Miracle-dz/UniFAR-FTUs huggingface dataset:
Pathogenic properties of fungal melanins

Abstract Melanins are complex black polymers of resonance stabilized cyclic subunits (including indoles, phenols, hydroxynaphthalenes) and are notoriously intractable to chemical analysis. Cell walls of numerous fungi are melanized, rendering many spores, vegetative hyphae, and certain fruit bodies opaque. Melanin deposition protects the pigmented cell from physical and biological stresses, excludes poisons, and helps limit leakage of certain metabolites. By forming a physical barrier between the cell and its surroundings, the production of a melanized wall layer has a profound effect upon the interactions between pathogenic fungi and their hosts. In many plant and animal diseases caused by melanotic fungi, melanin biosynthesis is an important determinant of pathogenicity and virulence. The mode of action of melanin in these diseases is the subject of intensive research, and a variety of mechanisms that link fungal melanin and disease have been discovered.
Detecção de anomalias utilizando métodos paramétricos e múltiplos classificadores

Anomalies or outliers are examples or group of examples that have a behaviour different from the expected. These examples may represent diseases in individuals or populations, as well as other events such as fraud and failures in banking systems. Several existing techniques seek to identify these anomalies, including adaptations of classification methods, statistical methods and methods based on information theory. The main challenges are that the number of samples of each class is unbalanced, the cases when anomalies are disguised among normal samples and the definition of normal behaviour associated with the formalization of a model for this behaviour. In this dissertation, we propose the use of a new space to help with the detection task, this space is called parameter space. We also present a new framework to perform anomaly detection by using the fusion of convex hulls in multiple parameter spaces to perform the detection. The method is considered a framework because it is possible to choose which parameter spaces will be used by the method according to the behaviour of the target dataset. For the experiments, two parameter spaces were used (mean and standard deviation; mean, variance, skewness and kurtosis) and the results were compared to some commonly used anomaly detection methods. The results achieved were comparable or better than those obtained by the other methods. Furthermore, we believe that a parameter space created great flexibility for the proposed method, since it allowed the user to choose a parameter space that best models the application. Both the flexibility and extensibility provided by the use of parameter spaces, together with the good performance achieved by the proposed method in the experiments, make parameter spaces and, more specifically, the proposed methods appealing when solving anomaly detection problems.
Effects of histone acetylation status on the early development of in vitro porcine transgenic cloned embryos.

Abstract The purpose of this study was to investigate the effects of the histone deacetylase (HDAC) inhibitor trichostatin A (TSA) on transgene expression and development of porcine transgenic cloned embryos, specifically focusing on effects derived from TSA-treated donor cells or TSA-treated reconstructed embryos. The results showed that TSA treatment on reconstructed embryos modified the acetylation status, which significantly improved the development of porcine somatic cell nuclear transfer (SCNT) embryos in vitro, but not donor cells. Furthermore, the treatment of reconstructed embryos with TSA enhanced expression of the pluripotency-related gene POU5F1 and stimulated expression of the anti-apoptotic gene BCL-2. Enhanced green fluorescent protein (EGFP) mRNA expression of every group dropped drastically from donor cells to blastocysts. Interestingly, TSA is likely to prevent a decline in EGFP expression in nuclear reprogramming of porcine SCNT embryos. However DNA hypomethylation induced by modified h.
DESIGNING AN IMAGE CRYPTOGRAPHY SYSTEM USING THE IMAGE ELEMENTS AS CIPHERING KEYS

A design and implementation of images' cryptography system is evaluated in this paper. This system depends on the idea of allocating a part of a digital image (possibly the first block of the image) so as to produce the cipher keys for the other parts. Circles generating algorithm is used to produce keys from the chosen block, then corresponding circles in other blocks will be encrypted using the located keys. So in this method encryption keys are brought from the plain-image (source image) it self using graphics shapes pixels.
Analysis and Synthesis of Real-Time Rule-Based Decision Systems

Real-time decision systems (RTDS''s) are computer-controlled systems that must react to events in the external environment by performing decision-intensive computation sufficiently fast to meet specified timing and safety constraints. This dissertation investigates a class of these systems where decisions are computed by an equational rule-based program. Two fundamental problems are identified: (1) the analysis of rule-based RTDS''s in order to verify that the specified timing and safety properties are satisfied prior to their execution, and (2) the synthesis of rule-based RTDS''s that are guaranteed to meet the specified timing constraints in addition to the safety constraints. Two complementary approaches have been developed to solve the first problem: (1) model checking of the global state transition graph representing the program, and (2) static analysis of the program. These approaches are combined to form the cornerstone of the General Iterative Analysis Algorithm. The applicability of this analysis technique is further enhanced by the development of a facility with which the rule-based programmer can specify domain-specific knowledge in the language Estella in order to validate the performance of an even wider range of programs. Two approaches also have been identified to tackle the second problem: (1) transforming the given equational rule-based program by adding, deleting, and/or modifying rules, and (2) optimizing the scheduler to select the rules to fire such that the variables in the program will always converge to stable values within the response time constraint. The complexity and size of real-time decision systems often necessitates the use of computer-aided design tools. This dissertation describes a suite of analysis tools based on our theoretical framework which have been implemented to ensure that equational rule-based programs written in the language EQL can indeed meet their specified timing constraints.
Altitude Patterns of Leaf Carbon Isotope Composition in a Subtropical Monsoon Forest

ABSTRACT Leaf carbon isotope composition (δ13C) of both vascular and non-vascular plants were investigated in order to assess their variability along an altitude gradient (414, 620, 850, 1086,1286 and 1462 m) from a subtropical monsoon forest located at Mt. Tianmu Reserve, eastern China. Leaf δ13C values of all plant species ranged from -34.4 to -26.6‰, with an average of -29.8‰. There is no significant difference in leaf δ13C between vascular plants and mosses, however, trees had significantly higher δ13C values than herbs. For pooled data, leaf δ13C was positively correlated with altitude. Leaf δ13C was significantly and negatively correlated with annual mean temperature and atmospheric pressure, while it was significantly and positively correlated with soil water content. Furthermore, there was no relationship between leaf δ13C and soil nitrogen content or soil phosphorus content. The altitudinal trend in leaf δ13C is the consequence of the interaction between temperature, atmospheric pressure and soil water content.
An empirical evaluation of lazy learning classifiers for text categorization

With the rapid growth of online documents available on the World Wide Web necessitate the task of classifying those documents into semantic categories. Text categorization is the task of automatically classifying the textual documents into a set of predefined categories. In this paper, we report the empirical evaluation of lazy learning classifier such as kNN and its variant like distance weighted kNN and our newly proposed evident theoretic kNN for text categorization task over two benchmark datasets. We observed the superiority of evident theoretic kNN method over others in all experiments we conducted.
Branching processes in disease epidemics

1 Power-law scalings are ubiquitous to physical phenomena undergoing a continuous phase transition. The classic Susceptible-Infectious-Recovered (SIR) model of epidemics is one such example where the scaling behavior near a critical point has been studied extensively. In this system the distribution of outbreak sizes scales as P (n) ∼ n−3/2 at the critical point as the system size N becomes infinite. The finite-size scaling laws for the outbreak size and duration are also well understood and characterized. In this work, we report scaling laws for a model with SIR structure coupled with a constant force of infection per susceptible, akin to a ‘reservoir forcing’. We find that the statistics of outbreaks in this system are fundamentally different than those in a simple SIR model. Instead of fixed exponents, all scaling laws exhibit tunable exponents parameterized by the dimensionless rate of external forcing. As the external driving rate approaches a critical value, the scale of the average outbreak size converges to that of the maximal size, and above the critical point, the scaling laws bifurcate into two regimes. Whereas a simple SIR process can only exhibit outbreaks This chapter and the material in Appendix C have been accepted for publication in Physical Review E with co-author Christopher R. Myers.
Hierarchical Bayesian classification of multimodal medical images

It has gradually been recognised that Bayesian algorithms are more widely applicable and reliable than ad hoc algorithms. Advantages include the use of explicit and realistic stochastic models making it easier to understand the working behind the algorithm and allowing confidence statements about conclusions. The authors propose a method, within a Bayesian framework, to assimilate information from images obtained from different modalities at different resolutions. The algorithm is used with a pair of images, from which a fused high resolution image and improved data reconstructions are simultaneously obtained. The authors illustrate their method by 2 examples, the first fuses a pair of SPECT and CT phantom images and the second a pair of MR brain scan images, obtained from different acquisition techniques. The authors provide a pseudo-comparison of the latter example with a commercially available package called ANALYZE. However, the phantom images from physical experiment given here provide a true validation and performance of the model.
Enhancement of in vitro Bioactivity by Surface Treatments of Ultra-thin Titanium Foils for Guided Periodontal Tissue Regeneration

This study developed a non-biodegradable membrane from commercial ultra-thin pure titanium (cpTi) foils as a guided tissue regeneration membrane for a potential modality in periodontal therapy. The etching behavior of ultra-thin cpTi foils in 40% sulfuric acid for various etching times was studied along with the effects of surface modification on in vitro bioactivity determined as well. Based on experimental results, we recommend an etching time of at least 30 min to maximize weight loss of ultra-thin cpTi foils. Scanning electron micrographs of the acid-etched titanium surface revealed a uniform distribution of extremely minute (3-4 μm) peaks and valleys. Additionally, machining (untreated) of the titanium surface yielded typical microscopically grooved surface features. Surface roughness increased with etching time and was closely related to weight loss. Etching for more than 30 min in 40% sulfuric acid substantially increased the X-ray diffraction (XRD) intensity of TiH2, as evidenced by the changes in weight loss and surface morphology. In vitro assessment revealed that adequate acid-etching treatments may increase in vitro titanium bioactivity in a simulated body fluid (SBF) solution and cell culture. Moreover, results of the tissue culture also established that treated (AE-Ti) ultra-thin foils promoted cell migration and repaired damaged bones more effectively than untreated (CP-Ti) ultra-thin foils. Results of this study demonstrate that etching treatment with concentrated sulfuric acid is an effective means of modifying the surfaces of ultra-thin cpTi foils and enhancing in vitro titanium bioactivity.
Ocular Motoneuron Pools Develop Along a Dorsoventral Axis in Zebrafish, Danio rerio

Both spatial and temporal cues determine the fate of immature neurons. A major challenge at the interface of developmental and systems neuroscience is to relate this spatiotempo-ral trajectory of maturation to circuit-level functional organization. This study examined the development of two ocular cranial motor nuclei (nIII and nIV), structures in which a motoneuron’s identity, or choice of muscle partner, defines its behavioral role. We used retro-orbital dye fills, in combination with fluorescent markers for motoneuron location and birth-date, to probe spatial and temporal organization of the oculomotor (nIII) and trochlear (nIV) nuclei in the larval zebrafish. We described a dorsoventral organization of the four nIII motoneuron pools, in which inferior and medial rectus motoneurons occupy dorsal nIII, while inferior oblique and superior rectus motoneurons occupy distinct divisions of ventral nIII. Dorsal nIII motoneurons are, moreover, born before motoneurons of ventral nIII and nIV. Order of neurogenesis can therefore account for the dorsoventral organization of nIII and may play a primary role in determining motoneuron identity. We propose that the temporal development of ocular motoneurons plays a key role in assembling a functional oculomotor circuit.
Ontology Based Android Mobile Search Engine

I propose a ontology based mobile search engine, OBMASE, that captures the users’ preferences in the form of concepts by mining their click through data. Due to the importance of location information in mobile search, OBAMSE classifies these concepts into content concepts and location concepts. In addition, users’ locations (positioned by GPS) are used to supplement the location concepts in OBMASE. The user preferences are organized in an ontology-based, multifacet user profile, which are used to adapt a personalized ranking function for rank adaptation of future search results. To characterize the diversity of the concepts associated with a query and their relevance’s to the users need, four entropies are introduced to balance the weights between the content and location facets. Based on the client-server model, we also present a detailed architecture and design for implementation of OBAMSE. In our design, the client collects and stores locally the click through data to protect privacy, whereas heavy tasks such as concept extraction, training and re-ranking are performed at the OBAMSE server. Moreover, we address the privacy issue by restricting the information in the user profile exposed to the OBAMSE server with two privacy parameters. We prototype OBAMSE on the Google Android platform. Experimental results show that OBAMSE significantly improves the precision comparing to the baseline. Moreover, we address the privacy issue by restricting the information in the user profile exposed to the server with two privacy parameters. We prototype OBMSE on the Google Android platform. Experimental results show that OBMSE significantly improves the precision comparing to the baseline.
Biosystematics of the Didymium squamulosum complex

Abstract Thirty-three isolates of the Didymium squamulosum morphospecies, from several geographic areas, were subjected to a biosystematic investigation that considered reproductive systems, plasmodial incompatibility, morphology and isozymes. Six of the isolates were heterothallic and the remaining 27 were nonheterothallic and presumably apomictic. The six heterothallic isolates represented three sexually incompatible biological species. Two of the biological species were represented by a single isolate, but the third biological species contained four isolates and displayed a multiple allelic mating series. A dendrogram derived from the isozyme difference data separated the isolates into two related groups. The first of these containing five heterothallic isolates, representing all three biological species, and a number of nonheterothallic isolates. The other containing a single heterothallic isolate, of the A2 biological species, and a number of nonheterothallic isolates. A second dendrogram, based upon morphological variations, did not correlate with the isozyme dendrogram, although several characters (peridial calcium carbonate, stalk color and plasmodial form) did conform to the two isozyme-defined groups. Thus, the D. squamulosum morphospecies is apparently a widespread species complex with large, but overlapping, morphological and genetic variations.
Diversity of Cenococcum geophilum isolates from serpentine and non-serpentine soils

Abstract Serpentine soils are characterized by a disproportionate level of Mg in relation to Ca and often contain phytotoxic levels of available Ni. Both of these factors may represent stresses to plants and fungi colonizing these soils. Ectomycorrhizal fungi play important roles in tree biology, and ecotypic adaptation in these fungi may be critical to the success of trees on serpentine soils. A collection of Cenococcum geophilum isolates was obtained from serpentine and non-serpentine soils by trapping isolates on the roots of Virginia pine (Pinus virginiana) seedlings. Restriction fragment length polymorphism (RFLP) analysis of the internal transcribed spacer region of ribosomal repeat exhibited certain common fragments among isolates and other fragments that varied in length. Additional polymorphic markers were obtained from PCR-amplified (β-tubulin gene fragments. UPGMA analysis of the RFLP data indicated that, with one possible exception, the serpentine isolates of C. geophilum are genetically more similar to each other than they are to the isolates from local or distant non-serpentine sites. AFLP analyses, sampling a greater number of loci across the genome, provided an even more distinct separation of the serpentine isolates from non-serpentine isolates. All serpentine isolates lacked a group I intron frequently found within the 18S ribosomal RNA gene in isolates of this species. The genetic divergence between serpentine and non-serpentine isolates may reflect adaptation to serpentine soil factors.
Q-enhanced tunable filter design with applications in receiver architectures

Q-enhanced Filters have been researched extensively, but have not been often implemented into receiver architectures due to inherent challenges in the design and stability of these filters. However, recent works have successfully addressed Q-enhanced filter designs which are viable for receiver implementation with tuning algorithms to achieve temperature stability. This work continues these efforts with the redesign of a Two-Pole Q-Enhanced BandPass filter tested at narrower fractional bandwidths than previous work of less than one percent and considers potential significant improvements in receiver performance using this filer. The Q-enhanced filter redesign ports the existing filter to a new integrated circuit technology which performs better at higher frequencies. The redesign in particular addresses problems in the previous design. The frequency divider design is modified, resistance tuning is added, and additional modifications to the overall filter functionality are implemented. General problems in obtaining an ideal passband shape by eliminating unwanted coupling are addressed. The supporting software for the tuning algorithm is modified to use analog controls and shown to achieve further narrowed bandwidths of 5 MHz and 2.5 MHz at center frequencies of 500 MHz, which are demonstrated to be temperature stable. Future software modifications are described to prepare the existing code base for the new filter design. Potential applications for a Q-enhanced filter include improving the performance of receiver designs. One of the most important performance parameters of a receiver is its spurious response rejection. To explore this behavior, an automated test system is developed to characterize receivers, and four receivers are tested. The test results are presented in a novel graphical display, which is used to evaluate receiver performance and compare receivers. These results motivated the development of a potential modified superheterodyne receiver architecture using the Q-enhanced filter as an image filter and an IF filter. The viability of this receiver design is tested and shown to provide significant improvements to receiver’s spurious rejection response.
Molecular phylogenetics of Ramaria and related genera: evidence from nuclear large subunit and mitochondrial small subunit rDNA sequences

Abstract Phylogenetic relationships of the genus Ramaria and additional related taxa were examined through phylogenetic analysis of mitochondrial and nuclear ribosomal DNA sequence data. Related genera included Clathrus, Clavariadelphus, Gautieria, Gomphus, Hysterangium, Kavinia and Pseudocolus. Outgroup genera included Bondarzewia, Favolus, Ganoderma, Lactarius and Russula. The nuclear large subunit ribosomal DNA (nuc LSU rDNA) (approx. 610 bp) from 78 collections including 34 Ramaria species was used to test generic, subgeneric and selected species concepts for Ramaria. The mitochondrial small subunit ribosomal DNA (mt SSU rDNA) (ca 470 bp) from 51 representative holobasidiomycetes including ten Ramaria species also was used to independently test the monophyly of the genus Ramaria. Parsimony analyses of both datasets indicated that the genus Ramaria was paraphyletic and that several morphologically distinct groups of holobasidiomycetes were derived from ramarioid ancestors. In the nuc LSU rDNA analyses, Gautieria was nested among the terricolous Ramaria species and was closely related to R. subg Ramaria. The nuc LSU rDNA results also indicated that R. subg Laeticolora and R. subg Lentoramaria formed paraphyletic grades. Ramaria subg Laeticolora was paraphyletic due to the terminally derived R. subg Ramaria/Gautieria clade and a nested Gomphus. Ramaria subg Lentoramaria was paraphyletic due to a nested Clavariadelphus, Kavinia, and R. abietina of subg Echinoramaria. Both the nuc LSU rDNA and the mt SSU rDNA analyses demonstrated strong bootstrap support for the inclusion of the Phallales with the ingroup taxa, but the relationship of the Phallales to the Gomphales was indeterminate. Selected species concepts were also tested (e.g., R. amyloidea and R. celerivirescens, and R. araiospora and R. stuntzii). These data rejected the monophyly of Ramaria and suggested that the ramarioid morphology and lignicolous substrate affinity were ancestral for the Gomphales.
An efficient design methodology for standard cell circuits

A novel standard cell design methodology is presented that is based on the implementation of interconnections over the gates to avoid dedicated connection channels. A priority scheme is used for the allocation of the metal layer. The result is a very compact layout. A standard cell library was designed using a double-metal CMOS technology. The topological structure and cell library are presented. The development of a software tool to compile integrated circuits using the available cells is also discussed, and the placement and routing strategies used in the implementation algorithm are described. <<ETX>>