Miracle-dz/UniFAR-FTUs huggingface dataset:
Screening and Identification of Therapeutic Targets for Pulmonary Arterial Hypertension Through Microarray Technology

Pulmonary arterial hypertension (PAH) is a rare but fatal disease characterized by vascular cell proliferation; the pathogenesis of PAH has yet to be fully elucidated. Publicly available genetic data were downloaded from the Gene Expression Omnibus (GEO) database, and gene set enrichment analysis (GSEA) was used to determine significant differences in gene expression between tissues with PAH and healthy lung tissues. Differentially expressed genes (DEGs) were identified using the online tool, GEO2R, and functional annotation of DEGs was performed using Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. Next, the construction and module analysis of the protein–protein interaction (PPI) network and verification of the expression level of hub genes was performed. Finally, prediction and enrichment analysis of microRNAs associated with the hub genes was carried out. A total of 110 DEGs were detected by screening PAH and healthy lung samples. The expression of nine genes [polo-like kinase 4 (PLK4), centromere protein U, kinesin family member 20B, structural maintenance of chromosome 2 (SMC2), abnormal spindle microtubule assembly, Fanconi Anemia complementation group I, kinesin family member 18A, spindle apparatus coiled-coil protein 1, and MIS18 binding protein 1] was elevated in PAH; this was statistically significant compared with their expression in healthy lung tissue, and they were identified as hub genes. GO and KEGG analysis showed that the variations in DEGs were abundant in DNA-templated transcription, sister chromatid cohesion, mitotic nuclear division, cell proliferation, and regulation of the actin cytoskeleton. In conclusion, this study has successfully identified hub genes and key pathways of PAH, with a total of 110 DEGs and nine hub genes related to PAH, especially the PLK4 and SMC2 genes, thus providing important clues for the in-depth understanding of the molecular mechanism of PAH and providing potential therapeutic targets.
Mixture models for clustering and dimension reduction

In Chapter 1 we give a general introduction and motivate the need for clustering and dimension reduction methods. We continue in Chapther 2 with a review of different types of existing clustering and dimension reduction methods. In Chapter 3 we introduce mixture densities and the expectation-maximization (EM) algorithm to estimate their parameters. Although the EM algorithm has many attractive properties, it is not guaranteed to return optimal parameter estimates. We present greedy EM parameter estimation algorithms which start with a one-component mixture and then iteratively add a component to the mixture and re-estimate the parameters of the current mixture. Experimentally, we demonstrate that our algorithms avoid many of the sub-optimal estimates returned by the EM algorithm. Finally, we present an approach to accelerate mixture densities estimation from many data points. We apply this approach to both the standard EM algorithm and our greedy EM algorithm. In Chapter 4 we present a non-linear dimension reduction method that uses a constrained EM algorithm for parameter estimation. Our approach is similar to Kohonen's self-organizing map, but in contrast to the self-organizing map, our parameter estimation algorithm is guaranteed to converge and optimizes a well-defined objective function. In addition, our method allows data with missing values to be used for parameter estimation and it is readily applied to data that is not specified by real numbers but for example by discrete variables. We present the results of several experiments to demonstrate our method and to compare it with Kohonen's self-organizing map. In Chapter 5 we consider an approach for non-linear dimension reduction which is based on a combination of clustering and linear dimension reduction. This approach forms one global non-linear low dimensional data representation by combining multiple, locally valid, linear low dimensional representations. We derive an improvement of the original parameter estimation algorithm, which requires less computation and leads to better parameter estimates. We experimentally compare this approach to several other dimension reduction methods. We also apply this approach to a setting where high dimensional 'outputs' have to be predicted from high dimensional 'inputs'. Experimentally, we show that the considered non-linear approach leads to better predictions than a similar approach which also combines several local linear representations, but does not combine them into one global non-linear representation. In Chapter 6 we summarize our conclusions and discuss directions for further research.
A Horizontal Intragravel Pipe for Sampling Water Quality in Salmonid Spawning Gravel

Abstract A new sampler, the horizontal intragravel pipe, was developed for collecting samples of intragravel water in salmonid spawning gravel. The device is a 2.54 x 76.2-cm length of slotted polyvinyl chloride pipe that is buried perpendicular to flow in the streambed. The slots (about 320/pipe) through which the intragravel water flows were cut perpendicular to the long axis of the pipe. Each slot is 1.9 cm long by 0.15 mm wide. A rigid plastic tube (0.64 cm inside diameter) centered axially within the intragravel pipe is perforated with three 3.2-mm holes equally spaced along its length to distribute equally the effect of pumping. The interior tube is connected by Tygon tubing to a peristaltic pump on a platform above the water surface. Intragravel water is pumped to containers for on-site measurement of dissolved oxygen, pH, and specific conductance, and for determination of other constituents in the laboratory. The principal advantages of a horizontal intragravel pipe are that a substantial quantity.
Ractopamine for finishing barrows fed restricted or ad libitum diets: performance and nitrogen balance

Supplementation of 5 ppm of ractopamine, associated or not to feed restriction in diets with a high total lysine content (1.04%) was evaluated on performance and nitrogen balance. In experiment 1, 60 hybrid castrated male swine (76.2 ± 2.3 kg) were housed in pairs according to a randomized complete block design in a factorial treatment arrangement (2 ×2 + 1) with or without ractopamine supplementation, two forms of feeding, ad libitum and feed restriction with 1.04% lysine, and an additional treatment (control), with ad libitum feed without ractopamine with 0.8% lysine, amounting to five treatments and six replications. The final live weight, daily weight gain, daily feed intake and feed conversion for 28 days were evaluated. There were improvements in supplementation with ractopamine for final live weight, daily weight gain and feed conversion. The ad libitum feeding improved both final live weight and daily weight gain compared with ractopamine. Compared with the control, there was a decrease in feed conversion with ractopamine supplementation and improvement for final weight (FW) in the treatment with the ractopamine and ad libitum feed. In experiment 2, 30 hybrid castrated male swine (74.1 ± 2.5 kg) were housed in metabolism cages and fed the same experimental treatments to evaluate the percentages of absorbed nitrogen (Nabs), retained nitrogen (Nret), nitrogen retained from the absorbed nitrogen (Nret/Nabs) and the plasma urea concentration at 14 and 28 days. At 14 days, there was an increase in the Nret/Nabs and plasma urea concentration with ractopamine supplementation. Compared with the control, there was a decrease in the plasma urea concentration for feed restriction with ractopamine. At 28 days, there was an increase in the Nret/Nabs with ractopamine supplementation. Thus supplementation with 5 ppm ractopamine improved the performance and efficiency of swine nitrogen use. Feed restriction interfered negatively in weight gain, but it improved the efficiency of the nitrogen use of barrows.
Finding homogeneous collections of dense subgraphs using constraint-based data mining approaches. (Découverte de collections homogènes de sous-graphes denses par des méthodes de fouille de données sous contraintes)

The work presented in this thesis deals with data mining approaches for the analysis of attributed graphs. An attributed graph is a graph where properties, encoded by means of attributes, are associated to each vertex. In such data, our objective is the discovery of subgraphs formed by several dense groups of vertices that are homogeneous with respect to the attributes. More precisely, we define the constraint-based extraction of collections of subgraphs densely connected and such that the vertices share enough attributes. To this aim, we propose two new classes of patterns along with sound and complete algorithms to compute them efficiently using constraint-based approaches. The first family of patterns, named Maximal Homogeneous Clique Set (MHCS), contains patterns satisfying constraints on the number of dense subgraphs, on the size of these subgraphs, and on the number of shared attributes. The second class of patterns, named Collection of Homogeneous k-clique Percolated components (CoHoP), is based on a relaxed notion of density in order to handle missing values. Both approaches are used for the analysis of scientific collaboration networks and protein-protein interaction networks. The extracted patterns exhibit structures useful in a decision support process. Indeed, in a scientific collaboration network, the analysis of such structures might give hints to propose new collaborations between researchers working on the same subjects. In a protein-protein interaction network, the analysis of the extracted patterns can be used to study the relationships between modules of proteins involved in similar biological situations. The analysis of the performances, on real and synthetic data, with respect to different attributed graph characteristics, shows that the proposed approaches scale well for large datasets.
Hierarchical modelling of population growth rate from individual capture–recapture data

Estimating rates of population change is essential to achieving theoretical and applied goals in population ecology, and the Pradel (1996, Biometrics, 52: 703.) temporal symmetry method permits direct estimation and modelling of the growth rate of open populations, using capture–recapture data from marked animals. We present a Bayesian formulation of the Pradel approach that permits a hierarchical modelling of the biological and sampling processes. Two parametrizations for the temporal symmetry likelihood are presented and implemented into a general purpose software in BUGS language. We first consider a set of simulated scenarios to evaluate performance of a Bayesian variable selection approach to test the temporal linear trend on survival and seniority probability, population growth rate and detectability. We then provide an example application on individual detection information of three species of burrowing nesting seabirds, whose populations cannot be directly counted. For each species, we assess the strength of evidence for temporal random variation and the temporal linear trend on survival probability, population growth rate and detectability. The Bayesian formulation provides more flexibility, by easily allowing the extension of the original fixed time effects structure to random time effects, an option that is still impractical in a frequentist framework.
Phylogeography of a mountain lizard species: an ancient fragmentation process mediated by riverine barriers in the Liolaemus monticola complex (Sauria: Liolaemidae)

Liolaemus monticola is a mountain lizard species, with a widespread distribution from central Chile that displays several highly polymorphic chromosomal races. Our study determined the phylogeographic structuring and relationships among three chromosomal races of L. monticola in Chile. Mitochondrial DNA (mtDNA) sequences of the cytochrome b gene were examined using the following phylogenetic methods: maximum parsimony, maximum likelihood, Bayesian inference and nested clade phylogeographic analyses (NCPAs). These methods revealed two major monophyletic clades (north and south) in the L. monticola species, with non-overlapping geographical locations separated by the Maipo and Yeso rivers (except one hybrid, from a zone of secondary contact). The NCPA showed that a past fragmentation process likely resulted in the separation of the two clades. The southern clade includes all samples of the ‘Southern, 2n = 34’ race; the northern clade is comprised of all remaining derived chromosomal races: the ‘Northern, 2n = 38–40 and the Multiple Fission, 2n = 42–44’ races. Our results support the hypothesis of a geographical and genetic split resulting from allopatric processes caused by riparian barriers acting over a long time period. The inferred biogeographical scenario shows that populations have moved from the south to the north using the Andean mountains as the primary corridor for dispersal. Resumen Liolaemus monticola es una especie de saurio de montana con una amplia distribucion en Chile central, con varias razas cromosomicas polimorficas. Nosotros determinamos la estructura y las relaciones filogeograficas entre tres razas cromosomicas de L. monticola. Secuencias del gen mitocondrial (mtDNA) citocromo b fueron analizadas usando metodos filogeneticos como maxima parsimonia, maxima verosimilutd e inferencia Bayesiana, ademas del analisis filogeografico de clados anidados (NCPA). Estos metodos mostraron dos principales clados monofileticos (Norte y Sur) en la especie L. monticola, los cuales presentan una distribucion disjunta separados por los rios Maipo y Yeso (exceptuando un ejemplar hibrido, perteneciente a una zona de contacto secundario). El NCPA mostro que un evento de fragmentacion en el pasado habria conducido a la separacion de ambos clados. El clado Sur incluye todas las muestras pertenecientes a la raza ‘Sur, 2n = 34’; el clado Norte comprende las restantes razas cromosomicas derivadas: ‘Norte, 2n = 38–40’ y ‘Multiples Fisiones, 2n = 42–44’. Los resultados respaldan la hipotesis de una division genetica y geografica como resultado de un proceso alopatrico causado por rios, el cual no seria un proceso reciente. El escenario biogeografico muestra que las poblaciones habrian colonizado hacia el norte, usando a la Cordillera de los Andes como el principal corredor para la dispersion.
An endophytic Taxol-producing fungus BT2 isolated from Taxus chinensis var. mairei

BT2, a newly isolated endophytic fungus from Taxus chinensis var. mairei, was observed to produce Taxol. Besides Taxol, a potent anticancer drug, BT2 could also yield taxane baccatin III, which was an important intermediate for Taxol and semi-synthesis of Taxol in industry. The isolation of such a fungus may provide a promising alterative approach to produce Taxol, and BT2 can serve as a potential material for fungus engineering to improve Taxol production
Susceptibility of cereal and non-cereal grasses to attack by Hessian fly (Mayetiola destructor (Say)).

Abstract The susceptibility of cereal, pasture, and wild grasses to attack by Hessian fly (Mayetiola destructor (Say)) was investigated by quantifying egglaying responses of adult females and the growth and survival of feeding larvae. A wide range of attractiveness to egglaying adult females was observed, not only between grass species but also within grass species (e.g., wheat). Larval growth and development occurred on all of the New Zealand wheat cultivars, New Zealand barley cultivars, and New Zealand barley breeding lines that were tested. A small number of the United States wheat cultivars and New Zealand wheat breeding lines that were tested did not support the growth of larvae and therefore were resistant to Hessian fly. In addition to wheat and barley, Hessian fly laid eggs and survived as feeding larvae on couch, barley grass, and prairie grass (both wild and cultivated species of the latter). Relative to wheat seedlings, seedlings of the cultivated prairie grass (Bromus willdenowii ’Grasslands .
Routing and performance evaluation of disruption tolerant networks. (Evaluation des performances des réseaux tolérants aux perturbations)

The thesis deals with the design and the evaluation of routing and medium access control protocols for wireless networks. The first part of the thesis focuses on the performance evaluation of routing protocols for disruption tolerant networks (DTNs) when these networks are augmented by fixed relays, termed throwboxes. As a first step, we show that successive instants of meeting between a throwbox and a mobile node moving according to some random mobility model can be well modeled by a Poisson process. We provide explicit formula for the rate of the Poisson process and we show that this rate depends among others on the spatial stationary probability density function of the mobility model as well as on the probability density function of throwboxes spatial distribution. As a second step, we study the impact of adding throwboxes on the performance of two common routing protocols, namely the epidemic and the multicopy two-hop relay protocols. We develop explicit expressions for the distribution and the mean of the delivery time of a packet, as well as for the number of generated copies. Following that, we propose five routing strategies that rely on the presence of throwboxes to perform packet forwarding. We therefore introduce an analytical framework that is based on a markovian model to compute and to compare analytically diverse performance metrics of these strategies. In the second part of the thesis, we concern ourselves with the design and the evaluation of an adaptive mechanism to enhance the performance of the backoff algorithm of IEEE 802.11 standard. We propose an extension of the backoff algorithm where the objective is to enhance the throughput and the delay performances in the case of high number of active users.
A new cytochrome b phylogroup of the common vole (Microtus arvalis) endemic to the Balkans and its implications for the evolutionary history of the species

The phylogeographic architecture of the common vole, Microtus arvalis, has been well-studied using mitochondrial DNA and used to test hypotheses relating to glacial refugia. The distribution of the five described cytochrome b (cyt b) lineages in Europe west of Russia has been interpreted as a consequence of postglacial expansion from both southern and central European refugia. A recently proposed competing model suggests that the 'cradle' of the M. arvalis lineages is in western central Europe from where they dispersed in different directions after the Last Glacial Maximum. In the present study, we report a new cyt b lineage of the common vole from the Balkans that is not closely related to any other lineage and whose presence might help resolve these issues of glacial refugia. The Balkan phylogroup occurs along the southern distributional border of M. arvalis in central and eastern Bosnia and Herzegovina, Montenegro, and eastern Serbia. Further north and west in Slovenia, Bosnia and Herzegovina, and Serbia, common voles belong to the previously-described Eastern lineage, whereas both lineages are sympatric in one site in Bosnia and Herzegovina. The Balkan phylogroup most reasonably occupied a glacial refugium already known for various Balkan endemic species, in contrast to the recently proposed model. South-east Europe is an absolutely crucial area for understanding the postglacial colonization history of small mammals in Europe and the present study adds to the very few previous detailed phylogeographic studies of this region.
Conserved CTCF Insulator Elements Flank the Mouse and Human β-Globin Loci

ABSTRACT A binding site for the transcription factor CTCF is responsible for enhancer-blocking activity in a variety of vertebrate insulators, including the insulators at the 5′ and 3′ chromatin boundaries of the chicken β-globin locus. To date, no functional domain boundaries have been defined at mammalian β-globin loci, which are embedded within arrays of functional olfactory receptor genes. In an attempt to define boundary elements that could separate these gene clusters, CTCF-binding sites were searched for at the most distal DNase I-hypersensitive sites (HSs) of the mouse and human β-globin loci. Conserved CTCF sites were found at 5′HS5 and 3′HS1 of both loci. All of these sites could bind to CTCF in vitro. The sites also functioned as insulators in enhancer-blocking assays at levels correlating with CTCF-binding affinity, although enhancer-blocking activity was weak with the mouse 5′HS5 site. These results show that with respect to enhancer-blocking elements, the architecture of the mouse and human β-globin loci is similar to that found previously for the chicken β-globin locus. Unlike the chicken locus, the mouse and human β-globin loci do not have nearby transitions in chromatin structure but the data suggest that 3′HS1 and 5′HS5 may function as insulators that prevent inappropriate interactions between β-globin regulatory elements and those of neighboring domains or subdomains, many of which possess strong enhancers.
Intraspecific geographic and seasonal physiological variability in an intertidal fish, Girella laevifrons, along a climatic gradient

Metabolic rate and condition factor (K) of juvenile Girella laevifrons were highest in southern populations along the Chilean coast. Since adults of G. laevifrons complete their life cycle in subtidal waters, the results suggest a metabolic cold adaptation in juveniles of this species and physiological compensation that enable them to move early to subtidal environments for reproduction.
Molecular Mechanism of HIV-1 Infection: Role of Viral and Host Determinants

16 1.INTRODUCTION 18 1.1 HIV-1 Structure and Biology 20 1.1.1 Virion structure and genome organization 20 1.1.2 HIV-1 life cycle and replication 23 1.2 HIV-1 Infection and Diversity 27 1.2. 1 HIV-1 pathogenesis 27 1.2. 2 Vertical Transmission 30 1.2. 3 Pediatric HIV-1 Infection 36 1.3 Role of viral determinants in HIV-1 pathogenesis and disease progression 37 1.3. 1 Viral diversity 37 1.3. 2 HIV-1 and its subtypes 43 1.4 Role of host factors in differential HIV-1 replication in neonatal and adult mononuclear cells 47
A Brain Controlled Wheelchair to Navigate in Familiar Environments. (Une chaise roulante contrôlée par ondes cérébrales pour la navigation dans un environnement familier)

HAL is a multi-disciplinary open access archive for the deposit and dissemination of scientific research documents, whether they are published or not. The documents may come from teaching and research institutions in France or abroad, or from public or private research centers. L’archive ouverte pluridisciplinaire HAL, est destinée au dépôt et à la diffusion de documents scientifiques de niveau recherche, publiés ou non, émanant des établissements d’enseignement et de recherche français ou étrangers, des laboratoires publics ou privés. A Brain Controlled Wheelchair to Navigate in Familiar Environments Brice Rebsamen
Response of young female prairie voles (Microtus ochrogaster) to nonresident males: implications for population regulation

We measured behavioral and physiological responses to nonresident males of young female prairie voles (Microtus ochrogaster) living in family groups. Although substantial variation both among families and among littermates was noted, females generally exhibited investigative and affiliative behavior toward nonresident males, and many were reproductive at the end of a 10-day period. Approximately 31 and 56% of females exposed to sexually inexperienced and experienced males, respectively, had uterine weights greater than or equal to 30 mg. Females exposed in the absence of their fathers to sexually experienced males displayed the highest levels of interaction with nonresident males, and 71% were classified as reproductive. Control females, exposed either to castrated nonresident males or not exposed to nonresident males, remained nonreproductive. Frequent interactions with nonresident males can thus override the reproductive suppression experienced by young female prairie voles at natal nests. The resultant.