Miracle-dz/UniFAR-FTUs huggingface dataset:
Synthesis and Biological Evaluation of Isosteric Analogs of Mandipropamid for the Control of Oomycete pathogens

A series of isosteric analogs of mandipropamid were designed and synthesized via ‘click chemistry’. The amide bond of mandipropamid was substituted by a 1,2,3‐triazole functional group. The bioassay results have indicated that some of the title compounds exhibited moderate fungicidal activity against Pseudoperonospora cubensis, and the activity has been systematically studied as a function of molecular structure. The low activity of the mandipropamid analog that contains a lipid chain is likely due to the presence of a weak hydrogen bond donor in the 1,2,3‐triazole. Furthermore, we have performed the molecular modeling and found that N‐methylamide could be more effective than amide as the surrogates to 1,2,3‐triazole, which ultimately leads to a longer distance (1.1 Å longer) between the two substitutes in the 1,4‐disubstituted 1,2,3‐triazole compound.
Novel computational techniques for mapping and classifying Next-Generation Sequencing data. (Nouvelles techniques informatiques pour la localisation et la classification de données de séquençage haut débit)

Since their emergence around 2006, Next-Generation Sequencing technologies have been revolutionizing biological and medical research. Quickly obtaining an extensive amount of short or long reads of DNA sequence from almost any biological sample enables detecting genomic variants, revealing the composition of species in a metagenome, deciphering cancer biology, decoding the evolution of living or extinct species, or understanding human migration patterns and human history in general. The pace at which the throughput of sequencing technologies is increasing surpasses the growth of storage and computer capacities, which creates new computational challenges in NGS data processing. In this thesis, we present novel computational techniques for read mapping and taxonomic classification. With more than a hundred of published mappers, read mapping might be considered fully solved. However, the vast majority of mappers follow the same paradigm and only little attention has been paid to non-standard mapping approaches. Here, we propound the so-called dynamic mapping that we show to significantly improve the resulting alignments compared to traditional mapping approaches. Dynamic mapping is based on exploiting the information from previously computed alignments, helping to improve the mapping of subsequent reads. We provide the first comprehensive overview of this method and demonstrate its qualities using Dynamic Mapping Simulator, a pipeline that compares various dynamic mapping scenarios to static mapping and iterative referencing. An important component of a dynamic mapper is an online consensus caller, i.e., a program collecting alignment statistics and guiding updates of the reference in the online fashion. We provide Ococo, the first online consensus caller that implements a smart statistics for individual genomic positions using compact bit counters. Beyond its application to dynamic mapping, Ococo can be employed as an online SNP caller in various analysis pipelines, enabling SNP calling from a stream without saving the alignments on disk. Metagenomic classification of NGS reads is another major topic studied in the thesis. Having a database with thousands of reference genomes placed on a taxonomic tree, the task is to rapidly assign a huge amount of NGS reads to tree nodes, and possibly estimate the relative abundance of involved species. In this thesis, we propose improved computational techniques for this task. In a series of experiments, we show that spaced seeds consistently improve the classification accuracy. We provide Seed-Kraken, a spaced seed extension of Kraken, the most popular classifier at present. Furthermore, we suggest ProPhyle, a new indexing strategy based on a BWT-index, obtaining a much smaller and more informative index compared to Kraken. We provide a modified version of BWA that improves the BWT-index for a quick $k$-mer look-up.
Improvement proposal of the effort estimation in software projects using use case points

This research makes a proposal that helps improve the accuracy of the effort estimation using the Use-Case Points method applied to software development projects. In order to determine the proposal a study of the factors that affect the accuracy of the estimation of the Use-Case Points method is carried out. As a result of the study of factors, the contributions of improvement of each author are rescued being used in a quasi-experiment, with the purpose of combining all the contributions that help to improve the Use Case Points method and as a final result to select the best combination of contributions that offers the slightest deviation in the precision of the estimate of the effort.
A novel MCDM combining DEMATEL technique for technology evaluation

This research aims to propose a hybrid process concerning the complex interactive relationship between different economic and industrial prospects towards a more effective evaluation on new technology. To achieve this purpose, the integration of the Decision Making Trial and Evaluation Laboratory (DEMATEL) technique and the analytic network process (ANP) is employed to construct a technology evaluation model regarding the economic and industrial prospects. The emerging organic light emitting diode (OLED) display technology is used as a case in order to verify the applicability of proposed a novel hybrid MCDM method for the technology evaluation. The result of this hybrid process can help top managers of technology-based companies or policy makers of governments to more objectively and effectively determine future research and development direction.
OPT3 Is a Phloem-Specific Iron Transporter That Is Essential for Systemic Iron Signaling and Redistribution of Iron and Cadmium in Arabidopsis[W][OPEN]

This work identifies a physiological substrate and a physiological function of the Arabidopsis oligopeptide transporter, OPT3, in iron (Fe) homeostasis, provides a mechanistic explanation of the role of OPT3 in systemic Fe signaling, and uncovers an aspect of crosstalk between Fe homeostasis and cadmium partitioning. Iron is essential for both plant growth and human health and nutrition. Knowledge of the signaling mechanisms that communicate iron demand from shoots to roots to regulate iron uptake as well as the transport systems mediating iron partitioning into edible plant tissues is critical for the development of crop biofortification strategies. Here, we report that OPT3, previously classified as an oligopeptide transporter, is a plasma membrane transporter capable of transporting transition ions in vitro. Studies in Arabidopsis thaliana show that OPT3 loads iron into the phloem, facilitates iron recirculation from the xylem to the phloem, and regulates both shoot-to-root iron signaling and iron redistribution from mature to developing tissues. We also uncovered an aspect of crosstalk between iron homeostasis and cadmium partitioning that is mediated by OPT3. Together, these discoveries provide promising avenues for targeted strategies directed at increasing iron while decreasing cadmium density in the edible portions of crops and improving agricultural productivity in iron deficient soils.
Ecological Energetics in Early Homo

Models for the origin of the genus Homo propose that increased quality of diet led to changes in ranging ecology and selection for greater locomotor economy, speed, and endurance. Here, I examine the fossil evidence for postcranial change in early Homo and draw on comparative data from living mammals to assess whether increased diet quality has led to selection for improved locomotor performance in other lineages. Body mass estimates indicate early Homo, both males and females, were approximately 33% larger than australopiths, consistent with archeological evidence indicating an ecological change with the origins of our genus. However, many of the postcranial features thought to be derived in Homo, including longer hind limbs, are present in Australopithecus, challenging the hypothesis that early Homo is marked by significant change in walking and running performance. Analysis of energy budgets across mammals suggests that the larger body mass and increased diet quality in early Homo may reflect an increase in the hominin energy budget. Expanding the energy budget would enable greater investment in reproduction without decreasing energy available for larger brains or increased activity. Food sharing and increased adiposity, which decrease variance in food energy availability, may have been integral to this metabolic strategy.
Gene Discovery Offers Tentative Clues to Parkinson's

Parkinson9s disease is caused by the gradual die-off of a set of brain neurons that make the neurotransmitter dopamine. Now, neurobiologists may have found a much-needed clue to what causes the death of those neurons. On page 2045, a research team reports identifying a gene that, when defective, causes an inherited form of Parkinson9s in a large Italian family. The gene, which encodes a brain protein of unknown function called-synuclein, will probably account for, at most, only a few percent of all cases of the disease. But if researchers can figure out just how the mutated-synuclein exerts its effects, they may also gain insight into the cause of the much larger number of cases of nonhereditary Parkinson9s disease.
Immune Regulation of Chlamydia trachomatis Infections of the Female Genital Tract

Tubal infertility and reproductive damage, preeclampsia and preterm births may potentially occur in many of the 50 million women who are annually infected with Chlamydia trachomatis [reviewed in 1; 2- 4]. C.trachomatis infections of the genital tract are also reported to increase the risk of human immunodeficiency virus type 1(HIV-1) susceptibility and viral shedding in the genital tract either directly by pro-inflammatory signalling pathways or indirectly by their effects on genital epithelial cells [5]. A dramatic increase in the number of HIV-1 chemokine co-receptor CXCR4- and CCR5-positive T cell targets has also been reported in the endocervix of C. trachomatis-positive women [6]. Gynecological cancer development is also suggested to be linked with Chlamydial genital tract infections. Epidemiological reports have proposed that C.trachomatis may act as a co-factor in the development of human papilloma virus (HPV)-induced squamous cell carcinomas (SCC), with an association between distinct serovariants of C. trachomatis (B, D, E, G, I, and J) and SCC being reported [7,8]. It is also likely that C. trachomatis co-infections of the lower genital tract (LGT) play a role in carcinogenesis of the female upper genital tract (UGT), particularly epithelial ovarian and type II carcinomas [9,10]. To explain the epidemiological associations of Chlamydial infections cervical and ovarian cancer development it has been hypothesised that the pathogen perhaps triggers epigenetic changes in host chromatin and impairs host DNA repair pathways [11] or that it changes host cell survival pathways by disrupting DNA damage signalling pathways associated with tumorigenesis [12].
A high performance engine for concurrent complex event processing

This paper describes the architecture, prototype implementation and performance analysis of a complex event processing engine that can scale up to very large numbers of concurrent events while keeping the requirements on system resources predictable and low. The main innovation of this approach is that each instantiated event pattern is handled by a dedicated Erlang process, instead of a single or shared operating system thread. This in turn, reduces the latency in processing the event processing as it avoids the overheads associated with resource contention. We demonstrate how this approach can achieve linear event processing times under high event loads, using modest computing resources. Copyright © 2013 John Wiley & Sons, Ltd.
TimeMatrix: Analyzing Temporal Social Networks Using Interactive Matrix-Based Visualizations

Visualization plays a crucial role in understanding dynamic social networks at many different levels (i.e., group, subgroup, and individual). Node-link-based visualization techniques are currently widely used for these tasks and have been demonstrated to be effective, but it was found that they also have limitations in representing temporal changes, particularly at the individual and subgroup levels. To overcome these limitations, this article presents a new network visualization technique, called “TimeMatrix,” based on a matrix representation. Interaction techniques, such as overlay controls, a temporal range slider, semantic zooming, and integrated network statistical measures, support analysts in studying temporal social networks. To validate the design, the article presents a user study involving three social scientists analyzing inter-organizational collaboration data. The study demonstrates how TimeMatrix may help analysts gain insights about the temporal aspects of network data that can be subsequently tested with network analytic methods.
CXCL10 Triggers Early Microglial Activation in the Cuprizone Model

A broad spectrum of diseases is characterized by myelin abnormalities and/or oligodendrocyte pathology. In most, if not all, of these diseases, early activation of microglia occurs. Our knowledge regarding the factors triggering early microglia activation is, however, incomplete. In this study, we used the cuprizone model to investigate the temporal and causal relationship of oligodendrocyte apoptosis and early microglia activation. Genome-wide gene expression studies revealed the induction of distinct chemokines, among them Cxcl10, Ccl2, and Ccl3 in cuprizone-mediated oligodendrocyte apoptosis. Early microglia activation was unchanged in CCL2- and CCL3-deficient knockouts, but was significantly reduced in CXCL10-deficient mice, resulting in an amelioration of cuprizone toxicity at later time points. Subsequent in vitro experiments revealed that recombinant CXCL10 induced migration and a proinflammatory phenotype in cultured microglia, without affecting their phagocytic activity or proliferation. In situ hybridization analyses suggest that Cxcl10 mRNA is mainly expressed by astrocytes, but also oligodendrocytes, in short-term cuprizone-exposed mice. Our results show that CXCL10 actively participates in the initiation of microglial activation. These findings have implications for the role of CXCL10 as an important mediator during the initiation of neuroinflammatory processes associated with oligodendrocyte pathology.
Deliberate imagery practice: the development of imagery skills in competitive athletes

The aim of this study was to examine mental imagery within the context of the deliberate practice framework. Altogether, 159 athletes from one of three different competitive standards (recreational, provincial and national) completed the Deliberate Imagery Practice Questionnaire, which was designed for the present study to assess the athletes' perceptions of the importance of imagery along the three deliberate practice dimensions of relevancy, concentration and enjoyment. The results indicated that national athletes perceived imagery to be more relevant to performing than recreational athletes. In addition, athletes of a higher standard (i.e. provincial and national) reported using more imagery in a recent typical week and they had accumulated significantly more hours of imagery practice across their athletic career than recreational athletes. Finally, the relationships among the dimensions of deliberate practice did not lend conclusive support to either the original conception of deliberate practice or a sports-specific framework of deliberate practice.
Determinantes de la propensión a emprender y del éxito en los emprendimientos

RESUMENEl crecimiento economico y la creacion de empleo en cualquier entorno economico se ven condicionados por los emprendimientos. El objetivo principal de este trabajo es determinar si la condicion de genero, edad, nivel de instruccion, nivel socioeconomico y la capacidad emprendedora influyen en la propension de emprender y en la probabilidad de exito en un nuevo emprendimiento. Con esta finalidad se realizo un estudio empirico sobre una muestra de la ciudad de Machala. Por la naturaleza de los datos se utilizo un modelo logit, siendo el proposito principal de encontrar la probabilidad de que el evento suceda. Esto es apropiado en la presente investigacion para las dos variables dependientes, ya que en la primera variable dependiente se mide la posicion relativa entre la intencion de generar un emprendimiento y no hacerlo, y, en el caso de la segunda variable dependiente se mide la posicion relativa de que un nuevo emprendimiento logre el exito. Los resultados alcanzados muestran que el genero, el nivel de instruccion, el nivel socio economico y la capacidad emprendedora influyen en la propension a emprender. Asi como el genero y el nivel de instruccion en la probabilidad de exito en un nuevo emprendimiento.
The Optimization of the Hermite transform: Application perspectives and 2D generalization

This paper studies the discrete Hermite transform applicability in concise representation of short-term and windowed sinusoidal signals. Namely, the Hermite functions show similar behavior with windowed multi-tone signals and filtered tones, which opens the possibility for signal sparsifation using an optimal transform scaling factor. In other words, the scaling factor is optimized in order to enhance the transform coefficients concentration. The scaling factor optimization method is based on concentration measures and it is further generalized to the case of 2D Hermite transform. Numerical examples illustrate the presented theoretical framework.
Sensor fault diagnosis method based on Hilbert marginal spectrum and supervised locally linear embedding and support vector machine

Sensor plays an important role in complex industrial environment. Therefore, researches on sensor fault diagnosis technology are important for improving the reliability of industry system. A sensor signal which is non-linear and non-stationary, has many kinds of structural characteristics and sensing properties. On the basis of supervised locally linear embedding (SLLE), support vector machine (SVM), and Hilbert marginal spectrum (HMS), as a means of sensor fault diagnosis is proposed in this thesis. HMS is put forward to feature analysis from obtained sensor signals. Then SLLE is put forward to reduce dimensionality of high dimensionality fault signal, that is more effective than other dimensionality reduction means, for example multi-dimensional scaling (MDS), locally linear embedding (LLE) and principal component analysis (PCA). In the end, support vector machine (SVM) is used to complete the sensor fault diagnosis on base of the obtained feature vector. The result shows that the above methods improve the feature extraction and recognition result observably. In the perspective of the results of the simulation, this mean may not merely be significantly used to the fault diagnosis of gas sensor but also offer a direction for other sensors.
3D digital relief generation

This thesis investigates a framework for generating reliefs. Relief is a special kind of sculptured artwork consisting of shapes carved on a surface so as to stand out from the surrounding background. Traditional relief creation is done by hand and is therefore a laborious process. In addition, hand-made reliefs are hard to modify. Contrasted with this, digital relief can offer more flexibility as well as a less laborious alternative and can be easily adjusted. This thesis reviews existing work and offers a framework to tackle the problem of generating three types of reliefs: bas reliefs, high reliefs and sunken reliefs. Considerably enhanced by incorporating gradient operations, an efficient bas relief generation method has been proposed, based on 2D images. An improvement of bas relief and high relief generation method based on 3D models has been provided as well, that employs mesh representation to process the model. This thesis is innovative in describing and evaluating sunken relief generation techniques. Two types of sunken reliefs have been generated: one is created with pure engraved lines, and the other is generated with smooth height transition between lines. The latter one is more complex to implement, and includes three elements: a line drawing image provides a input for contour lines; a rendered Lambertian image shares the same light direction of the relief and sets the visual cues and a depth image conveys the height information. These three elements have been combined to generate final sunken reliefs. It is the first time in computer graphics that a method for digital sunken relief generation has been proposed. The main contribution of this thesis is to have proposed a systematic framework to generate all three types of reliefs. Results of this work can potentially provide references for craftsman, and this work could be beneficial for relief creation in the fields of both entertainment and manufacturing.
Autonomous strategy organization in the dynamical quantitative environment

This paper proposes a system, which manages both efficiency and flexibility in the manufacturing system. It has been considered that an autonomous distributed system is superior to a centralized system in terms of fail-proof expansion, load dispersion, flexibility, and the possibility of the evolution. However, it is difficult to manage both efficiency and flexibility according to conventional method in an autonomous distributed system. To solve the problem, we propose a method. The method is that the carrier organizes the whole number of the carrier in the system, according to the volume of the task and the complexity of it. And we evaluate the proposed method of self-organizing behavior by a multi-AGV autonomous system in the quantitative dynamic environment. It shown that the system has higher efficiency in this system than in the centralized system with self-organization in the quantitative dynamic environment.