Miracle-dz/UniFAR-FTUs huggingface dataset:
Detection of polymorphism in xenobiotic metabolising enzymes using database analysis

The link between genomic variation and disease was first recognised over 50 years ago, fuelling research into the underlying genetic basis of rare and complex genetic disorders, disease susceptibility and altered drug response. Interest in polymorphis1n studies has undergone a rapid revival with the recent completion of the Human Genome Project, the advent of sequence databases and the development of computer-based tools designed to detect polymorphisms, all of which are expected to facilitate this area of research. Of particular interest in the study of disease susceptibility and adverse drug responses are enzymes involved in the 1netabolism of xenobiotics such as the glutathione Stransferases (GSTs). The GST superfa1nily belongs to the group of phase II detoxification enzymes that facilitate the detoxification of various carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress with which hu1nans are daily faced. Eight classes of soluble human GSTs, with as many as five isoforms per class, have been defined (Alpha, Kappa, Mu, Omega, Pi, Sigma, Theta and Zeta). Although there is some overlap between classes, each GST isoform possesses unique substrate specificities hence the GSTs are able to provide an effective defence against the potentially damaging effects of a range of xenobiotics and endogenously produced toxic compounds. Polyinorphisn1s in the GSTs have the potential to alter an individual's susceptibility to carcinogens and toxins, and influence the efficacy and toxicity of drug treatment. A nun1ber of polymorphisms have been described in the human GSTs and whilst some appear innocuous, others have been implicated in altering susceptibility to diseases such as cancer and Parkinson's Disease, and influencing response and resistance to drugs, simply through altered activity and expression levels. As these polymorphisms have generally been identified by chance, the extent of genetic polymorphism in the human GST genes remains unknown. The recent developments in bioinformatic approaches to polymorphism detection were therefore applied to the GST superfamily. The following chapters describe the discovery of polymorphisms in the Alpha (Chapter 3), Mu (Chapter 4) and O1nega (Chapter 5) class GSTs using this approach.
SNP identification and validation in two invasive species: zebra mussel (Dreissena polymorpha) and Asian clam (Corbicula fluminea)

espanolEl desarrollo de las plataformas asequibles de secuenciacion masiva en paralelo (SMP) ha reducido el coste y el tiempo en la identificacion de marcadores de polimorfismos de nucleotido unico (PNU) para su uso en estudios de genetica de poblaciones y de conservacion. Tras la SMP, suele ser necesaria una segunda validacion. El analisis de las curvas de fusion a alta resolucion (HRMA en su sigla en ingles) es un metodo rapido y sencillo para escanear mutaciones y, por tanto, es un protocolo adecuado de validacion de dichos marcadores, especialmente en especies no modelo. En este trabajo se presenta un juego de nueve marcadores polimorficos de PNU nuevos identificados mediante SMP y validados con el HRMA en dos especies invasoras (el mejillon cebra Dreissena polymorpha y la almeja asiatica Corbicula fluminea), que pueden utilizarse en estudios de genetica de poblaciones para evaluar y entender correctamente los episodios de invasion pasados y los que podrian ocurrir en el futuro. EnglishThe development of affordable massive parallel sequencing (MPS) has reduced both time and costs of SNP identification for use in conservation and population genetic studies. After MPS, a second validation is usually required. High resolution melting analysis (HRMA) is a fast and simple method for mutation scanning, and thus a suitable validation protocol, particularly in non–model species. We present a set of nine novel polymorphic SNPs identified by MPS and validated with HRMA in two invasive species (the zebra mussel Dreissena polymorpha and the Asian clam Corbicula fluminea). These SNPs can be used in genetic studies to accurately assess and understand past and future invasion events.
The Effect of Hawthorn Berry Phenolics and Parsley Roots Fermented Juice on Frankfurters’ Shelf-Life

Plant extracts rich in phenolics and vegetal fermented juices rich in nitrite may be used as preservatives in the meat industry. The aim of this study was to evaluate the effects of hawthorn berry phenolics and nitrite from parsley roots fermented juice, on unsmoked frankfurters. Seven lots of frankfurters were prepared. Two lots were prepared using ascorbate and parsley juice nitrite (each preservative 50 ppm, L1; each preservative 25 ppm, L4), two lots were prepared using hawthorn berry phenolics and parsley juice nitrite (each preservative 50 ppm, L2; each preservative 25 ppm, L5), two lots were prepared only with parsley juice nitrite (50 ppm, L3; 25 ppm, L6), while L7, control lot, was prepared with 50 ppm ascorbate and 50 ppm synthetic nitrite. pH, thiobarbituric acid reactive substances, cure efficiency, residual nitrite, total viable count, Enterobacteriaceae and coliform bacteria were determined at 3-day intervals for 15 days. During storage, comparatively with control, the best physico-chemical parameters were found for L4 and L5 of frankfurters, while the best microbiological parameters were found for frankfurters treated with ascorbate and parsley juice nitrite (L1 and L4). The addition of natural antioxidants and nitrite was able to improve unsmoked frankfurters’ shelf-life.
A Reemerging Lassa Virus: Aspects of Its Structure, Replication, Pathogenicity and Diagnosis

Lassa virus is a linear, bisegmented, single-stranded RNA virus, which belong to the Arenaviridae family that causes viral hemorrhagic fever transmitted by rats. The virus is endemic in West African countries, which may be due to its zoonotic nature. Lassa virus infection occurs through contact with the vector Mastomys natalensis or infected humans and can lead to wide symptoms from a mild infection to Lassa fever and to a severe fatal viral hemorrhagic fever, which include delayed cellular immunity resulting to fulminant viremia. The virus replicates through a strategy known as the Ambisense, where two RNA strands code for genes in both the sense and antisense direction that is rapid and demonstrate temporal control in replication. Different diagnostic tests for the virus are available, which range from viral culture to serological and molecular diagnostic tests. There is an urgent need to develop drugs and vaccines against the virus because the World Health Organization (WHO) has identified Lassa virus as one of the viruses that is likely to cause a future epidemic, although a research is ongoing to evaluate Lassa virus vaccine immunogenicity in the CBA/J-ML29 mouse model. This chapter gives an overview on the structure, replication cycle, pathogenesis, and diagnosis of the virus.
Data Stream Clustering Methods: A Review

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. Data Stream Clustering Methods: A Review Nathalie A Barbosa, Louise Travé-Massuyès, Victor Hugo Grisales
Isolation and characterization of Ty1-copia retrotransposons in Saccharum officinarum

Background. Saccharum officinarum is the most significant resource for sugar and high-yield genes in sugarcane breeding programs. However, the unknown information of evolution and genome organization remain largely in the sugarcane, which has limited progress in sugarcane breeding. Retrotransposons occupy a large proportion of the plant genome; therefore, characterization of Ty1-copia retrotransposons will improve understanding of the evolution and organization of plant genomes. Methods. The present study isolated conserved domains of Ty1-copia retrotransposon-encoded reverse transcriptase genes from S. officinarum to characterize their phylogenetic diversity, genomic abundance, and chromosomal distribution. Results. In total, 42 Ty1-copia reverse transcriptase sequences with 35-100% similarity and high levels of heterogeneity were obtained. Of them, 11 (26%) were disrupted by stop codons and/or frameshift mutations. Phylogenetic analysis revealed these sequences could be split into four distinct evolutionary lineages (Tork/TAR, Tork/Angela, Sire/Maximus, and Retrofit/Ale). Dot blot analysis showed that Ty1-copia retrotransposons represent a significant portion of the S. officinarum genome, with copy numbers as high as 1.7 × 105. Fluorescence in situ hybridization revealed that Ty1-copia retrotransposons were dispersed within heterochromatic regions among all S. officinarum chromosomes, with around 30 obvious signals clustering in terminal regions. However, Ty1-copia retrotransposons were not found in nucleolar organizing regions of 45S rDNA. Discussion. These results serve to enhance our understanding of the chromosomal distribution and evolution of the S. officinarum genome as well as promote possible utilization of retrotransposons in sugarcane breeding programs.
Active receptor tyrosine kinases, but not Brachyury, are sufficient to trigger chordoma in zebrafish

ABSTRACT The aberrant activation of developmental processes triggers diverse cancer types. Chordoma is a rare, aggressive tumor arising from transformed notochord remnants. Several potentially oncogenic factors have been found to be deregulated in chordoma, yet causation remains uncertain. In particular, sustained expression of TBXT – encoding the notochord regulator protein brachyury – is hypothesized as a key driver of chordoma, yet experimental evidence is absent. Here, we employ a zebrafish chordoma model to identify the notochord-transforming potential of implicated genes in vivo. We find that Brachyury, including a form with augmented transcriptional activity, is insufficient to initiate notochord hyperplasia. In contrast, the chordoma-implicated receptor tyrosine kinases (RTKs) EGFR and Kdr/VEGFR2 are sufficient to transform notochord cells. Aberrant activation of RTK/Ras signaling attenuates processes required for notochord differentiation, including the unfolded protein response and endoplasmic reticulum stress pathways. Our results provide the first in vivo evidence against a tumor-initiating potential of Brachyury in the notochord, and imply activated RTK signaling as a possible initiating event in chordoma. Furthermore, our work points at modulating endoplasmic reticulum and protein stress pathways as possible therapeutic avenues against chordoma. Summary: An injection-based chordoma model in zebrafish shows that the hypothesized chordoma oncogene brachyury is insufficient, whereas EGFR and VEGFR2 are sufficient, to trigger notochord hyperplasia in our model.
Stable maps and quasimaps to toric Fano varieties

We analyze the relationship between two compactifications of the moduli space of maps from curves to a toric fano varieties: the Kontsevich moduli space of stable maps and the Ciocan-Fontanine--Kim moduli space of stable quasi-maps. We exhibit the moduli space of stable maps as a union of two (reducible) components: the moduli space of relevant maps and the moduli space of irrelevant maps. We equip these spaces with virtual classes such that their sum equals the virtual class of the moduli space of stable maps. The moduli space of relevant maps is birational to the space of qusi-maps and the enumerative invariants defined as virtual intersection numbers on the space of relevant maps are equal to the quasi-maps invariants. On the other hand, the virtual intersection numbers on the space of stable irrelevant maps are zero. This shows that Gromov--Witten invariants agree with quasi-map invariants for toric Fano varieties.
Growth, feed utilization and metabolic responses of three gibel carp (Carassius gibelio
) strains to fishmeal and plant protein-based diets

The utilization of plant-based diets in fishes could be affected by their genetic backgrounds. To examine this, three strains of one-year-old gibel carp, Dongting (strain DT: 30.42 +/- 0.05 g), CAS III (strain A: 43.34 +/- 0.08 g) and CAS & (strain F: 61.78 +/- 0.10 g), were fed fishmeal (FM), soybean meal (SBM) and rapeseed meal (RM) diets for 8 weeks. The present results showed that growth performances, feed utilization, body composition, postprandial kinetics of plasma metabolites and gene expression of lipid metabolism markers in the three strains were affected by diets and strains (p 0.05). Strain A had higher SGR than strain DT and F (A > F > DT) with the three diets, whereas strain F had higher FE than the other two strains with FM and RM diets (p 0.05). Compared to FM diet, plant protein-based diets resulted in poor growth, feed use and nutrient retention in all the three strains, and different strains showed differing changes in fatty acid synthesis and oxidation to different dietary proteins. Overall, strain A showed better growth performances than the other two strains irrespective of diet, and all the three strains could utilize RM diet better than SBM diet.
Comparing KISS1 and GPR54 genes between the two breeds of goats with low and high prolificacy

There is increasing evidence that kisspeptin, the peptide product of KISS1 gene and its receptor (GPR54), regulate reproductive processes through actions on other organs than hypothalamus. Therefore, the study for the first time, was conducted to investigate the nucleotide sequences and mRNA expression levels of KISS1 and GPR54 genes in pituitary, endometrium, ovary and oviduct of prolific Jintang black goat (JTG) and non-prolific Tibetan goat (TBG) during pro-estrus. By RT-PCR strategy, we obtained that the KISS1 cDNA sequence was 408-bp long, encoding a putative peptide of 135 amino acids. The GPR54 cDNA sequence was 244-bp long, encoding a putative peptide of 81 amino acids. There were two base changes in KISS1, and one base change in GPR54, but these base changes did not result in amino acid substitution between these two breeds. Real-time PCR analyses revealed that both KISS1 and GPR54 genes were expressed in all four tissues examined. KISS1 was most highly expressed in pituitary (p<0.05) and its expression was greater in JTG than TBG (p<0.05). In conclusion, a high KISS1 expression level in pituitary of prolific goat breed might be associated with its great litter size.
A New Species of Pholidobolus (Squamata: Gymnophthalmidae) from the Paramo Ecosystem in the Northern Andes of Colombia

Abstract. On the basis of morphological and molecular evidence, we describe a new species of lizard of the genus Pholidobolus, previously conflated with P. vertebralis, from a paramo ecosystem in the northern Cordillera Central of Colombia. Our results support the recognition of the new species and suggest it is not closely related to P. vertebralis. Morphologically, the new species is distinguished from its congeners by coloration pattern, scutelation and hemipenial morphology. In light of the new evidence, we discuss the validity of available names, putative synapomorphies and the biogeography of the genus Pholidobolus in its northern distribution.
Effects of humidity on the adsorption of coating solvent (m-xylene) on activated carbon.

Control of coating solvent vapors by adsorption on activated carbon in the automotive industry can be affected by the presence of humidity. As a foundation to better understand the adsorptive behavior of these organic solvents, in this investigation, adsorption of mxylene in the presence of water vapor on granular activated carbon was studied. Single component (m-xylene and water vapor) adsorption experiments were first conducted as prerequisites for the binary component (m-xylene with water vapor) studies. The dynamic method of gas adsorption technique (passing a flux composed of carrier gas and adsorbate vapor through a fixed bed adsorbent and subsequently analyzing the outlet adsorbate concentrations) was used throughout this research. The experimental results were then compared with predictive models to capture the dominant features of the data. For the equilibrium and kinetic studies of water vapor adsorption, an online digital hygrometer was used in conjunction with an electronic balance. Relative humidity values from 18 to 96% were examined. The adsorption isotherm was found to resemble a type V isotherm (Brunauer classification system). The adsorption capacities from the gravimetric measurement were within 14% of the values obtained from the kinetic studies based on the area integration of the breakthrough curves. The m-xylene adsorption system design was similar to the water vapor adsorption system, except the online measurement of the adsorbate was done by gas chromatograph with the help of a six-port valve. The concentration range studied was 52 to 1030 ppm. The limiting pore volumes resulting from the m-xylene adsorption experiments (0.56 mL/g)
NeuroImage: Clinical Decreased integration of EEG source-space networks in disorders of consciousness

, Increasing evidence links disorders of consciousness (DOC) with disruptions in functional connectivity between distant brain areas. However, to which extent the balance of brain network segregation and integration is modi ﬁ ed in DOC patients remains unclear. Using high-density electroencephalography (EEG), the objective of our study was to characterize the local and global topological changes of DOC patients' functional brain networks. Resting state high-density-EEG data were collected and analyzed from 82 participants: 61 DOC patients re-covering from coma with various levels of consciousness (EMCS ( n =6), MCS+ ( n =29), MCS- ( n =17) and UWS ( n =9)), and 21 healthy subjects (i.e., controls). Functional brain networks in ﬁ ve di ﬀ erent EEG frequency bands and the broadband signal were estimated using an EEG connectivity approach at the source level. Graph theory-based analyses were used to evaluate their relationship with decreasing levels of consciousness as well as group di ﬀ erences between healthy volunteers and DOC patient groups. Results showed that networks in DOC patients are characterized by impaired global information processing (network integration) and increased local information processing (network segregation) as compared to controls. The large-scale functional brain networks had integration decreasing with lower level of consciousness.
Morphological variability patterns in the Balearites-Pseudothurmannia genera boundary (Ammonoidea, late Hauterivian): taxonomic and biostratigraphic implications

As for many other ammonoid groups, the Hauterivian family Crioceratitidae has been traditionally approached from a strictly typological viewpoint, leading to considerable taxonomic oversplitting. Balearites angulicostatus (d’Orbigny, 1841) and Pseudothurmannia ohmi (Winkler, 1868) are two successive species within this lineage, which are used as index species in biostratigraphy. In order to clarify the taxonomic position of the two aforementioned species, the present study carries out morphometric analyses on 111 stratigraphically controlled specimens from the Arroyo Gilico section (SE Iberian Peninsula), enabling us to conclude that the diagnoses of both species should be broadened to encompass the continuous morphological variations occurring within their populations. A phenotypic variability model among eight extreme poles is described for B. angulicostatus, whereas P. ohmi ranges between two extreme poles. The detailed study of shell morphology through time recognizes the evolutionary changes between the two species: anagenetic processes such as the increase of whorl height growth rate and tachymorphosis of ontogenetic stages, coupled with punctuated changes such as the loss of heteromorphic coiling and an allometric hypermorphosis. Some of these may be inherent to the variation of the species themselves, but others such as the loss of heteromorphism seem to be related to palaeoenvironmental factors such as changes in nutrient supply to the sea.
Feeding of plankton in turbulent oceans and lakes

Analytical models for the statistical distribution of the gut content of fish larvae in a turbulent ocean environment are compared to data obtained in a field experiment. The proposed model allows the nutrition state and thereby the survival probability of plankton populations to be estimated for given conditions and parameters characterizing their environment, i.e., prey concentrations and turbulence levels. These parameters are all available in the field data. Other parameters such as the capture range and fields of view together with a characteristic time for digesting prey are assumed to be known. The analysis allows an estimate for the probability density of the gut content of plankton in terms of the number of nauplii in the gut. In particular, the analytical results give a basis for evaluating the average gut content of a given plankton population on the basis of basic information concerning the prey concentration and the turbulence intensity. Also analytical models for the prey capture rates are compared with results based on the field data. The analysis emphasizes the effects of turbulence.
Attitude Towards Green Packaging and Its Impact on Purchase Intention of Green Packaged Consumer Products among Undergraduates in Bangkok Metropolitan, thailand

The fundamental accomplishment of moving towards the green concept is the use of green packaging in a product. Consequently, this study explores the attitude towards green packaging with two influence factors involved: attitude towards environmental issue and knowledge of green packaging, as well as how they affect the purchase intention of green packaged consumer products. The qualitative method used in this study was to conduct a survey of 257 undergraduates over 18 years old and studying at a university in the Greater Bangkok area. The data is analyzed by using regression modeling. The results indicate that Thai teenagers have a moderately positive attitude towards green packaging, which is significant to the purchase intention of green packaged consumer products. Moreover, the attitude towards green packaging can be influenced by attitude towards environmental issue and partially by knowledge about green packaging. However, attitude towards environmental issue alone also directly predicts the purchase intention of green packaging.