Miracle-dz/UniFAR-FTUs huggingface dataset:
The complete chloroplast genome of Wakame (Undaria pinnatifida), an important economic macroalga of the family Alariaceae

Abstract We decoded the complete chloroplast DNA (cpDNA) sequence of the Wakame (Undaria pinnatifida), an important economic macroalga of the family Alariaceae, by using next-generation sequencing technology. The genome consists of 130 336 bp containing a pair of inverted repeats (IRs) of 4790 bp, which was separated by a large single-copy region and a small single-copy region of 77 821 and 42 934 bp, respectively. The genic regions account for 77.7% of whole cpDNA, and the GC content of the cpDNA was 30.6%. The U. pinnatifida cpDNA encodes 153 unigenes (129 protein-coding genes, 3 rRNA genes and 21 tRNA genes). There are 1 PCG (rpl33) and 1 tRNA genes (trnL) containing an intron. A phylogenetic analysis of the four complete cpDNA from Phaeophyceae showed that U. pinnatifida is closely related to Saccharina japonica with high bootstrap value supported. The complete cpDNA of U. pinnatifida provides essential and important DNA molecular data for further phylogenetic and evolutionary analysis for brown algae.
Use of Wild Foods During the Rainy Season by a Reintroduced Population of Scarlet Macaws (Ara Macao Cyanoptera) in Palenque, Mexico

The scarlet macaw (Ara macao cyanoptera) is an endangered species in Mesoamerica due to illegal traffic, habitat loss, and hunting. In Mexico, its range has been reduced by 98%. Between April 2013 and June 2014, a population of 96 individuals of A. m. cyanoptera was reintroduced (six releasing events), in the tropical rainforests of Palenque, southeast Mexico, where this macaw had been extinct for the last 70 years. This study documents the use of wild foods and range use by the reintroduced macaws for the rainy season period June to November, 2014. The macaws used 140 trees of 31 species (19 families; 84% native species) as a source of food. Seeds and fruit accounted for 70% of their diet. The remaining 30% consisted of bark, stems, leaves, insect galls, flowers and shoots. A subset of five tree species was highly dominant in their diet (regarding number of trees used, months used and feeding records). Spatial data showed that food trees used by the macaws were dispersed over 36 ha and had a highly clumped distribution. The macaws used an additional 23ha for non-feeding activities. The dietary diversity and breadth (as indicated by Levin's Index) of the reintroduced macaws closely approaches that of wild macaws. The capacity of the reintroduced macaws to use wild foods, a very low mortality in the released population (9%), and the occurrence of nine successful nesting events, attests to a short-term success of the reintroduction. We discussed the observed patterns of use of wild foods and habitat by the reintroduced scarlet macaws in the context of the soft-release protocol used and of behavioral flexibility, accumulated social learning and a high cognitive capacity typical of psittacines, aspects essential for a successful adaptation to the wild.
Synthèse par ingénierie métabolique d'oligosaccharides sialylés pour l'élaboration de glycoconjugués d'intérêt médical

Les structures sialylees sont presentes a la surface des cellules sous forme de glycoconjugues,couples a des proteines ou des lipides. Ces structures jouent un role important dans divers processusbiologiques que ce soit a travers l’interaction avec des lectines, ou de par leurs proprietes physicochimiques.Ces structures sont egalement impliquees dans diverses pathologies et on constatenotamment une forte augmentation du taux d’acides sialiques chez les individus atteints de cancer,due a une surexpession de structures naturelles mais aussi a l’apparition de nouveaux motifs,naturellement absent chez l’individu sain. L’ensemble de ces structures sialylees presente un interetsoit par leur role biologique soit a cause de leur expression specifique dans les cancers. Leurobtention est tres difficile par voie chimique et la synthese enzymatique in vitro est efficace mais trescouteuse en nucleotide-sucre et ne sont pas adaptees a une production a l'echelle preparative.Dans un premier temps, ces travaux de these s’interessent a la synthese bacterienne par ingenieriemetabolique d'acides polysialiques fonctionalises. Ces polysaccharides presentent divers interets.Tout d’abord il est possible de les coupler a des proteines actives pour en augmenter le temps dedemi-vie in vivo. Mais ces polysaccharides peuvent egalement etre utilises dans le cadre de therapievaccinale, soit contre des bacteries pathogenes de types Neisseria meningitidis qui le presententcomme polysaccharide capsulaire, soit contre les cellules cancereuses surexprimant cette structure.Ensuite nous avons cherche a obtenir des oligosaccharides specifiques des cancers, les motifssialylTn, et siallTF, toujours par ingenierie metabolique d’E. coli. Le sialylTn a ete couple a uneplateforme peptidique immunogene afin de construire un candidat vaccin qui a ete teste in vitro et invivo sur la souris.
Exploiting expression patterns across multiple gene isoforms to identify radiation response biomarkers in early-stage breast cancer patients

In an effort to understand the underlying biology of radiation response along with whole transcriptome effects of preoperative radiotherapy in early-stage breast tumors, we propose two efficient score-based statistical methods that exploit gene expression patterns across all available gene transcript isoforms and identify potential biomarkers in the form of differentially expressed genes and differentially enriched gene-sets. We demonstrate the effectiveness of these two methods using extensive simulation studies that show that both of our methods give improved performance, in terms of statistical power, over the most commonly used methods. By exploiting radiation-induced changes in all available gene transcript isoforms, we identified several statistically significant differentially expressed genes related to PI3K-AKT and JAK-STAT signaling pathways along with radiation-induced oncogenic signaling pathways and tumor microenvironment gene signatures that could be potential targets to improve response to radiotherapy in breast tumors.
Variability of the agronomic indicators of Pennisetum purpureum cv. Cuba CT-115 with the sampling distance

An experiment was conducted during two years to establish the variability of the agronomic indicators of Pennisetum purpureum cv. Cuba CT-115. Samples were taken at different sampling distances (1, 2, 3, 4 and 5 m length). The data of an experiment with random block design and four replicates were used. The lowest variance, standard deviation and coefficient of variation were obtained with sampling distance of five meters for the height (4.3, 2.1 and 1.88, and 1.1, 1.0 and 0.99 for the rainy and dry season, respectively). Similar performance had the per cent of leaves and dry matter of the whole plant. The sampling distance of five meters propitiated lower yield variability (18.04 and 12.35 % in the rainy season and dry season, respectively). Similar performance had the number of bunches/m (8.34 and 12.27, in that same order). In all the indicators, the lowest width of the values range was obtained, in general, in the distance of five meters. When sampling the population, five bunches/m recorded the lowest variability compared with 11 bunches/m. It is concluded that for the best estimation of the agronomic indicators, the samplings should be conducted in five linear meters. No less than five bunches as sample units should be taken. Similar studies in grasslands with different growing habits are recommended. Key words: sample, yield, grass .
ANTIOXIDANT ACTIVITY AND SECONDARY METABOLITES IN SELECTED VEGETABLES IRRIGATED WITH SEWAGE WATER

The study was conducted to investigate the impact of various concentration of domestic waste water on growth, physiological, and biochemical characteristics of tomato, okra and pumpkin. Sewage water was applied of 50% and 100% on vegetables grown under field conditions. Irrigation with tubewell water was considered as control. At maturity data for growth attributes was recorded. Maximum fresh weight of root, shoot and fruit was in tomato at 50% sewage water treatment followed by control. Dry weight also exhibited a considerable increase at 50% sewage water application. However, a decline in chlorophyll a, b and carotenoid contents was observed at 100% sewage water. Antioxidants and secondary metabolites increased and their maximum values were recorded at 100% sewage treatment in all the three vegetables.
The role of glycerol-3-phosphate acyltransferase 1 in mitochondrial phospholipid biosynthesis of cold-bodied fishes

Mitochondrial biogenesis is induced by low temperature in many fish species. For example, cold acclimation of Gasterosteus aculeatus (threespine stickleback) increases mitochondrial densities in oxidative skeletal muscle. Oxidative muscles of Antarctic icefishes (suborder Notothenioidei) also have high mitochondrial densities characterized by higher densities of phospholipids compared to red-blooded notothenioids. Mitochondrial biogenesis has been well studied in mammals yet it is unknown how mitochondrial phospholipid synthesis is regulated. I hypothesized that both activity and mRNA levels of glycerol-3-phosphate acyltransferase (GPAT), the rate-limiting enzyme in glycerolipid biosynthesis, would increase in oxidative muscle of stickleback, where mitochondrial biogenesis occurs, but not in liver, in response to cold acclimation, and that GPAT1 and /or GPAT2 mRNA levels would be higher in hearts of icefishes compared to red-blooded species. To test these hypotheses, maximal activity of GPAT and mRNA levels of GPAT1 and GPAT2 were measured in liver and oxidative muscle of coldand warmacclimated stickleback. GPAT1 and GPAT2 mRNA levels were also quantified in hearts and livers of redand white-blooded Antarctic notothenioids. Additionally, cDNA of GPAT1 was sequenced in Antarctic and sub-Antarctic notothenioids to gain insight to the evolution of a mitochondrial membrane protein and identify candidate amino acid residues responsible for maintaining function at cold temperature. GPAT activity increased in oxidative muscle but not in liver, and transcript levels of GPAT1 increased in liver but not in oxidative muscle, in response to cold acclimation in stickleback. GPAT2 transcripts were undetectable in both tissues. GPAT1 mRNA levels were highest in liver of red-blooded Antarctic notothenioids and did not differ in hearts between redand white-blooded fishes, and GPAT2 transcripts were undetectable. GPAT protein levels may not change concurrently with GPAT1 and GPAT 2 mRNA levels because GPAT3 or 1-acylglycerol-3-phosphate acyltransferase (AGPAT), the enzyme subsequent to GPAT, may be involved in regulating phospholipid synthesis during mitochondrial biogenesis. The amino acid sequence of GPAT1 is highly conserved (97.94­ 98.06%) among Antarctic and sub-Antarctic notothenioids, with three potential sites in the cytosolic region that may be important for maintaining function at cold temperature: Ser415Ala, Asp603Glu and Thr648Ala.
Population genetics and reproductive strategies of two Notostraca (Crustacea) species from winter ponds in Israel

Fluorescent-amplified fragment length polymorphism (FAFLP) fingerprinting assay was used to compare the genetic diversity within and between tadpole shrimps (Notostraca) populations of Lepidurus apus (n=7) and Triops cancriformis (n=2) from rain pools in Israel. Each ephemeral water body has revealed a unique fingerprint pattern with an entailed genetic drift between nearby ponds. High similarity of genotypic diversity within each geographic area led to three clusters of water bodies, north, south and center of Israel. FAFLP assays on several newly hatched individuals of T. cancriformis revealed high identity amongst kin, as compared to L. apus where newly hatched from the same maternal source showed high diversity. Results indicate that T. cancriformis populations from Israel are probably parthenogenetic as indicated by clonal structures. The higher genetic variability in the L. apus populations and in laboratory-hatched specimens indicates the existence of sexual reproduction.
Nonlinear scaling of foraging contacts with rodent population density

Density-dependent shifts in population processes like territoriality, reproduction, dispersal, and parasite transmission are driven by changes in contacts between individuals. Despite this, surprisingly little is known about how contacts change with density, and thus the mechanisms driving density-dependent processes. A simple linear contact-density function is often assumed, but this is not based on a sound basis of empirical data. We addressed this question using a replicated, semi-natural experiment in which we measured contacts at feeding stations between multimammate mice, Mastomys natalensis, across ten distinct, linearly increasing densities between 10 and 272 animals/ha. Unexpectedly, unique contacts increased not linearly but sigmoidally with density, which we attribute to the species' scramble competition mating system, small-scale dominance/avoidance and absence of territoriality. These results provide new insights into how species' characteristics can relate to density-dependent changes in contacts, and the unexpected shape of the contact-density function warrants that density-dependence in ecological models, such as parasite transmission models, must be parameterized with care.
Divergent migratory behaviours associated with body size and ocean entry phenology in juvenile sockeye salmon

Survival during early marine life stages is hypothesized to contribute disproportionately to variation in salmonid recruitment, yet estimates of cumulative mortality are constrained by knowledge of how long juveniles reside in specific regions. We used otolith microstructure techniques to examine the relationship between migratory rate and ocean entry characteristics of juvenile sockeye salmon (Oncorhynchus nerka). We observed differences in migratory rate between catch locations that are consistent with divergent migratory behaviours. Individuals captured in northern regions were typically older, larger at ocean entry, and migrated more rapidly. Migratory rate was also correlated with entry size, phenology, population group, and year. Next, we compared “lingering” individuals captured nearshore during fall surveys to juveniles from the same populations captured during the peak summer migratory period. We determined that individuals that entered after 24 May and at smaller sizes (<85 mm) had a greater pro.
New Way of Production of Cyclopentanone

The paper describes the mode of preparation of cyclopentanone. The principle of this procedure lies in pyrolysis /thermic decarboxylation/ and simultaneously run hydrolysis of the reaction mixture. The reaction mixture consists of dimethyl adipate, methyl hydrogen adipate and adipic acid, together with methanol and water. The reactions runs on heterogeneous catalyst at temperatures around 450°C
STUDY OF PREVALENCE SOME PATHOGENICITY-ASSOCIATED VIRULENCE FACTOR GENES IN UROPATOGENIC E.COLI ISOLATES AND ABILITY OF TRANSFERRING THEM TO OTHER RELATED AND NON-RELATED SPECIES IN AL NAJAF PROVINCE- IRAQ

Background: The generally accepted hypothesis today is that UPEC involved from nonpathogenic strains by acquiring new virulence factor from accessory DNA horizontal transfer located at the chromosome or plasmid level. Aim of study: investigate the genetic determination of some pathogenicity-associated virulence factors (PAVFs) genes such as fimH, hlyA and iucC genes in UPEC and capability of transferring of them from UPEC to related and non related species such as E.coli JM 109 and P. aeruginosa as well as evaluation of genes transferring effeciency. Method: During the period from May 2014 to November 2014.a total of 290 samples has been collected from patients suffering from Urinary tract infections (170 samples) and burn infections (120 samples) from Alzahraa and Alsadr teaching Hospital as well as private clinics analytical laboratories and Central Health Laboratory in Al-Najaf Al- Ashraf City Results: seventy (41.2%) of isolates were belong to Uropathogenic E.coli whereas out of 120 burn infection samples only 60(50%) isolates were belong to P.aeruginosa depending on identification by microscopic, morphologic, genetic and biochemical tests. So fimH, hlyA and iucC revealed that 48(69%), 6(9%) and 56(80%) isolates were possess these gene respectively, while 12(17%) isolates showed negative results (absence of any target genes) , to confirm ability of these gene to transferred from local UPEC isolates to E.coli JM 109 as well as to local cured P.aeruginosa that selected from conjugation and transformation possess, results of that showed fimH had ability to transfer by conjugation and transformation to E.coli JM 109 while
Influence of Reaction Temperature on the Controlled Growth of Mg-Al LDH Film

The Mg-Al layered double hydroxides (Mg-Al LDH) film was fabricated on anodized magnesium alloy AZ31 at different reaction temperature by in-situ hydrothermal treatment method. The reaction solution contained only one kind of trivalent cation Al 3+ , and the divalent cation Mg 2+ is provided by the anodic oxide films. The structure, composition and morphology of the Mg-Al LDH films were investigated via XRD, FI-IR and SEM, respectively. The corrosion resistance of films was studied using potentiodynamic polarization and electrochemical impedance spectroscopy. The SEM images show that the compactness of LDHs increases with the increase of the reaction temperature. The results of XRD and FT-IR indicate that the crystallinity of films was improved with the increase of reaction temperature. The results of potentiodynamic polarization and electrochemical impedance spectrum show that the corrosion resistance was improved with the increase of reaction temperature. The influence mechanism of reaction temperature on the controlled growth of Mg-Al LDH films was investigated subsequently.
Interactions flavivirus-moustiques : diversité et transmission

Les flavivirus sont des virus a ARN parmi lesquels certains sont des arbovirus transmis entre hotes vertebres par des vecteurs arthropodes, notamment des moustiques. L'interaction avec les moustiques est centrale dans la biologie des flavivirus par son influence sur leur diversite genetique et transmission, mais certains de ses aspects restent meconnus. Au cœur de cette these, des approches basees sur les « big data », generees par des technologies modernes ou par compilation de travaux plus anciens, ont eclaire d’un jour nouveau la complexite des relations moustique-flavivirus. En explorant des genomes de moustiques anopheles, nous avons identifie et caracterise des elements viraux endogenes d'origine flavivirale chez Anopheles sinensis et An. minimus, suggerant l'existence de flavivirus infectant les anopheles et revelant une facette insoupconnee de leur diversite. Par ailleurs, nous avons explore, par sequencage haut-debit, la fine interaction entre le genotype du moustique Aedes aegypti et la diversite intra-hote du virus de la dengue-1. Nos resultats montrent un fort effet de la derive genetique lors de l'infection initiale, diminuant l'importance relative de la selection naturelle, et une modulation de la diversite genetique intra-hote du virus par le genotype du moustique. Enfin, nous avons compile la litterature sur la transmission verticale des arbovirus chez les moustiques, c'est-a-dire de la femelle infectee a sa descendance, afin d'identifier des facteurs techniques et biologiques sous-jacents. Nos resultats ameliorent la comprehension de ce mode de transmission et des strategies employees par les arbovirus pour persister dans l’environnement.
Evaluating conversational success: Weighted Message Exchange Games

We analyze evaluations of conversational success and how such evaluations relate to notions of discourse content and structure. To do so, we extend the framework of Message Exchange (ME) games by adding weights or scores to the players’ moves and then accumulating these weights using discounting to evaluate a conversationalist’s performance. We illustrate our analysis on a fragment of a recent political debate.
Parasite infection in a central sensory organ of fish does not affect host personality

Among the ecological factors acting on the evolution and expression of animal personalities and behavioral syndromes, parasitism has received comparatively little attention. However, infection and host behavior are often strongly intertwined, because host behavior can predict the risk of infection and can also be changed by an infection. We conducted a controlled experimental infection study to explore the effects of infection on host boldness, exploration and activity using rainbow trout Oncorhynchus mykiss and its trematode parasite Diplostomum pseudospathaceum, which infects a central sensory organ of the fish, the eye lens. Contrary to our expectation, infection did not change the within-individual consistency of the personality traits or the relationships between the traits, but infected individuals were less bold than uninfected control individuals. We also found no relationship between personality in uninfected fish and resistance against parasite infection, suggesting that behaviors which increase parasite encounter do not select for improved resistance. Thus, we found only weak support for parasite-mediated effects on animal personalities.
Introduction to Conservation Genetics

Review(s) of: Introduction to Conservation Genetics, by Frankham, R. , Briscoe, D. A. and Ballou, J. 2002 - ISBN Pending Cambridge University Press, 600+pp with lots of Figures and Tables, RRP will be Aud$100.00 paperback Aud$250.00 hardback. Includes footnotes.
Diversity of branched Halymenia (Halymeniales, Rhodophyta) species on the Brazilian coast: molecular and morphological analyses reveal three new species

Abstract: The diversity of branched Halymenia species in Brazil was assessed by molecular analyses and morphological examination to clarify the status of taxa previously identified as Halymenia floresii and H. pseudofloresii. Molecular tools included sequencing the COI-5P molecular marker for DNA barcoding and rbcL for phylogenetic inferences. Both molecular and morphological results demonstrated that Brazilian specimens previously attributed to H. floresii and H. pseudofloresii do not correspond to these species but constitute three distinct lineages that we propose as the new species: Halymenia ignifera sp. nov., Halymenia pinnatifida sp. nov. and Halymenia silviae sp. nov. We propose that H. floresii and H. pseudofloresii be removed from the Brazilian marine flora. We highlight that without the use of molecular tools, the morphological divergences observed in Brazilian specimens could be misinterpreted as morphological plasticity and lead to incorrect species determinations.