Miracle-dz/UniFAR-FTUs huggingface dataset:
Supertree methods for phylogenomics

Phylogenetics is the field of evolutionary biology that studies the evolutionary relationships between species through morphological and molecular data. These relationships can be summarized in the so- called "species tree". A gene tree is an evolutionary tree constructed by analyzing a gene family. Species trees are mainly estimated using gene trees. However, for both methodological and biological reasons, a gene tree may differ from the species tree. To estimate species tree, biologists then analyze several data sets at a time, letting the weight of the evidence decide. This thesis focuses on the "supertree" approach to combine data sets. This approach consists first in constructing trees (commonly called source trees) from primary data, then assembling them into a larger and more comprehensive tree, called supertree. When using supertree construction in a divide-and-conquer approach in the attempt to reconstruct large portions of the Tree of Life, conservative supertree methods have to be preferred in order to obtain reliable supertrees. In this context, a supertree method should display only information that is displayed or induced by source trees (induction property - PI) and that does not conflict with source trees or a combination thereof (non contradiction property - PC). In this thesis we introduce two combinatorial properties that formalize these ideas. We proposed algorithms that modify the output of any supertree methods such that it verifies these properties. Since no existing supertree method satisfies both PI and PC, we have developed two methods, PhySIC and PhySIC_IST, which directly build supertrees satisfying these properties. An application of PhySIC_IST to the complex problem of the history of Triticeae is presented. Since duplication events often result in the presence of several copies of the same genes in the species genomes, gene trees are usually multi-labeled, i.e., , a single species can label more than one leaf. Since no supertree method exists to combine multi-labeled trees, until now these gene trees were simply discarded in supertree analyses. Yet, they account for 60% to 80 % of the gene trees available in phylogenomic databases. In this thesis, we propose several algorithms to extract a maximum amount of speciation signal from multi-labeled trees and put it under the form of single-labeled trees which can be handled by supertree methods. An application to the hogenom database is presented
A comparative evaluation of the effect of four desensitizing agents (strontium chloride, potassium nitrate, pro-argin, bioactive glass) on dentinal occlusion: An ex-vivo SEM study

Aim: The aim of this study was to compare and evaluate the effect of four desensitizing agents (Strontium Chloride, Potassium Nitrate, Pro-Argin, Bioactive Glass) on dentinal occlusion. Materials and Methods: Forty freshly extracted mandibular molars were selected. Dentine discs measuring 6x6x3mm were cut off from cervical 1/3 of molars. The occlusal surface of each dentine disc was abraded with silicon carbide paper for 1 minute and then immersed in 17% Ethylenediaminetetra-acetic acid for 5 minutes. The specimens were then randomly distributed into 4 groups: Strontium Chloride(G1), Potassium Nitrate(G2), Pro-argin (G3) and Bioactive Glass(G4) and brushed with undiluted tooth paste (1 gm) with colgate actibrush 2 minutes daily for 7 days and stored in artificial saliva. Dentine discs were then analyzed by scanning electron microscope. Results: Data were statistically analyzed by one-way Analysis of Variance (ANOVA) and Tukey’s test. The P value for each group was <0.001 showing that highly significant difference existed among the groups. The Bioactive Glass showed maximum amount of dentinal tubule occlusion among all the groups. The least amount of dentinal tubule occlusion was observed in potassium nitrate. The Energy Dispersive X-ray microanalysis showed highest peaks of Calcium and Phosphorous along with presence of Sodium, Magnesium, Potassium, Carbon, Silicon, Oxygen, Phosphorous, Sulphur, Chlorine, and Fluorine. Conclusion: It was concluded that tooth brushing with dentifrice containing bioactive glass showed maximum amount of dentine tubule occlusion. Clinical Relevance: Dentinal hypersensitivity is a significant clinical problem which can cause considerable concern for patients. Appropriate and combine use of various clinically effective both synthetic and natural desensitizing agents may considerably help to manage the problem. Key-words: Dentinal hypersensitivity, Dentinal occlusion, Desensitizing agent.
Phylogeography of Simulium siamense Takaoka and Suzuki complex (Diptera: Simuliidae) in Thailand

The phylogeography of Simulium siamense complex was inferred from mitochondrial DNA sequences. A 586‐bp fragment of the cytochrome oxidase I was sequenced for 92 individuals from 13 populations throughout Thailand, representing five cytoforms (A, B, C, F and G). The cytoforms are not genetically different at the molecular level except for cytoform B, which is genetically distinct from the others. This might indicate that cytoform B is a distinct species. Further morphological and molecular work using other genes is needed to clarify this. Our results also argue for the need of integrated approach, both cytological and molecular studies to understanding biodiversity of black flies. The star‐like shape of the mtDNA genealogy is consistent with the sudden population expansion of the mismatch distribution analysis and large negative values of Fu's Fs and Tajima's D‐tests, indicating a population demographic expansion. The expansion time is estimated to be in the late Pleistocene (about 120 000 years ago). Therefore, the overall low level of genetic structure could be due to sharing a recent history. The ancestral haplotype was found in the mountainous area in northeastern Thailand, suggesting that this area could have been the refugium of the species complex during the Pleistocene glaciations. Our results are consistent with previous findings about population expansion in response to the Pleistocene climatic change, thus revealing the importance of this historical event in shaping the genetic structure and diversity of Southeast Asian mainland species.
Avaliação da diferenciação osteoblástica de células-tronco mesenquimais de ratos tratados cronicamente com bifosfonatos

Apesar dos bifosfonatos (BPs), fármacos antirreabsortivos, atuarem principalmente nos osteoclastos, a ação desses medicamentos em osteoblastos tem sido demonstrada em experimentos in vitro. Porém, na maioria desses experimentos, há exposição das culturas de osteoblastos aos BPs. Na presente investigação, foram avaliados osteoblastos diferenciados a partir de células-tronco mesenquimais (CTMs) de ratos tratados in vivo com alendronato de sódio (ALE: 1mg/ml/kg/semana), ácido zoledrônico (ZOL: 0,3mg/ml/kg/semana) ou solução salina (VEH: 0,009mg/ml/kg/semana) durante 13 semanas. As CTMs da medula óssea dos fêmures direitos dos animais foram cultivadas em meio osteogênico, na densidade de 5.000 células/200μl/poço. Após 21 dias de cultura, osteoblastos foram avaliados quanto à viabilidade celular e à formação de matriz mineralizada. Foram observadas viabilidades celulares semelhantes nos grupos BPs (ALE e ZOL) e superiores ao controle (VEH). Quanto à formação da matriz mineralizada, houve maior mineralização no grupo ZOL em relação ao grupo ALE, sendo ambas inferiores ao observado no grupo VEH. Os resultados obtidos sugerem que a exposição in vivo das CTMs ao ALE e ao ZOL influenciou a atividade dos osteoblastos in vitro. Ambos os medicamentos utilizados são BPs nitrogenados; contudo, na dose empregada, o ALE afetou mais significativamente a formação de matriz mineralizada.
Aprendizagem empreendedora como suporte para o desenvolvimento de competências de identificação de oportunidade: um estudo entre os empresários inseridos no Armazém da Criatividade Caruaru.

Entrepreneurs are constantly searching for knowledge and tend to participate in spaces such as the Armazem da Criatividade Caruaru, which fosters local economic development and integrates in an operational, functional and spatial manner the main actors of society. This space tends to concentrate knowledge, people and experiences that can generate learning, helping the entrepreneur in the development of entrepreneurial skills and in the ability to identify new business opportunities. Thus the present study aims to understand how entrepreneurial learning contributes to the process of generation and development of opportunity skills in micro and small entrepreneurs of the Armazem da Criatividade Caruaru. For the analysis was carried out a qualitative research, with explanatory character, carried out through a case study and that had its data reviewed through content analysis. The results obtained in the study show that participating in the ecosystem of the Armazem da Criatividade contributes positively to the entrepreneur, promoting the learning and development of new behaviors that allow greater potential to identify new business opportunities that could contribute to regional economic growth.
The fly neuromuscular junction : structure and function

Introduction on the use of the Drosophila embryonic/larval neuromuscular junction as a model system to study synapse development and function, and a brief summary of pathfinding and target recognition. Development and structure of motoneurons. The development of the Drosophila larval body wall muscles. Organisation of the efferent system and structure of neuromuscular junctions in Drosophila. Development of electrical properties and motor output. Transmitter release at the neuromuscular junction. Vesicle trafficking and recycling at the neuromuscular junction: Two pathways for endocytosis. Glutamate receptors at the NMJ. Scaffolding proteins at the Drosophila neuromuscular junction. Plasticity and second messengers during synapse development. Retrograde signaling that regulates synaptic development and function at the Drosophila neuromuscular junction. Activity-dependent regulation of transcription during development of synapses. Experience-dependent potentiation of NMJs. Selected methods for the anatomical study of Drosophila embryonic and larval neuromuscular junctions.
Animating emotions in ECA’s for interactive applications

: Within interactive applications, emotions expressed through animations are often overlooked and when animating for a mobile platform, certain constraints have to be considered, such as a limited amount of polygons and bones in the model. This master’s thesis, aims to investigate how to apply emotional expressions through body language by the use of animation to an embodied conversational agent (ECA), used for an interactive application on a mobile device. The research suggests the three most suited emotions to test as being: angry, sad and happy. Furthermore a list of emotional expressions to implement in the animations was identified, and a test was then conducted to validate the findings, by asking the participants how they perceived the emotional states of the ECA. The results indicate that it is possible to implement emotions through body language to an ECA, when constrained by a mobile platform.
Bioaditivos e aditivos naturais em alimentos: Corantes, antioxidantes e aromatizantes

Os aditivos naturais representam uma alternativa interessante a ser adotada pelas indústrias de alimentos em substituição aos compostos artificiais, sendo que existe uma tendência crescente na busca por alimentos saudáveis entre os consumidores. Dessa forma, métodos para extração de aditivos naturais e obtenção de bioaditivos estão sendo alvo de pesquisas e seu uso vem se demonstrando bastante eficiente para proporcionar cor, aroma e conservação aos alimentos de maneira natural. Esse artigo de revisão traz estudos que buscam compostos naturais com potencial aditivo para uso em alimentos, bem como aborda aspectos relacionados com a extração e a biotransformação dessas substâncias naturais, dando ênfase nos compostos com potencial para conferir aroma, cor e atividade antioxidante em alimentos. Palavras-chave: Biotecnologia. Radicais livres. Compostos naturais.
The role of the GRB2 family of adaptor proteins in T cell receptor-mediated signaling

CD4+ T cells are critical in the fight against parasitic, bacterial, and viral infections, but are also involved in many autoimmune and pathological disorders. Ligation of the T Cell Receptor (TCR) is the primary signal required for T cell activation proliferation, differentiation and cytokine release. Upon TCR activation, several kinases and adaptor proteins are assembled at the TCR/linker for activation of T cells (LAT) signaling complexes, a process indispensable for optimal signal transduction. One important group of proteins recruited to the TCR/LAT complexes is the GRB2 family of adaptors. Due to their role in mediating signaling complexes, the GRB2 family of adaptors are critical for development, proliferation, and survival of diverse cell types. These proteins have been linked to the initiation and progression of numerous pathological conditions including diabetes, asthma/allergy, and solid and hematopoietic malignancies. Therefore, it is essential to characterize and understand the complete functions of these proteins for the generation of safe and efficient targeting treatments for diseases mediated by these proteins. In T cells, GRB2 and its homologs, GADS and GRAP, are crucial for the propagation of signaling pathways through the TCR and adaptor protein LAT. These proteins recruit distinct sets of proline-rich ligands to LAT thereby inducing multiple signaling pathways such as MAP kinase activation, calcium influx and cellular adhesion. However, the role of GRB2 family members in controlling TCR and LAT mediated signaling in mature human T cells is not completely understood. Moreover, the relative role of GRB2 family members in the extent and timing of the
Inference of Progressive Loop Invariants for Array Programs

Formal verification of programs that utilize loops typically requires the user to provide inductive loop invariants. Providing such invariants can be cumbersome which is why a wide range of inference techniques have been proposed. These techniques are, however, limited with respect to array programs. In this thesis we introduce progressive loop invariants – an abstraction that captures information about which loop iterations have already been executed and which ones will be executed in the future. We, furthermore, discuss a series of analyses based on progressive loop invariants that let us infer useful information about the behaviour of array programs and help us verify such programs. Based on a set of examples we, furthermore, show that these analyses work well in practice.
Identification and cloning of amplified DNA sequences by a modified-in-gel renaturation technique: Isolation of an amplified DNA sequence from a human sarcoma.

A modified in gel renaturation technique has been developed which detects DNA sequence amplifications of ≥10-fold without prior identification of the target gene. In order to determine the sensitivity of detection and applicability of modified in gel renaturation, primary human tumor cultures and drug resistant human cell lines with identified cellular gene amplifications were assayed. The modified in gel renaturation technique was then used to screen 71 human tumor cell lines and direct tumor biopsies for amplified sequences. Particular emphasis was placed on screening cell lines derived from human melanoma and direct tumor samples from adult sarcomas. Four of 55 cell lines tested had amplification ≥10-fold of previously known cellular oncogenes. None of the 25 melanoma short term cultures tested positive by this assay. One of 16 adult sarcoma samples (a malignant fibrous histiocytoma (MFH)) tested positive for DNA sequence amplification >10-fold. The amplified DNA present in this MFH, (termed ST-23987), was not identified by Southern blot analysis with a panel of oncogene probes previously reported as amplified in other human malignancies. In order to further characterize the amplified DNA in ST-23987, DNA was subjected to in gel renaturation cloning procedures followed by PCR modified cloning. Of 55 clones isolated and analyzed, four cloned inserts (termed pMAC895, pMAC15, pMAC20, and pMAC30) were amplified between 10-to-15-fold in ST-23987DNA. Several other adult sarcomas were probed with these four clones and three other instances of amplification were identified by Southern blot analysis with probes generated from pMAC15 and pMAC30 (found in tumors ST-24609, 870141 and ST-23493). A bacteriophage lambda genomic library was constructed from DNA isolated from a ST-23493. Four clones representing ∼34 kb of the amplified domain (designated 493.1, 493.2, 493.4, and 493.5) were isolated using clones pMAC15 and pMAC30 as probes. Plasmid subclones generated from the EcoRI fragments of the amplified bacteriophage lambda clones (termed p10.5, p6.0, p5.2, p5.0, p4.7, p2.8, and p0.5) were used as probes against Northern blots of sarcoma mRNA in an attempt to identify transcribed sequences within the cloned regions of the amplification unit. The hypothesized target gene carried within the amplification unit will likely be important to the progression, diagnosis and treatment of adult sarcoma, irrespective of the target gene identity.
PARTICLE SIZE CHARACTERIZATION OF NANOPARTICLES–A PRACTICALAPPROACH

Most properties of nanoparticles are size-dependent. In fact, the novel properties of nanoaprticles do not prevail until the size has been reduced to the nanometer scale. The particle size and size distribution of alumina nanoparticle, as a critical properties, have been determined by transmission electron microscopy (TEM), photon correlation spectroscopy (PCS), surface area analysis (BET) and x-ray diffraction peak broadening analysis. The particle size was found to be in the range of 5-95nm. Cumulative percentage frequency plot of the data extracted form TEM images indicates that particle size distribution obeys the log-normal function. The TEM images also reveal that particles are spherical in shape and loosely agglomerated. Comparing of the XRD and TEM results shows that the particles are single-crystal. The HRTEM images also verify that the particles have a single-crystal nature. In comparison, there is a good correlation between the BET, XRD and TEM measurements other than PCS that is sensitive to the presence of the agglomerates.
Communication In International Alliances And Effects On Their Goals Achievement

This study shows the extent to which the communication between allies affects the goals achievement of their alliance. A quantitative empirical analysis, adopting a hypothetico-deductive approach, was carried out in order to validate the causal model. The results, declined from a collected data by a survey distributed to 114 international alliances, evince that communication has a positive effect on three objectives of alliances namely cost reduction, risk reduction and the development of new skills but not new technologies development.
The Unpatchable Silicon: A Full Break of the Bitstream Encryption of Xilinx 7-Series FPGAs

The security of FPGAs is a crucial topic, as any vulnerability within the hardware can have severe consequences, if they are used in a secure design. Since FPGA designs are encoded in a bitstream, securing the bitstream is of the utmost importance. Adversaries have many motivations to recover and manipulate the bitstream, including design cloning, IP theft, manipulation of the design, or design subversions e.g., through hardware Trojans. Given that FPGAs are often part of cyber-physical systems e.g., in aviation, medical, or industrial devices, this can even lead to physical harm. Consequently, vendors have introduced bitstream encryption, offering authenticity and confidentiality. Even though attacks against bitstream encryption have been proposed in the past, e.g., side-channel analysis and probing, these attacks require sophisticated equipment and considerable technical expertise. In this paper, we introduce novel low-cost attacks against the Xilinx 7-Series (and Virtex-6) bitstream encryption, resulting in the total loss of authenticity and confidentiality. We exploit a design flaw which piecewise leaks the decrypted bitstream. In the attack, the FPGA is used as a decryption oracle, while only access to a configuration interface is needed. The attack does not require any sophisticated tools and, depending on the target system, can potentially be launched remotely. In addition to the attacks, we discuss several countermeasures.
Students' Admission Prediction using GRBST with Distributed Data Mining

Data is the most important asset of any organization which is further processed to produce useful information. Data mining techniques are widely used for industrial sectors to generate the useful pattern helpful for earning more profits and expand business. Since last few years, lots of research works have been done by applying data mining techniques on educational data for improvement in Education System. Data Mining can be useful for predicting such as the students’ admission, faculty performance, student performance, identifying the group of students of similar behavior. Very large educational institute’s data are geographically spread and increase every year. It is very time consuming and tedious task of processing these large volume of data. In this paper, the new algorithm has been presented with Binary Search Tree which stores the global rules by consolidating the local rules generated at each site. This Global Rule Binary Search Tree (GRBST) can then be used in prediction of Students' admission to college.
Analyse et simulation numérique par méthode combinée Volumes Finis - Éléments Finis de modèles de type Faible Mach

Dans cette these, nous etudions des ecoulements caracterises par un faible nombre de Mach. Dans une premiere partie, nous developpons un schema numerique permettant la resolution des equations de Navier-Stokes a faible nombre de Mach. L’equation de continuite est resolue par une methode de volumes finis, tandis que l’equation de conservation de la quantite de mouvement et l’equation d’evolution de la temperature sont resolues par elements finis. Le schema ainsi developpe assure la preservation des etats constants. Dans une seconde partie, nous faisons l’analyse d’un modele de type faible Mach specifique, dans lequel la pression thermodynamique est consideree constante, et la viscosite est une fonction particuliere de la temperature. Nous montrons l’existence, l’unicite et la regularite des solutions, ainsi qu’un resultat de principe du maximum pour la temperature. Enfin dans une troisieme partie, nous developpons un schema numerique permettant de simuler les equations de ce modele. L’accent est mis sur la discretisation de l’equation de temperature, qui est de type volumes finis. Plusieurs schemas sont etudies et compares sur des criteres de precision et de respect du principe du maximum. L’equation de conservation de la quantite de mouvement est discretisee par elements finis, definissant un nouveau schema combine.
Optimization of adsorptive desulfurization process conditions for FCC gasoline

In order to study the desulfurization of FCC gasoline, Zn/NaY zeolite FCC gasoline adsorbent was synthesized by impregnation method. The effects of space velocity, adsorbent bed temperature, adsorbent roasting temperature and roasting time on the desulfurization rate of FCC gasoline were investigated by adsorbent and fixed bed process. The results showed that the desulfurization rate of FCC gasoline reached about 85% under the conditions of 0.5 h-1 air velocity, 35°C adsorbent bed temperature, 700°C adsorbent roasting temperature and 4 h roasting time. Adsorption desulfurization as a technology with many advantages, such as low investment, low operation cost, complete desulfurization, had good application prospects and popularization value. To develop a fixed bed adsorption desulfurization technology for FCC gasoline which meets the requirements of V gasoline quality standards of producing countries.