Miracle-dz/UniFAR-FTUs huggingface dataset:
Identificación de nombres de genes en la literatura biomédica

An enormous complexity arises in the identification of gene terms in biomedical literature. With the discovery of huge quantities of genes, and the Human Genome Project (HGP), the scientists have remained without easy and intuitive names. In the genomic information many forms of variation occur due to lack of standardization of gene names. Although nomenclature and ontological specifications are valuable for processing, efforts toward the systematic naming of genes have been made, but the difficulty still exists. The development of procedures that resolve these problems would benefit the progress of molecular pathways, the extraction of gene-gene and gene-disease interactions, the delimitation of the structure of the genomic research domain through gene-document relations and the knowledge discovery that is hidden in the biomedical literature. Our proposal relies on approximate pattern-matching techniques, adopted of natural language processing (NLP), to find and filter gene variants matches. To perform the gene-matching, we apply finite-state transducers (FSTs). To implement our prototype system, we were using publicly available gene and text databases, such as FlyBase (biological database of the Drosophila genome projects) and PubMed (US National Library of Medicine).
Effect of Leuconostoc kimchii GJ2 Isolated from Kimchi (Fermented Korean Cabbage) on Lipid Metabolism in High Cholesterol-Fed Rats

The present study investigated the effect of Leuconostoc kimchii GJ2 (Leu. kimchii GJ2), an exopolysaccharide-producing lactic acid bacterium isolated from kimchi, on serum and liver lipid metabolism in rats fed a high-cholesterol diet. Male Sprague-Dawley rats were divided into four groups: a normal diet group (ND), a high-cholesterol diet group (HCD), a high-cholesterol diet and 200 mg/kg Leu. kimchii GJ2-administered group (HCD-LKL), and a high-cholesterol diet and 400 mg/kg Leu. kimchii GJ2-administered group (HCD-LKH). No between-group differences were found in body weight gain, food intake, or food efficiency ratio. The serum GOT and ALP activities that were elevated by the high-cholesterol diet were significantly decreased after Leu. kimchii GJ2 administration. Serum HDL-cholesterol level was markedly increased in the Leu. kimchii GJ2-administered groups, whereas the serum total cholesterol and LDL-cholesterol levels were lower in the Leu. kimchii GJ2-administered animals. Liver levels of total cholesterol and triglyceride were also markedly lower in the Leu. kimchii GJ2-administered groups. In addition, increased activities of HR-LPL and TE-LPL in adipose tissue, caused by the high-cholesterol diet, fell to normal after administration of Leu. kimchii GJ2, in a dose-dependant manner. These results suggest that Leu. kimchii GJ2 isolated from kimchi exerts an antiatherosclerotic effect by reducing serum and liver cholesterol levels.
Locomotion et morphologie du labyrinthe osseux chez les hominoïdes actuels. Application à Sahelanthropus tchadensis (Hominidae, 7 Ma, Tchad)

L’espece humaine est caracterisee par une forme de locomotion bipede qui lui est propre. Toumai, l’holotype de l’espece Sahelanthropus tchadensis decouverte au Tchad, est le plus ancien representant connu du rameau humain. Date de 7 millions d’annees, il est tres proche de la dichotomie entre ce rameau et celui des chimpanzes. C’est donc un temoin precieux des premieres phases de l’evolution de la locomotion dans ce groupe. Le but de ce travail est de reconstituer le comportement locomoteur de Sahelanthropus tchadensis a partir de l’etude de la partie osseuse de son labyrinthe, organe de l’equilibre.Pour cela, les relations entre locomotion et morphologie du labyrinthe osseux sont recherchees chez les hominoides actuels. Les covariations entre le labyrinthe et le crâne sont etudiees chez Homo sapiens afin de determiner l’influence sur la morphologie du labyrinthe de son integration dans le crâne. Ces resultats sont enfin appliques au labyrinthe de Toumai, compare a d’autres hominines fossiles.La morphometrie geometrique discrimine l’ensemble des especes actuelles par l’orientation, la taille et la forme relatives de chacune des parties du labyrinthe. Cependant, la torsion et l’orientation relative des canaux semi-circulaires sont majoritairement liees a l’integration du labyrinthe dans le crâne (orientation des pyramides petreuses et de la face par rapport a la ligne medio-sagittale du basicrâne). Au contraire, l’excentricite des canaux et leur taille sont uniquement liees a la locomotion.Chez Sahelanthropus tchadensis, la taille des canaux semi-circulaires indique une espece relativement plus agile que les grands singes. En revanche, il ne presente pas les rotations de canaux caracteristiques du genre Homo. La forme de ses canaux constitue une combinaison unique de caracteres : canal posterieur rond et canal anterieur legerement etire, comme les humains et les australopitheques, mais canal lateral legerement projete postero-lateralement, comme les gorilles et les babouins. Ceci indiquerait un comportement locomoteur associant le grimper vertical dans les arbres a des deplacements au sol bipedes mais aussi quadrupedes.
Can Tweets Predict TV Ratings?

We set out to investigate whether TV ratings and mentions of TV programmes on the Twitter social media platform are correlated. If such a correlation exists, Twitter may be used as an alternative source for estimating viewer popularity. Moreover, the Twitter-based rating estimates may be generated during the programme, or even before. We count the occurrences of programme-specific hashtags in an archive of Dutch tweets of eleven popular TV shows broadcast in the Netherlands in one season, and perform correlation tests. Overall we find a strong correlation of 0.82; the correlation remains strong, 0.79, if tweets are counted a half hour before broadcast time. However, the two most popular TV shows account for most of the positive effect; if we leave out the single and second most popular TV shows, the correlation drops to being moderate to weak. Also, within a TV show, correlations between ratings and tweet counts are mostly weak, while correlations between TV ratings of the previous and next shows are strong. In absence of information on previous shows, Twitter-based counts may be a viable alternative to classic estimation methods for TV ratings. Estimates are more reliable with more popular TV shows.
A call for statistical pluralism answered

We welcome Lukacs et al.'s (2007) response to our paper calling for pluralism in inferential approaches. These are important issues and we sought to clarify the strengths and weaknesses of two inferential approaches in an atmosphere that avoided denigrating either, while emphasizing that poor application of any statistical approach is a weak basis for disregarding it as a tool for science. Lukacs et al.'s (2007) contribution is helpful, clarifying the arguments in favour of information theoretic (IT) approaches. The single-parameter example is useful and does much to illustrate the application of the approach. In general, we applaud statistical formalization of the method of multiple working hypotheses, as well as the focus on acknowledging model selection uncertainty, which we see as a principal advantage of that method. In spite of our broad concurrence with Lukacs et al. (2007), it is unsurprising that areas of disagreement remain. Here, we focus on four. First, we question their apparent view that arguments regarding null hypothesis testing (NHT) and IT are widely understood, and that confusion over statistical methods is dissipating. Second, we believe that, whether or not it is the best method for a given problem, NHT can represent a far richer approach to analysis than represented by Lukacs et al. (2007). We clarify why this is the case. Third, we are concerned that, by denigrating the statistical theory underlying NHT as relatively weak, Lukacs et al. (2007) overstate the degree to which elements of their suggested IT algorithms are established, and their performance known. Last, in disparaging exploratory data analysis (EDA), Lukacs et al. (2007) confuse different stages of scientific endeavour. We explain what we see as the purpose of EDA and its role in science.
Proteins and Antigens of Mycobacterium tuberculosis

The proteins of the causative agent of tuberculosis, Mycobacterium tuberculosis, have been a major research topic almost since the days of the discovery of the organism by Robert Koch in 1882. The goals of subsequent efforts have been to identify antigens that may be important in conferring protection against tuberculosis. The search for improved diagnostic reagents such as improved skin test reagents and/or serological markers is another aspect of such studies. Obviously, each protein of M. tuberculosis, like proteins of any other organism, serves different functions. As discussed in this chapter, many bacterial proteins are highly conserved, not only within the genus Mycobacterium but also in a broad range of other bacterial species. One example is the group of stress or heat shock proteins that are produced in abundant quantities by M. tuberculosis and that exhibit at least 50% homology at the amino acid level with stress proteins from other bacterial species. A new group of researchers were thereby recruited to the field from other disciplines, and the microorganism was soon approached at both the DNA level and the protein level by the development of monoclonal antibodies (MAbs) raised against M. tuberculosis. Five recombinant antigens have been produced in large enough quantities to be distributed to interested researchers through a WHO-organized "antigen bank". In gram-negative bacteria, the cell wall consists of three layers: the cytoplasmic membrane, the peptidoglycan layer, and an outer lipopolysaccharide-containing cell membrane.
Karyotype Analysis of Japanese Burmannia (Burmanniaceae)

Cytological studies on four myco-heterotrophic species of Burmannia (Burmanniaceae) in Japan were carried out. The finding of a chromosome number of 2 n = 176 = 88II (88 bivalents) in B. championii dif-fered significantly from previous reports of 2 n = 12, 64–72. Chromosome numbers of 2 n = 120 for B. cryptopetala , 2 n = 60 for B. itoana and 2 n = 24 for B. nepalensis are reported here for the first time. Wide variation in chromosome number, chromosome length and karyotype at resting stage and metaphase was observed among the four Japanese species of Burmannia .
POPULATION REGULATION IN WOLVES

of social regulation of wolf populations Some of the first studies of wolves indicated that their populations did not increase as rapidly as was theoretically possible, and that they reached a saturation point apparently not set by food. Subsequent captive studies demon strated the existence of social mechanisms possibly capable of regulat ing population growth. However, the importance of these factors in wild populations has not been established. This paper has four objec tives: (1) to evaluate the existing concept of "intrinsic limitation," (2) to propose that wolf population dynamics may be better understood by considering feedback between the prey resource and the wolf popula tion, (3) to evaluate group selection explanations regarding evolution of limiting mechanisms," and (4) to propose an alternative explanation based on individual selection.
Future Development of Customer Analytics in Marketing

Customer Analytics is a fairly new part of business analytics. It has brought new, granular approach to customers. Since it is developing along with technology, a lot has changed since its beginnings in the 60's and 70's. As marketing relies on customer analytics, it is important to know where the analytics are heading and how marketing can benefit from it. The goal of this paper is to show the possible future development of customer analytics in marketing. It is going to be achieved by an extensive literature review on this topic, with the focus on the latest findings in these fields.
The Evolution of plant physiology : from whole plants to ecosystems

Coupled with biomechanical data, organic geochemistry and cladistic analyses utilizing abundant genetic data, scientific studies are revealing new facets of how plants have evolved over time. This collection of papers examines these early stages of plant physiology evolution by describing the initial physiological adaptations necessary for survival as upright structures in a dry, terrestrial environment. The "Evolution of Plant Physiology" also encompasses physiology in its broadest sense to include biochemistry, histology, mechanics, development, growth, reproduction and with an emphasis on the interplay between physiology, development and plant evolution. It has contributions from leading neo- and palaeo-botanists from the Linnean Society. Focus is on how evolution shaped photosynthesis, respiration, reproduction and metabolism. There is coverage of the effects of specific evolutionary forces - variations in water and nutrient availability, grazing pressure, and other environmental variables.
Importance of secreted lipases for virulence of the phytopathogenic fungus Fusarium graminearum

Two secreted lipases FGL1 and FgLIP1 of Fusarium graminearum have been characterized as important factors for plant infection and for nutrition acquisition, respectively. In this report, we identified 15 more putatively secreted lipases of the fungus which share the same lipase motif of five amino acids GXSXG. Disruption of the entire coding sequence of the secreted lipase genes by gene replacement techniques revealed their function during plant infection. While most of the lipases were not required for fungal infection, disruption of lipase genes FGL2 and FGL5 led to the reduced infection on wheat heads and maize cobs, indicating that these lipases are general virulence factors required for plant infection. Measurements of the gene transcripts by real-time PCR during plant infection revealed that transcription of the characterized lipase FGL1 is highly induced after 3 days post inoculation (dpi). Interestingly, we observed the decreased induction of FGL1 in the reduced virulence mutants delta FGL2 and delta FGL5 but not in the delta FGL4, a virulent strain, after 3 dpi. This implicates that lipase activity of FGL2 and FGL5 is required for induction of FGL1. By complementing the delta FGL2 and delta FGL5 inoculums with different free fatty acids, it iswas revealed that gamma-linolenic acid induced the expression of the gene FGL1 in the delta FGL2 inoculums. Therefore, we hypothesized that free fatty acids liberated from FGL2 and FGL5 activity are required for activation of the important virulence factor FGL1 during plant infection.
Research regarding the lactating period of the bitch.

Breastfeeding shows for all species the most important period for both the female and the new generation of products. Milk produced by a bitch, by his the qualities it is, offers puppies a considerable growth rate. Research conducted on 10 female breeds: German Shepherd Dog, Caucasian Shepherd, Labrador and West terrier showed qualitative differences in colostrum and matern milk. The differences were both studied the chemical composition of each race and in different periods of lactation. Protein percentage was higher in colostrum at 8.1% in female German Shepherd breed and lowest 3.7% in West terrier breed. Regarding the entire period of lactation, the highest percentage of protein was recorded at Caucasian Shepherd females (7.5%) and the lowest breed West terrier (3.5%). Correlations between body weight and quantity of milk is strongly positive, with a value of 0.72, and also the correlation between the amount of milk and prolificacy was positive, being +0.61.
Myc-p27 expression and interactions in chronic lymphocytic leukemia and in myeloid cells differentiation

[EN]: We studied expression levels of cell cycle inhibitor p27 and Myc (an oncogenic transcription factor) in more than 100 chronic lymphocytic leukemia (CLL) patients. p27 and Myc levels were inversely correlated. Thus, the ratio between p27 (overexpressed) and Myc (downregulated) appears inverted in CLL with respect to the other tumors so far known. Moreover, low p27 and high Myc expression correlated with the expression of Skp2, which is the main responsible for p27 degradation, suggesting a pathway Myc-Skp2-p27 in CLL. To investigate why p27 is expressed in CLL we overexpressed it in a CLL-derived cell line (MEC1) and observed that high levels of p27 provide resistance to fludarabine treatment. Also, we studied the erythroid differentiation in human K562 cells induced by two different p27 mutants (p27CK- and p27 Nt). p27 Nt transfection resulted in erythroid differentiation, but p27CK- only induced differentiation when Myc expression was low. Thus, we studied the correlation between both Myc and p27 in this process and we found that p27 induced erythroid differentiation through Myc downregulation.
A multimeric complex of adenoviral small e1a and host cell proteins condenses chromatin

Author(s): Johnson, Sarah Anne | Advisor(s): Berk, Arnold J | Abstract: Classically, transcriptional regulation is discussed as the recruitment and assembly of RNA Polymerase II (Pol II) and its pre-initiation complex (PIC) on promoter regions of DNA. However, upstream of this event, transcriptional regulation also requires the regulation of chromatin structure between repressive, condensed forms of chromatin and active, decondensed chromatin to allow transcription of cellular genes. Chromatin structure is regulated via modifications on the histone tails by histone modifiers, such as the lysine acetyltransferase p300/CBP(P300). The actions of repressive and activating transcriptional regulators binding to chromatin result in the highly regulated expression of genes in cells. Adenovirus infects the terminally differentiated cells of the human respiratory epithelium. In order to create a conducive environment for the viral life cycle, the first viral protein expressed, e1a interacts with RB and p300 proteins to reprogram the host cell's epigenetic landscape. This dissertation shows that in order to repress some host cell genes, small e1a rearranges host cell chromatin into higher order condensed chromatin. Furthermore, the condensation of chromatin by small e1a requires the RB and P300 interaction, the maintenance of RB in its repressive state and e1a interactions with host cell chromatin modifiers. This work also hopes to refine the e1a-P300 interaction in e1a-induced chromatin condensation, and through those studies illuminate understanding of P300 and its protein domains. Overall, further studies are required, but this work furthers understanding of the precise impact of adenoviral small e1a interactions with host cell proteins. More broadly, these studies further knowledge not only in how adenovirus oncogenic transformations, but overall cellular functions, that when mis-regulated, lead to cancer.
Nutritional value and utilization of plants with antimicrobial properties as components of the diet of dairy sheep

The aim of these thesis was to evaluate the nutritional characteristics and the productive and health effects of several aromatic plants with known high antimicrobial activity supplied to sheep. The review of the literature explored the characteristics and nutritional the effects of aromatic plants and of their extracts. In the first chapter, 18 herbs with known antimicrobial activity -- Achillea millefolium L. (aerial parts), Anethum graveolens L. (seeds), Carum carvi L . (seeds), Chamaemelum nobile All . (aerial parts), Coriandrum sativum L . (seeds), Hyssopus officinalis L . (aerial parts), Lavandula angustifolia Mill . (vegetative parts), Lavandula angustifolia Mill . (flowers), Melissa officinalis L . (vegetative parts), Ocimum basilicum L . (vegetative parts), Origanum vulgare L . (vegetative parts), Pimpinella anisum L . (seeds), Pinus Silvestris L . (young shoots), Rosmarinus officinalis L . (vegetative parts), Salvia officinalis L . (vegetative parts), Satureja montana L . (vegetative parts), Thymus serpyllum L . (vegetative parts) and Thymus vulgaris L . (vegetative parts) – were evaluated to asses their nutritional characterisitics and values utilizing chemical analysis and in vitro fermentation studies. Based on the results of this Chapter, 7 plant species were selected for further studies. In the second and in the third chapters these 7 species were used in two experiments to assess their palatability when used alone or mixed with other concentrates. Based on the results of these studies, one plant was discarded and 5 plants were used in a productive short term experiment. Indeed, the fourth chapter deals with the experiments carried out on lactating ewes in order to evaluate the intake of the mixes including the plants, and the effects on milk production and composition, health status of the animals, and rumen function. Based on the results of the short term productive experiment, 3 plants were considered superior: Carum carvi , Coriandrum sativum and Satureja Montana . These plants need to further studies to asses their productive and health effects when used in long term studies and to assess their ability to transfer active microbial compounds to the milk and the cheese.
Relations between mycorrhizas and fruitbodies of mycorrhizal fungi in Douglas fir plantations in The Netherlands.

SUMMARY Relations between above-ground fruitbodies of mycorrhizal fungi and mycorrhizas in the soil were studied in 23 Douglas fir stands of various ages in The Netherlands. In the autumn of 1986, fruitbody and mycorrhiza density and diversity were determined. Quantitative relations were found between above-ground fruitbodies of mycorrhizal fungi and below-ground mycorrhizas. Mycorrhiza density explains fruitbody density better than mycorrhiza frequency, but fruitbody density is an unreliable estimator of mycorrhiza density. Density of root tips does not influence the density of fruitbodies. The above-ground diversity, in number of species of fruitbodies, is reflected by the below-ground diversity, in number of mycorrhiza types, but the below-ground diversity is not explained simply by the number of species fruiting. The strong decline in density and diversity of fruitbodies and mycorrhizas with age of the stands cannot be explained yet.
Variation in Mitochondrial DNA Sequences of Black Porgy, Acanthopagrus schlegeli, in the Coastal Waters of Taiwan

22urgent need to resurrect these stocks through con-servation, management, and mariculture. Definingthe systematic status and population structure of aspecies is a basic prerequisite for making informeddecisions regarding rational exploitation and man-agement, as well as for correct interpretation ofecological investigations (Ferguson and Mason1981). Due to maternal inheritance and a relativelyfaster evolutionary rate, mitochondrial DNAs(mtDNA) have been used to provide insights intopopulation genetic structure, gene flow, hybridiza-tion, biogeography, and phylogenetic relationshipsof various animals (Avise et al. 1986, Moritz et al.1987, Bartlett and Davidson 1991, Bowers et al.1994, Sang et al. 1994, Taylor and Dodson 1994,Jean et al. 1995a).