Miracle-dz/UniFAR-FTUs huggingface dataset:
THESIS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY Bayesian inference for detection problems in biology

This thesis is about different kinds of detection problems in biology: detection of DNA sequences in crime scene samples, detection of harmful bacteria in feed and food stuff and detection of epidemical diseases in animal populations. In each case, biological data is produced or collected in order to determine which DNA sequences, bacteria types or diseases are present, if any. However, the state of nature will often remain uncertain due to limited amounts of samples, low quality samples and imperfect methods for detection and classification. For correct and efficient interpretation of such data it is therefore often necessary to use statistical methods, taking the different sources of uncertainty into account. Several Bayesian models for analysis of such data, for determining the performance of detection methods, and for deciding on the optimal analysis procedure are developed and implemented. In paper I of this thesis it is investigated how the quality in forensic DNA profiles, such as allele dropout rates, changes with different analysis settings, and how the results depend on features in the DNA sample, such as the DNA concentration and marker type. Regression models are developed and the better analysis setting is determined. In paper II Bayesian decision theory is used to determine the optimal forensic DNA analysis procedure, after the DNA concentration and level of degradation in the sample have been estimated. It is assumed the alternatives for DNA analysis are 1) using a standard assay, 2) using the standard assay and a complementary assay, or 3) the analysis is cancelled. In paper III detection models for bacteria are developed. It is shown how heterogeneous experimental data can be used to learn about the sensitivity of detection methods for specific bacteria types, such as Bacillus anthracis. As exemplified in the paper, such results are useful e.g. when evaluating negative analysis results. Finally, in paper IV a Bayesian method for early detection of disease outbreaks in animal populations is developed and implemented. Based on reported neurological syndromes in horses, connected e.g. with the West Nile Virus, the probability of an outbreak is computed using a Gibbs sampling procedure.
A review on experimental investigations of peat stabilization.

Thorough experimental investigation of stabilized peat is of great importance in order to formulate an effective mix design that can be applied for deep peat stabilization, which forms economical deep foundation for supporting highway embankments and light structures constructed on deep peat ground. Unsuitable and inadequate binders mixed with peat was often found to be the main reason for the failure in the formation of high strength stabilized peat columns. Since the properties of peat differ from location to location, reactivity of peat to a binder to form high strength stabilized peat is very site specific and requires detail laboratory mix design investigation. Despite of that, not much research is done on stabilized peat mainly because peat is problema tic due to its high organic content. Consequently, it is not easy to stabilize the soil as the soil is highly acidic and stabilization of peat with cement only is often unsucessful due to insufficient binder dosage resulting in the retardation of hydration and secondary pozzolanic reactions in the stabilized soil. In order to develop a proper understanding on the reactivity of peat with various types of binder, this paper reviews the results of experimental investigation of stabilized peats developed by some researchers.
THE ANALYSIS OF RECIRCULATION ZONE AND IGNITION POSITION OF NON-PREMIXED BLUFF-BODY FOR BIOGAS MILD COMBUSTION

Combustion ignition study is important due to the combustion process becoming more lean and efficient. This paper studied the recirculation zone and ignition location for the bluff-body non-premixed MILD burner with biogas used as fuel. The location of the ignition was critical to ensure the spark energy supply during the ignition process is successful ignite the mixture of air and fuel. The numerical calculations were done using the commercial code ANSYS-Fluent to simulate the furnace with bluff-body burner to determine the recirculation zone. The turbulence model used was the realizable k-e model. The inner recirculation zone between the air and fuel nozzle is the best location for the ignition point since low velocity of air and fuel mixing will assist the ignition process. This is because the ignition energy will have time to ignite the mixture in the low speed of turbulent swirl flow. The most suitable location with the highest possibility of ignition is the centre of the recirculation zone.
Trends and regime shifts in climatic conditions and river runoff in Estonia during 1951–2015

Abstract. Time series of monthly, seasonal and annual mean air temperature, precipitation, snow cover duration and specific runoff of rivers in Estonia are analysed for detecting of trends and regime shifts during 1951–2015. Trend analysis is realised using the Mann–Kendall test and regime shifts are detected with the Rodionov test (sequential t-test analysis of regime shifts). The results from Estonia are related to trends and regime shifts in time series of indices of large-scale atmospheric circulation. Annual mean air temperature has significantly increased at all 12 stations by 0.3–0.4 K decade−1. The warming trend was detected in all seasons but with the higher magnitude in spring and winter. Snow cover duration has decreased in Estonia by 3–4 days decade−1. Changes in precipitation are not clear and uniform due to their very high spatial and temporal variability. The most significant increase in precipitation was observed during the cold half-year, from November to March and also in June. A time series of specific runoff measured at 21 stations had significant seasonal changes during the study period. Winter values have increased by 0.4–0.9 L s−1 km−2 decade−1, while stronger changes are typical for western Estonia and weaker changes for eastern Estonia. At the same time, specific runoff in April and May have notably decreased indicating the shift of the runoff maximum to the earlier time, i.e. from April to March. Air temperature, precipitation, snow cover duration and specific runoff of rivers are highly correlated in winter determined by the large-scale atmospheric circulation. Correlation coefficients between the Arctic Oscillation (AO) and North Atlantic Oscillation (NAO) indices reflecting the intensity of westerlies, and the studied variables were 0.5–0.8. The main result of the analysis of regime shifts was the detection of coherent shifts for air temperature, snow cover duration and specific runoff in the late 1980s, mostly since the winter of 1988/1989, which are, in turn, synchronous with the shifts in winter circulation. For example, runoff abruptly increased in January, February and March but decreased in April. Regime shifts in annual specific runoff correspond to the alternation of wet and dry periods. A dry period started in 1964 or 1963, a wet period in 1978 and the next dry period at the beginning of the 21st century.
Analysis of Public Participation in Sustainable Waste Management Practice in Abuja, Nigeria

It is widely accepted that solid waste management is a global problem. This problem is even more pronounced in developing countries such as Nigeria where solid waste management is a major concern. In recent times, however, there has been a concerted effort towards engaging members of the public in solving the waste management crisis. This effort is centred on public participation in sustainable waste management practice across the country. Nevertheless, in Abuja there seems to be low public participation in sustainable wastes and environmental management practice. This paper therefore seeks to investigate the rate of participation in sustainable waste and environmental management activities in Abuja. In order to achieve the aim of the study, the paper relied on a sample of 57 participants to obtain some primary data. The paper employed a mixed method approach with the aid of a questionnaire. The questions were designed to gather data on demographics of the participants, their awareness and attitude to sustainable waste management, the barriers preventing public participation in a sustainable solid waste management and measures that can encourage public participation in sustainable waste management in Abuja. The study revealed that increase funding, provision of recycling collection points, enforcement of laws and policies, the development of effective policies and regulatory framework amongst others are some of the measures that can encourage public participation in sustainable waste management programs in Abuja.
Pro-Poor Mobile Financial Services

There has been significant growth and penetration of mobile financial services across the globe especially in developing countries. The poor are the target customers and beneficiaries of the mobile financial services as it provides the much needed access which formal financial service providers could not. The dominant paradigm is the conventional top-down models such as technology adoption model (TAM) and unified theory of acceptance and use of technology (UTAUT). These theoretical models are mainly based on individual factors such as perceived ease of use, perceived usefulness, perceived credibility and perceived financial cost to study access, adoption and usage of mobile financial services. These conventional top-down models are insufficient in explaining the access, adoption and continued usage of mobile financial services by the poor. The pro-poor perspective is a bottom up approach that seeks to understand the poor specific issues of pro-poor access, adoption and continued usage of mobile financial service by the poor. The pro-poor contextual factors influence the pro-poor access, community factors influence the pro-poor adoption and cultural factors influence the propoor continued usage of mobile financial services by the poor. We establish gaps in literature in the light of the pro-poor perspective and propose an alternative pro-poor conceptual model to better explain the pro-poor access, adoption and continued usage of mobile financial services among the poor. The proposed model could unearth the influence of pro-poor factors and their relationships with pro-poor access, adoption and usage of mobile financial services. Once validated the model could enrich the mobile financial services studies and will be of valuable use by researchers in the field of mobile financial services among poor.
Microquasars: A Galactic-Extragalactic Connection?

Abstract Microquasars are Galactic X-ray binaries which show radio emission from relativistic outflows. Here we argue that the origins of radio emission from microquasars and compact extragalactic radio sources are similar. In particular, both can be explained qualitatively by a model in which shocks are propagating in the relativistic jets. The microquasar GRO J1655–40 is used to illustrate that the spectral evolution of its 1994 radio outburst can be explained by the growth phase of the generalised-shock model, similar to the case of the quasar 3C 273.
A polynomial-time algorithm for LO based on generalized logarithmic barrier functions

We present a polynomial-time primal-dual interior-point algorithm for solving linear optimization (LO) problems, based on generalized logarithmic barrier function. The growth term depends on a parameter p ∈ [0, 1]. The kernel functions are neither self-regular nor strongly convex. The classical logarithmic barrier function occurs if p = 1. The goal of this paper is to investigate such class of kernel functions and to show that the interior-point methods based on these functions have favorable complexity results. In order to achieve these complexity results, several new techniques had to be used for the analysis. Complexity issues are discussed and they are O ( n log n ) , and O (√ n log n ) , for large-update and small-update methods, respectively. Numerical tests show that the iteration bounds are influenced by p. We conclude that a gap still exists between the theoretical complexity and practical behavior of the algorithm. AMS Subject Classification: 90C05, 90C31
FEASIBILITY OF USING WAX BLOCKS TO MEASURE RAT AND POSSUM ABUNDANCE IN NATIVE FOREST

Rats and possums are the predominant pest species in New Zealand forests and forest managers need to know when to control them and the success of control. This requires an accurate and practical census method. Existing census methods using footprint tracking tunnels and traps are time-consuming, which lowers the precision of the measures of pest abundance. We examined the feasibility of using a new census method based on the frequency of rat and possum bite marks in wax blocks. Results showed that rat and possum bite marks could be individually identified and appeared to give realistic estimates of pest abundance when compared to existing census methods.
The preservation of total organic carbon of the Silurian Pridoli strata in the Milaičiai-103 well core of Western Lithuania

The Pridoli series is one of the thickest and most complete stratigraphic intervals of the Silurian as well as other systems of the Lithuanian part of the Baltic sedimentary basin. In this study we present a sequence stratigraphic model of the sedimentary succession in the Milaiciai-103 core section. High resolution trend of concentrations of total organic carbon is presented in the developed stratigraphic context. The variability in the total organic matter amount in different sequence stratigraphic system tracts was statistically evaluated using the generalized linear mixed-effect modeling approach. The statistical analysis revealed that the highest concentrations of total organic carbon in the studied section are expected in a highstand and transgressive system tracts and significantly lower concentrations are expected in a lowstand and falling stage system tracts.
MID TERM EVALUATION OF RDPs IN ITALY: COMPARING MODELS

With the reforms of Structural Funds there has been a considerable tightening of the guiding principles of Community actions. Among these, a primary role has been given to evaluation. In this context, the paper deals with what has been realized for the evaluation of rural development policy, comparing various experiences in Italy with reference to the Rural Development Plans. The aim is to verify, on the basis of (meta) criteria, the methodological contents of the mid term evaluation reports of 14 RDPs in the centre-north of Italy. Through the analyses and the comparisons of these reports, the paper is an attempt to reconstruct the “quality” of the evaluations with specific reference to the methodological aspects, the models and the procedures adopted by the evaluators.
GENERALIZED COHEN-MACAULAY MONOMIAL IDEALS

We give a generalization of Hochster's formula for local cohomolo- gies of square-free monomial ideals to monomial ideals, which are not necessarily square-free. Using this formula, we give combinatorial characterizations of gener- alized Cohen-Macaulay monomial ideals. We also give other applications of the generalized Hochster's formula.
A molecular dynamics investigation of water migration in a lipid bilayer for microalgae drying

Robby Manrique, Aristotle Ubando, Al Rey Villagracia, Jennifer Corpuz, Allan Abraham Padama, Melanie David, Nelson Arboleda Jr.*, Alvin Culaba, and Hideaki Kasai Mechanical Engineering Department, De La Salle University, 2401 Taft Avenue, Malate 1004, Manila, Philippines Physics Department, De La Salle University, 2401 Taft Avenue, Malate 1004, Manila, Philippines Department of Precision Science & Technology and Applied Physics, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
A New System of Contactless Power Transfer with Low Voltage Stress and Parasitic Capacitors Effect

In this paper, a high frequency contactless power transfer (CPT) system is designed with ∅2 inverter drive. This system works in 30MHz frequency and 380W power with low voltage stress and considers the inductive link parasitic capacitor effect. In the design, we formulated the inverter equations first and then suggested another design for the transmitter and the receiver coils as the energy transfer medium. Following the inverter equations, structures of proper coil are designed for a CPT system. The results of the coil and ∅2 inverter designs are implemented as a bipolar circuit model which is equal to considering the inductive link parasitic capacitors. The system characteristics such as the stress, efficiency, mutual induction, field scattering, magnetic field distribution and the parameters’ variations are evaluated along with analysis. The results demonstrate that the presented CPT system has high efficiency, low switching voltage stress, small passive energy storage elements and fast dynamic response.
Colloquium: Quantum interference of clusters and molecules

We review recent progress and future prospects of matter wave interferometry with complex organic molecules and inorganic clusters. Three variants of a near-field interference effect, based on diffraction by material nanostructures, at optical phase gratings, and at ionizing laser fields are considered. We discuss the theoretical concepts underlying these experiments and the experimental challenges. This includes optimizing interferometer designs as well as understanding the role of decoherence. The high sensitivity of matter wave interference experiments to external perturbations is demonstrated to be useful for accurately measuring internal properties of delocalized nanoparticles. We conclude by investigating the prospects for probing the quantum superposition principle in the limit of high particle mass and complexity.
Transfer Function Analysis of Epidemiological Data Un ’ Analisi di Dati Epidemiologici mediante Modelli a Funzione di Trasferimento

Riassunto: Nel presente lavoro si propone l’uso di modelli a funzioni di trasferimento per l’analisi di serie storiche epidemiologiche. La metodologia proposta prevede due fasi: nella prima fase, le serie storiche relative alla risposta ed alle variabili esplicative vengono individualmente depurate dell’effetto di confondimento temporale e meteorologico. Successivamente, si utilizzano le serie dei residui derivanti dalla prima fase per costruire un nuovo modello. In entrambe le fasi, si utilizzano modelli a funzioni di trasferimento selezionati tramite algoritmi genetici. L’utilit à della strategia viene esplorata nel contesto degli studi di associazione inquinamento atmosferico–effetti sulla salute.
Computation of Thermal Conductivity of Gas Diffusion Layers of PEM Fuel Cells

Polymer electrolyte membrane (PEM) fuel cells are promising candidates for automotive applications due to the low operating temperature which allows for relatively short start-up times and the high flexibility of the delivered power. In PEM fuel cells, gas diffusion layers (GDL) – in combination with bipolar plates – are usually employed to distribute the reactants over the electrode surfaces. The GDL has not only the function to provide gas access to the catalyst layer, but also to allow the removal of the product water, to mechanically stabilize the membrane-electrode assembly and to provide electronic and finally also thermal conductivity between catalyst layer and bipolar plate. The thermal conductivity of the GDL plays an important role in the management of the heat transfer in PEM fuel cells and therefore is important for simulation of fuel cell performance and for fuel cell design. While the measurement of thermal conductivity by experimental means is possible, it remains challenging due to the anisotropy and the high porosity and the available experimental data is rather limited. In the following, the numerical computation of effective thermal conductivity of GDLs based on 3D structure data – with spatial resolution on the µm-scale – will be discussed. The 3D structure data is derived using two different approaches: 1) the 3D GDL structure is measured experimentally applying x-ray computed tomography [1, 2]; 2) the 3D GDL structure is simulated by a randomly generated fiber geometry [3]. The computation of thermal conductivity requires the solution of the steady state, purely diffusive three-dimensional heat transfer equation. In the present approach, the convection and radiation transport, as well as thermal contact resistance and phase changes were not taken into account. Usually porous carbon fiber papers or cloths are used as gas diffusion layers and they are infiltrated with polytetrafluoroethylene (PTFE) to improve the GDL's ability to remove product water. Typical carbon fiber diameters are between 5 and 10 µm, typical porosities of GDLs are between 70 and 90 %. The GDL can contain a microporous layer (MPL) to improve the water management within the PEM fuel cell. Commercially available gas diffusion layers were investigated by x-ray computed tomography (CT). This lab-based technique allows for a non-destructive determination of 3D structure with a resolution well below 1 µm. The sample is placed between x-ray source and 2D detector and a projection image of the sample is acquired. This is repeated for different orientations of the sample with respect to the x-ray/detector setup and based on this series of projection images, the 3D structure of the sample is reconstructed. Each voxel has now to be assigned to a certain material in the sample or to air, based on the gray level of the voxel in combination with morphological information.
Assessing Virtual Collaborative Environment performance mediated by web-based conversational mechanisms

The aim of this Work in Progress (WiP) is to assess the effect of using chat and thread discussion on effectiveness of collaboration through Web-Based Collaborative Environments (WBCEs), particularly platform wikis. In order to prove that, this WiP will describe the experiment with four different scenarios that will be conducted in the following days. Each scenario is formed by 16 groups of three random students from Technical studies at the ETSEIAT, an UPC Engineering School, particularly candidates from Industrial and Aeroespace Engineering. Some of the groups will work in face-toface basis (control group) and the others will use the WBCEs. The groups that are using the WBCEs scenario will be using whether the wiki platform only or the wiki platform integrated with an online communication tool (chat or forum). In the last three scenarios, each member will have one computer and the communication among the members of the group will be made through the assigned WBCE. These groups have to deliver the final team collaboration report through the wiki space. On the other hand, the Face-to-Face group has to deliver the final collaboration report in a paper format. We expect that this WiP would bring up new insights on WBCEs effectiveness. We expect that the groupware performance will improve by means of the online communication tools, because they promote social interaction, discussion and collaboration in online environments. However, we are dealing with students that are “technology based learners” and a preliminary results conducted in a pre-pilot experiment show that some of our assumptions differ from what we expected.