Miracle-dz/UniFAR-FTUs huggingface dataset:
Evaluation of LAMP for detection and/or screening of Leptospira spp. infection among domestic animals in the Philippines

Objective: This study assessed the applicability of loop-mediated isothermal amplification (LAMP) for the detection of leptospirosis among domesticated animals and sewage rats. Specifically, it evaluated the ability of LAMP to amplify Leptospira spp. targeting the 16s rRNA gene in boiled urine samples. Materials and methods: A total of 140 samples from different domestic animals were tested for the presence of the antigen. A nested-polymerase chain reaction (nPCR) protocol was used to compare and determine the sensitivity of LAMP in detecting Leptospira spp. The LAMP was also evaluated by comparing its amplification result using agarose gel electrophoresis and color change using dye. Results: Positivity rate of Leptospira spp. antigen was 29.0% (40/140) for LAMP and 9.3% (13/140) for nPCR. Also, LAMP results for gel electrophoresis and dye color change varied in some samples that may be due to the interpretation of the result in dye color change. Conclusion: Overall, LAMP is a rapid, sensitive, and cost-effective diagnostic method compared with nPCR. Also, LAMP has a potential application as pen-side screening, surveillance, and clinical diagnostic kits of infectious diseases without requiring advance equipment and skilled personnel.
Managing uncertainty in movement knowledge for environmental decisions

Species’ movements affect their response to environmental change but movement knowledge is often highly uncertain. We now have well‐established methods to integrate movement knowledge into conservation practice but still lack a framework to deal with uncertainty in movement knowledge for environmental decisions. We provide a framework that distinguishes two dimensions of species’ movement that are heavily influenced by uncertainty: knowledge about movement and relevance of movement to environmental decisions. Management decisions can be informed by their position in this knowledge‐relevance space. We then outline a framework to support decisions around (1) increasing understanding of the relevance of movement knowledge, (2) increasing robustness of decisions to uncertainties and (3) improving knowledge on species’ movement. Our decision‐support framework provides guidance for managing movement‐related uncertainty in systematic conservation planning, agri‐environment schemes, habitat restoration and international biodiversity policy. It caters to different resource levels (time and funding) so that species’ movement knowledge can be more effectively integrated into environmental decisions.
TURBULENT MIXING AND BURNING OF COAXIAL STREAMS INSIDE A DUCT OF ARBITRARY SHAPE

Abstract : A theoretical investigation of the ducted turbulent mixing of coaxial streams is presented. The effects of equilibrium chemical reactions in the mixing layer are included in the analysis. In Part I, the theory is developed for ducted mixing systems in which the inviscid portions of the flow are assumed to be one-dimensional. The integral method is used, and the mixing zone velocity profiles are assumed to be similar. Turbulent Prandtl and Lewis numbers are assumed to be unity, and the turbulent shear stress along one control surface in the mixing layer is computed by use of a semi-empirical model for the eddy viscosity. The theory is formulated to include the downstream regime where the mixing layer extends across the entire duct. The system of integral equations is transformed into a form suitable for numerical solution by standard methods. In Part II, the theory is extended to include the influence of a nonuniform supersonic inviscid core flow. A technique is developed for coupling the numerical solution of the inviscid core flow (from the method of characteristics) with the solution of the integral equations for the mixing layer. The theory is correlated with low speed experiments, with supersonic air-air ejector experiments and with experiments on ducted rocket-air mixing. The correlations show that the theory gives satisfactory results for the performance of ducted rocket-air mixing systems which are representative of air augmented rockets.
Comparative genomics, transcriptome analysis and characterization of selected regulatory genes of Burkholderia glumae

vi CHAPTER 1: Introduction.1 CHAPTER 2: Genome sequencing and comparative genomics of Burkholderia glumae, strain 336gr-1.6 CHAPTER 3: Characterization of ECF sigma 70 gene and sigma 54 dependent response regulator gene (tepr) in Burkholderia glumae, strain 336gr-1. 50 CHAPTER 4: RNA-seq based transcriptome analysis to study the gene expression of Burkholderia glumae, strain 336gr-1.64 CHAPTER 5: Conclusions.79 REFERENCES: . 82 APPENDIX: . 88 VITA: . 95
Airline Seats Allocation Optimization Through Revenue Management

Revenue Management has recently gained a solid recognition in Airline industry. It acts as a strategic and tactic provider to manage the uncertainty in demand for their perishable products in the most profitable manner as possible. The Airline Revenue Management tries to attain an effective seat inventory control by utilizing the forecasts of future bookings, the revenue values related with each fare class, and the booking requests by the passengers which in turn will maximize the total revenue of a flight. This paper attempts to propose a novel approach in optimizing the seat inventory control by jointly utilizing the statistical forecasting together with revenue management. The revenue value associated with each point of sale (origin) has been considered when locating seats for a future departure instead of concerning the revenue values of each fare class. Further, it describes a method to obtain optimal seat protection levels that should be reserved from a lower fare origin for a higher fare origin and the nested structure of booking limits for each fare origin so as to optimize the seat allocation in a future departure. A novel approach using Functional Principal Component Regression (FPCR) was carried out to model and forecast the future demand and revenue value for each origin, using historical bookings and revenue values. The Expected Marginal Seat Revenue (EMSR) decision model was developed to address the uncertainty associated with this forecasted future demand and to gain the nested structure of booking limits. Finally, the forecasted booking limits were updated with actual booking requests prior to the flight departure. At the point of verification, it showed a remarkably maximized total revenue over the existing method. Thus, it is suggested that the optimal seat allocation for a better seat inventory control in airlines can be achieved by jointly utilizing the proposed FPCR and EMSR methods.
Default Probability of the Medical Imaging Service Providers in Hungary

Medical imaging, providing Magnetic Resonance Imaging (MRI) services have a special, oligopolistic market in Hungary. A majority of the MRI machines are operated by private contractors in a Public Private Partnership form in major healthcare centres with defined machine-hours for public healthcare services while they can sell their remaining capacities on the market as well. Current paper analyses the default probability of this firms via Ohlson-O and Altman-Z’ ratios, based on their annual financial report data. Then, default ratios are compared to market segment- and macro-specific variables trough panel regression analysis to identify the key factors of this technolo-gy-intense sector. Finally, results are compared to public default-rate databases.
A Perspective of the Machine Learning Approach for the Packet Classification in the Software Defined Network

Packet classification is a major bottleneck in Software Defined Network (SDN). Each packet has to be classified based on the action specified in each rule in the given flow table. To perform classification, the system requires much of the CPU clock time. Therefore, developing an efficient packet classification algorithm is critical for high speed inter networking. Existing works make use of exact matching, range matching and longest prefix matching for classification and these techniques sometime enlarges rule databases, thus resulting in huge memory consumption and inefficient searching performance. In order to select an efficient packet classification algorithm with less memory consumption and high classification accuracy, Machine Learning (ML) algorithms are used. For performance comparison, ML algorithms are used, namely Multi-layer Perceptron (MLP), K-Nearest Neighbor (KNN), Decision Tree (DT), Random Forest (RF), AdaBoost classifier (AB) and Support Vector Machine (SVM). All these algorithms build network for packet classification and train the network with the use of Access Control List (ACL) netbench dataset. 5-features of IPv4 packet header are used and the algorithms classify the packets based on action/flow of each packet. Experimental results show that among six algorithms, RF algorithm gives better improvement in accuracy performance for permitted packets.
Rhithronic and potamonic fishes coexist in wadeable streams under distinct metacommunity processes

Recent metacommunity ecology research has demonstrated that local communities can be divided into different guilds. We hypothesised that wadeable streams are occupied by fishes that follow distinct metacommunity processes. The mainstem is a river corridor for the potamonic fish guild (PFG) but represents a nonhabitat matrix for the rhithronic fish guild (RFG). Accordingly, the PFG should be filtered out from the headwaters by dispersal limitations or environmental filtering along the longitudinal gradient, and the guild should have a nested pattern of beta diversity. The RFG should be structured by the local species sorting, and the species turnover component should prevail. We sampled fishes in 42 streams distributed in four subbasins that were separated by at least one mainstem channel. We modelled the influences of spatial and environmental predictors using a partial redundancy analysis and variance partitioning and by quantifying the components of beta diversity that were associated with species turnover and nestedness. Both environment and space affected the structure of the RFG, owing to the influence of substrate type, riparian cover and presence of downstream barriers. The PFG was structured by only the influence of downstream barriers. Species turnover predominated within the RFG, and species nestedness dominated within the PFG. Our results support the hypothesis that potamonic and rhithronic guilds coexist in wadeable streams and follow distinct metacommunity assembly mechanisms. Potamonic guilds are structured by regional dispersal from the mainstem channels, whereas rhithronic guilds are sorted by local filtering along the longitudinal gradient in a spatially structured environment.
Religious instruction in Polish public schools in light of universal and European standards

The study is devoted to the analysis of legal regulations at a national level (Poland), the jurisprudence (case-law) of the Constitutional Tribunal and the practices of central and local government in matters related to public education, as perceived from the point of view of universal and European standards protecting freedom of conscience and religion. The author justifies the claim that the standards set by the Polish Constitutional Tribunal in this field are fundamentally different from the standards established in the case-law of the UN Human Rights Committee and the European Court of Human Rights. This leads to tolerance of repeated violation of the principle of ideological impartiality of public authorities. The principle, declared in Article 25 (2) of the Constitution of the Republic of Poland,1 is violated both by state-level legislation pertaining to the sphere of religion, and by biased practices of educational administration. What is particularly abnormal is the inertia of public authorities that are obliged to supervise religious education and/or instruction, and their indifference to the unlawful activities of the entity interested in ideological domination over the education sector. The author expresses the conviction that a fundamental change of the approach of the Polish legislator should take place, especially as regards the role and tasks of state entities in protecting freedom of conscience and religion in the educational activities of public schools. This would guarantee the philosophical and religious neutrality of education in state schools.
Structural Remodeling of Alpha-Synuclein by Small Molecules: A Novel Path to Neuroprotective Therapeutics

Neurodegenerative diseases share the unifying features of insoluble protein aggregates and irreversible neuron loss. Parkinson’s disease (PD) is defined by proteinaceous Lewy bodies—which contain α-synuclein—and loss of dopamine neurons leading to motor dysfunction. Growing evidence implicates α-synuclein aggregation as a causal driver of neurodegeneration in certain forms of PD. However, the precise mechanism(s) by which the process or products of α-synuclein aggregation drive neuron death remains unknown. Better understanding of this key question might further development of neuroprotective therapies for PD and related disorders. To address this gap, we reviewed how the native conformation of α-synuclein relates to its physiological function and roles in pathology. We also examined how the mouse brain proteome and phosphoproteome change in response to α-synuclein aggregation using quantitative proteomics. This revealed that proteomic changes were not widespread, but instead were enriched within certain functional areas. For the first time, we found that the immunoproteasome is induced during aggregation, providing a new tunable target for studying α-synuclein aggregation and its connection to toxicity. We also employed nordihydroguaiaretic acid (NDGA) and analogs to study the chemistry and products of phenolic inhibitors of α-synuclein aggregation. We discovered that oxidation-dependent cyclization is required for NDGA analogs to inhibit α-synuclein aggregation and that this inhibition is caused by modification of α-synuclein monomers that retain their conformational dynamics and lipid interactions. Further, we found that these NDGA analogmodified monomers exert a dominant negative effect on aggregation of untreated α-synuclein, exposing a novel mechanism for inhibiting α-synuclein aggregation. Using transgenic Caenorhabditis elegans, we showed that cyclized NDGA can prevent neurodegeneration driven by α-synuclein. These findings outline a novel paradigm for small molecule inhibition of α-synuclein aggregation wherein they act by stabilizing dynamic αsynuclein monomers, preventing aggregation. This in turn prevents aggregation of untreated α-synuclein and reduces neurodegeneration. Together this work underscores the importance of α-synuclein’s native structural dynamics and provides several novel tools for future use in untangling the relationship between α-synuclein aggregation and neuron loss in PD and related disorders. Degree Type Dissertation Degree Name Doctor of Philosophy (PhD) Graduate Group Pharmacology First Advisor Harry Ischiropoulos
Phylogeny of the family Cladoniaceae (Lecanoromycetes, Ascomycota) based on sequences of multiple loci

Cladoniaceae is a family of lichenized fungi that belongs to the Lecanorales, Ascomycota. The family is distributed widely, although several genera are restricted to the Southern Hemisphere. The circumscriptions of the genera and species in the family have traditionally been based on thallus morphology, the type of vegetative propagules and the secondary metabolites. However, numerous species are highly variable phenotypically, making their delimitation problematic. In the present study a new phylogeny of Cladoniaceae is constructed using five loci (ITS rDNA, IGS rDNA, RPB2, RPB1, EF‐1a) from a worldwide sample of 643 specimens representing 304 species. Cladoniaceae was resolved as a monophyletic group. The circumscription of the genera and the relationships among them are discussed. Pycnothelia, Carassea and Metus are closely related, forming a sister clade to the larger genus Cladonia. Cladia in its recent wide sense turned out to be paraphyletic, including species that have been recognized in Thysanothecium and Notocladonia. Cladonia was resolved as monophyletic, with C. wainioi as the earliest diverging lineage. Eleven major clades were resolved in Cladonia. No synapomorphies were found for most of them. We propose the new genera Pulchrocladia and Rexia, as segregates of Cladia, five new combinations, and the resurrection of the genus Heterodea.
Sentence processing is modulated by the current linguistic environment and a priori information: An fMRI study

Words are not processed in isolation but in rich contexts that are used to modulate and facilitate language comprehension. Here, we investigate distinct neural networks underlying two types of contexts. Firstly, the current linguistic environment, presented as the relative frequencies of two syntactic structures (prepositional object (PO) and double-object (DO)), which would either follow everyday linguistic experience or not. Secondly, preference towards one or the other structure depending on the verb; learned in everyday language use and stored in memory. German participants were reading PO and DO sentences in German while brain activity was measured with functional magnetic resonance imaging. Firstly, the anterior cingulate cortex (ACC) showed a pattern of activation that integrated the current linguistic environment with everyday linguistic experience. When the input did not match everyday experience, the unexpectedly frequent structure showed higher activation in the ACC than the other conditions and more connectivity from the ACC to posterior parts of the language network. Secondly, verb-based surprisal of seeing a structure given a verb (PO verb preference but DO structure presentation) resulted, within the language network (left inferior frontal and left middle/superior temporal gyrus) and the precuneus, in increased activation compared to a predictable situation. In conclusion, 1) beyond the canonical language network, brain areas engaged in cognitive control, such as the ACC, might use the statistics of syntactic structures to facilitate language comprehension, 2) the language network is directly engaged in processing verb preferences. These two networks show distinct influences on sentence processing.
Energy-efficient data collection and fusion in wireless body sensor networks for continuous health monitoring

Plusieurs defis existent dans les reseaux de capteurs corporels sans fil tels que la collecte et la fusion de donnees physiologiques dans un environnement contraignant. En effet, les nœuds de capteurs sans fil ont des ressources limitees en energie, traitement et memoire. En outre, une grande quantite de donnees est collectee. Ces donnees sont heterogenes, ambigues et imprecises. Ajoutons que l'interpretation des donnees est influencee par plusieurs facteurs externes tels que les informations contextuelles fournies par la personne surveillee. En consequence la prise de decisions et l'analyse des informations extraite sont influencees.Tout d'abord une technique de collecte de donnees est proposee. Celle-ci a pour interet de reduire la quantite de donnees collectee et la consommation d'energie. Dans le modele propose, l'energie consommee par les nœuds capteurs sans fil pour capter et pour transmettre les signes vitaux est particulierement ciblee. Il s'agit a la fois d'un mecanisme temps-reel pour l'adaptation du taux d'echantillonnage et d'un systeme de detection local permettant aux nœuds de transmettre uniquement les donnees indiquant un changement dans l'etat de sante de la personne.Deuxiemement, un modele de fusion de donnees pour l'evaluation de l'etat de sante de la personne surveillee est propose. Les donnees fusionnees sont les signes vitaux de la personne qui proviennent de plusieurs capteurs. Ces donnees sont interpretees de maniere humaine et sont caracterisees par l'ambiguite et l'imprecision. Ainsi, nous proposons d'utiliser un systeme d'inference floue.Ensuite, nous proposons d'evaluer l'etat de sante de la personne surveillee tout en prenant en compte le contexte dans lequel elle se trouve. Etant donne que les signes vitaux de l'etre humain ainsi que son contexte tels que : son activite physique, son dossier medical et ses informations personnelles sont fortement correles, interpretation des signes vitaux est largement influencee. Plus particulierement, nous proposons d'utiliser les ensembles flous hesitants pour determiner subjectivement l'intensite de l'activite physique de la personne. L'approche proposee prend en consideration le profil de la personne ainsi que les caracteristiques de l'activite physique en cours.Finalement, une application medicale specifique est ciblee. Nous proposons de detecter et d'evaluer le stress en temps reel tout en considerant la consommation d'energie. Shimmer 3 GSR + est utilise comme capteur sans fil pour capter le signal Photoplethysmogram (PPG) et la conductance cutanee. Une application mobile Android est developpee pour extraire du signal PPG les signes vitaux qui sont correles au stress tels que la frequence cardiaque, la frequence respiratoire et la pression arterielle.
Exploring Saccharomyces cerevisiae in the light of novel small-scale cultivation techniques

In recent years, small-scale bioreactors became more important due to an increasing need in screening capacities as well as in simplified and parallelized cultivation experiments. Screening experiments are frequently performed in batch cultivation mode, while industrial production processes prefer fed-batch operating conditions allowing to control the delivery of substrate to the culture. The discrepancy between the initial screening in batch and final cultivation operation in fed-batch mode may therefore result in inadequate strain selection and process conditions. Here, we present a simple and easy-to-operate fed-batch mimicking cultivation system at microliter range tailored for yeast cultivation at pH 3.8 and 6.4. The system is based on the gradual enzymatic release of glucose from a polymer. We demonstrate the robustness and transferability of important bioprocess parameters from the small-scale fed-batch cultivation system to fully automated stirred tank bioreactors using two different Saccharomyces cerevisiae strains engineered for 3hydroxypropionic acid production, where product yields on glucose showed comparable values for the two systems.
Dynamic earthquake ruptures on multiscale fault and fracture networks

Multiscale fault structures consist of macroscopic major fault networks surrounded by mesoscopic and microscopic fracture networks, considered as off-fault damage. Such geometrical complexity of natural fault structure modifies the rupture dynamics, the seismic wave radiation and the overall energy budget associated with earthquakes. Here we propose a continuum-discontinuum approach framework with combined finite-discrete element method (FDEM) to model dynamic earthquake rupture with the coseismic off-fault damage along natural fault networks. We firstly modeled the dynamic earthquake rupture with the coseismic off-fault damage on a single planar fault. We showed the mechanism of dynamically generated off-fault fracture networks, the decrease in rupture velocity and the enhancement of high-frequency radiation in near-field ground motion. The overall energy budget is modified due to the additional radiation, and dissipation of the energy, associated with the secondary off-fault cracks. We then conducted a dynamic earthquake rupture modeling on the 2016 Kaikōura earthquake, which shows a great potential to narrow down a subset of hypothetical rupture scenarios by comparing the displacement field perturbed by the coseismic off-fault damage with the observations. Overall, this work has opened an avenue to model the dynamic earthquake ruptures with the continuum-discontinuum approach framework, which elucidates the effect of coseismic off-fault damage on the earthquake rupture dynamics and has shown the potential of further applications to natural fault systems.