMO-RS), a model based on unimolecular quantum chemistry calculations, was evaluated for the prediction water activity coefficient at infinite dilution, gamma(infinity)(w), in several classes of ILs. A critical evaluation of the experimental and predicted data using COSMO-RS was carried out. The global average relative deviation was found to be 27.2%, indicating that the model presents a satisfactory prediction ability to estimate gamma(infinity)(w) in a broad range of ILs. The results also showed that the basicity of the ILs anions plays an important role in their interaction with water, and it considerably determines the enthalpic behavior of the binary mixtures composed by Its and water. Concerning the cation effect, it is possible to state that generally gamma(infinity)(w) increases with the cation size, but it is shown that the cation-anion interaction strength is also important and is strongly correlated to the anion ability to interact with water. The results here reported are relevant in the understanding of ILs-water interactions and the impact of the various structural features of its on the gamma(infinity)(w) as these allow the development of guidelines for the choice of the most suitable lLs with enhanced interaction with water.

Spotter: towards a unified search interface in IDEs

Program comprehension requires developers to reason about many kinds of highly interconnected software entities. Dealing with this reality prompts developers to continuously intertwine searching and navigation. Nevertheless, most integrated development environments (IDEs) address searching by means of many disconnected search tools, making it difficult for developers to reuse search results produced by one search tool as input for another search tool. This forces developers to spend considerable time manually linking disconnected search results. To address this issue we propose Spotter, a model for expressing and combining search tools in a unified way. The current implementation shows that Spotter can unify a wide range of search tools. More information about Spotter can be found at scg.unibe.ch/research/moldablespotter