Miracle-dz/UniFAR-FTUs huggingface dataset:
Bioproduction of itaconic acid by biomass valorization, towards material elaboration

In the context of sustainable development, the bioproduction of building blocks (chemical platforms) from biomass is way to substitute the current fossil-based chemical molecules. This thesis is focused on the use of lignocellulosic biomass, renewable and abundant, towards the production of two organic acids (potential building blocks): itaconic acid and fumaric acid. These molecules have been chosen especially because they can generated polymers with interesting properties. The experimental work consisted in using wheat bran and corn cobs, agricultural wastes, as substrates for fermentation by four strains of filamentous fungi from Aspergillus genus. Screenings of the best fermentation conditions show that enzymatically pretreated corn cobs, especially in solid state fermentation achieve higher yields, especially in solid state fermentation. Among other notable results, we have shown for the first time the ability of Aspergillus oryzae to produce itaconic acid. Overall, our results show that the use of lignocellulosic biomass is a promising alternative for the production of these two building blocks of industrial interest.
Development and basic properties of the viral preparation viroden

: Laboratory studies demonstrated the effectiveness of viroden preparation in different doses against preimago stages of Aedes aegypti mosquitoes. After treatment of larvae of instar 1 at preimago stages about 77% of the insects died. The preparation is stable on storage and resistant to unfavourable environmental factors: sun radiation, heating, pH variations, without significant loss of activity. The study of the host range of densonucleosis virus, the active principle of the viroden preparation, showed that it was not harmful for other animals. Large-scale trials of the preparation in different climatic zones are necessary for the elucidation of its effectiveness against naturally occurring mosquito species.
Complete mitochondrial genome of Pseudogastromyzon fasciatus (Osteichthyes: Gastromyzontidae)

Abstract Pseudogastromyzon fasciatus belonging to the family Gastromyzontidae is a good model for phylogeny and zoogeography research. The complete mitochondrial genome of P. fasciatus was sequenced in this study. The genome sequence is 16,563 bp in length, comprising 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and one control region. Overall base composition is 29.70% A, 25.16% T, 16.53% G, and 28.60% C. The result of phylogenetic analysis indicates that P. fasciatus mitogenome is close to that of P. myersi.
Long‐term population dynamics reveal that survival and recruitment of tropical boobies improve after a hurricane

Variability in population numbers is a central issue in evolutionary ecology and also in biodiversity conservation. However, for most seabirds this information is lacking and tropical populations are virtually unstudied. Long-term studies are warranted because world's seabird populations exhibit an overall declining trend since 1950. Using data spanning 23 yr, we investigated how adult survival, local recruitment, and their relative contributions to population growth (λ) vary over time in the blue-footed booby Sula nebouxii, a long-lived locally foraging seabird that breeds in tropical waters. In addition, we investigated whether booby demographic rates exhibit the same declining trend observed in other seabirds, whether these rates are impacted by hurricanes, and whether these potential impacts differ between sexes. Our analysis of 4608 capture–recapture histories revealed that survival and recruitment were nearly equal between males and females, exhibited a declining trend over the last 23 yr, and in both sexes, these vital rates improved after a hurricane. The declining trend in recruitment was slightly more attenuated in males. These results add to the current evidence for an overall declining trend in world's seabird populations and extend its confirmation to the warm eastern tropical Pacific. Moreover, they provide the first evidence that hurricanes may favor natural populations. As a result of the declining trend and variation in survival and recruitment, λ exhibited a slight decline and substantial variation over the 23 yr. However, most λ values were equal to or higher than 1, and the long-term average indicates population increase. The ability of blue-footed boobies to maintain a positive population balance despite of negative trends in their vital rates might result from canalization of adult survival (the vital rate that contributes most to λ and shows lower variation compared to recruitment) against environmental variability.
Feynman diagrams and $Ω$-deformed M-theory

We derive the simplest commutation relations of operator algebras associated to M2 branes and an M5 brane in theΩ-deformed M-theory, which is a natural set-up for Twisted holography. Feynman diagram 1-loop computations in the twisted-holographic dual side reproduce the same algebraic relations. Copyright J. Oh and Y. Zhou. This work is licensed under the Creative Commons Attribution 4.0 International License. Published by the SciPost Foundation. Received 07-10-2020 Accepted 01-02-2021 Published 05-02-2021 Check for updates doi:10.21468/SciPostPhys.10. 2.029
A new Amazonian species of Rhaebo ( Anura: Bufonidae) with comments on Rhaebo glaberrimus (Günther, 1869) and Rhaebo guttatus (Schneider, 1799)

We describe a new species of toad of the genus Rhaebo from the Amazonian lowlands of Colombia and Ecuador. The newspecies is characterized by have a large-size (SVL 156.7 mm in adult female, 92.8–127.0 mm in adult males), lacking apreocular ridge and most cephalic crests except for the low parietals crests; having the cloacal opening towards the middlelevel of thighs; rounded to slightly oval parotoids; and dark to cream brown groin. The new species was previouslyconfused with Rhaebo glaberrimus, but the latter differs by having the cloacal opening at the ventral level of the thighs,small body size, skin texture mainly smooth, and a pink or yellowish color in the groin. The new species is also similar to Rhaebo guttatus that differs by having a preocular ridge and a different ventral coloration (throat, chest and belly withcream round spots). We also comment on the identity of R. glaberrimus and R. guttatus, correct some reports published in the literature, and present new information on their natural history and distribution.
Production and characterization of spherical thermostable silver nanoparticles from Spirulina platensis (Cyanophyceae)

Abstract: Biological production of silver nanoparticles (SNP) has recently received considerable attention because of their therapeutic applications. The present study reports the production and characterization of spherical-thermostable SNP from Spirulina platensis. Wet biomass harvested from optimized logarithmic-phase culture was used for production of SNP in 1, 3, or 5 mM silver nitrate solution. Formation and concentration of spherical SNP was highest when S. platensis was treated with 3 mM silver nitrate. Fourier transform infrared spectra of SNP indicate that vanillin, coumarins, tannins, amide, and glycogen may act as stabilizing agents for bioreduction. The crystalline nature of the produced SNP was evidenced from X-ray diffractometer analysis. Weight loss of SNP occurred at 210°C, 310°C, and 510°C as shown by thermogravimetric analysis. This study shows that S. platensis may be used as an efficient tool for production of spherical, crystalline, and thermostable SNP.
Nutritional impact of crude glycerine infusion into the rumen of wethers fed a tropical or a temperate forage grass

SUMMARY The current study evaluated the nutritional impact of crude glycerine (CG) supplementation to wethers fed only forage grass. Eight Polwarth wethers were used in a replicated 4 × 4 Latin Square. Treatments consisted of no CG (control, CON) or intra-ruminal infusion of CG at daily rates of 0·5, 1·5 or 3·0 ml/kg body weight (BW). In each Latin Square, four animals were fed Avena strigosa and four were fed Cynodon sp. hay ad libitum. The actual concentration of glycerol in diet was similar for both forage types and varied from 21 to 364 g/kg dry matter. No interactions between forage type and CG treatments were detected and no differences were observed between the CON and 0·5 CG treatment for most variables. Both the organic matter (OM) and the digestible OM intake decreased linearly at increased levels of CG infusion, whereas no treatment effect was observed on OM and neutral detergent fibre (NDF) digestibility. The duodenal flow of rumen microbial nitrogen (N) was not affected, whereas the duodenal flow of α-amino N decreased linearly at increased levels of CG infusion. In conclusion, CG supplementation at a rate of up to 0·5 ml/kg BW/day did not change the nutrient supply whereas greater amounts of CG supplementation negatively impacted the nutrient supply to wethers fed only grass forage. The forage digestibility, in turn, was not affected by CG supplementation.
De novo assembly, characterization and comparative analysis of entelegyne spider transcriptomes (Araneae: entelegynae)

OF THE THESIS De Novo Assembly, Characterization and Comparative Analysis of Entelegyne Spider Transcriptomes (Araneae: Entelegynae) by David E. Carlson Master of Science in Biology with Evolutionary Biology San Diego State University, 2015 Next-generation sequencing technology is rapidly transforming the landscape of evolutionary biology. Transcriptome sequencing in particular has become a cost-effective and efficient means of collecting exome information for non-model organisms. Due to their taxonomic diversity, production of interesting venom and silk proteins, and the relative scarcity of existing genomic resources, spiders in particular are excellent targets for NGS methods. In this study, the transcriptomes of six entelegyne spider species from three genera (Cicurina travisae, C. vibora, Habronattus signatus, H. ustulatus, Nesticus bishopi and N. cooperi) were sequenced and de novo assembled. Each assembly was assessed for quality and completeness and functionally annotated using gene ontology information. Approximately 100 sequences with evidence of homology to venom proteins were also discovered. After identifying more than 3,000 putatively orthologous sequences across all six taxa, comparative analyses using multiple methods revealed evidence for positive selection in up to 229 of these orthologs. In addition, between ~ 400 and 1,100 unique orphan genes were found to be present in each congeneric lineage. These sequences exhibited elevated rates of amino acid substitution, consistent with previous hypotheses suggesting that orphan genes may be involved with lineage-specific adaptive evolution.
Revised nomenclature of Cortinarius taxa with type specimens deposited in the Innsbruck (IB) Mycological Herbarium

A nomenclatural study of the names associated with type collections deposited in the mycological collection of IB was undertaken. Many of these names were invalidly published (Art. 34.2.) or had never been officially recombined. Our Mycological Type Collection Database can now be searched on the world-wide-web, and thus we decided to validate or recombine the following 18 species epithets in Cortinarius. Cortinarius aineus, C. atrocoeruleus, C. atropurpureus, C. betuletorum, C. caesiostramineus var. amarissimus, C. chrysophthalma, C. corynecystis, C. duramarus, C. fagetorum, C. flavotomentosus, C. heterochromus, C. multicolor, C. nothovenetus, C. obscurooliveus, C. obscurooliveus var. brunneus, C. olivipes, C. subtriumphans var. cephalixoides, C. viridipes. We give an overview of the valid names of nomenclatural types regarded as synonyms and of nomenclatural types, which have already been recombined. Three names proposed in an earlier paper turned out to be later Cortinarius homonyms. Therefore, they are replaced by the new names C. singerianus C. glabriceps and C. deminutus.
Interferon-γ liposomes : drug binding properties and antiviral in vitro activity

Recombinant human interferon-γ (IFN-γ), a promising protein drug with immunomodulating properties, was adsorbed to the surface of multilamellar liposomes by simple incubation (adsorption method) or encapsulated in liposomes (encapsulation method), in order to identify crucial parameters for the formulation of a potential liposomal IV-dosage form. By incorporating negatively charged phospholipids (e.g. dipalmitoylphosphatidylserine) into the liposomal membrane, the amount of liposome-bound interferon-y was multiplied compared with uncharged liposomes, due to electrostatic interactions between the cationic protein and the anionic liposomes. The specific antiviral activity of interferon- ? adsorbed to negatively charged liposomes increased with increasing drug loading. The adsorption to liposomes prepared from negatively charged phospholipids caused a lower reduction in biological activity than the adsorption to neutral liposomes. The encapsulation method resulted in approximately 50-180% higher binding rates than the absorption method. The stability profile of liposome-bound interferon-γ, monitored in vitro as a decrease in antiviral activity, was comparable to that of aqueous drug solutions. Interferon-γ solutions with a concentration < 25 μg ml -1 lost part of the dissolved protein by adsorption to the container walls, two other interferon fractions had a different storage stability profile. Desorption of interferon-γ from the liposome surface at 37 °C was slow and the presence of human serum albumin did not lead to a significant displacement of liposome-bound interferon-γ.
The combined effects of purified fiber and dietary threonine on chick growth, and gut health, when infected with coccidiosis

The characterization of intestinal health in poultry has become imperative as specialized ingredients (e.g., grain by-products) become common feedstuffs in poultry diets. We tested whether purified fiber affects dietary threonine (Thr) requirements and intestinal structure of young chicks. In Experiment 1, three diets containing 7% added silica sand (control), cellulose, or high-methoxy pectin were used. Six replicate pens of 6 chicks received dietary treatments through day (d) 14 post-hatch, at which time, growth performance and nutrient digestibility were determined. In Experiment 2, the impact of purified fiber on dietary Thr requirements was determined using a Thr-deficient basal diet (3.2 g/kg diet) and 7 graded levels of supplemental Thr (0 to 9.6 g/kg of diet). Six replicate pens of 5 chicks were tested from d 8-21 post-hatch, and ileal tissue was collected at study conclusion for histological evaluation. In Experiment 1, pectin reduced (P < 0.05) weight gain and feed efficiency by 32% and 39%, respectively. Pectin inclusion resulted in a reduction (P < 0.05) in dry matter (DM) digestibility, as well as apparent metabolizable energy (AMEn), compared with the control diet. No differences in feed intake due to fiber inclusion were observed. In Experiment 2, supplemental Thr requirements were estimated by fitting growth performance data to a one-slope, broken-line (i.e., piece-wise) regression model. For the control, and celluloseand pectin-containing diets, supplemental Thr requirements were estimated at 3.64, 2.60, and 2.38 g Thr/kg diet, and at 778, 737, and 576 mg
Isolation of cDNAs for Gonadotropin-II of Flounder (Paralichthys olivaceus) and Its Expressions in Adult Tissues

Gonadotropin (GTH) is a pituitary glycoprotein hormone that regulates gonadal development in vertebrates. In teleosts, two types of gonadotropins, GTH-I and GTH-II, are produced in the pituitary, and they comprised of common α and distinct β subunits. In the present study, the cDNAs encoding GTH a and GTH-IIβ subunits were cloned and sequenced from flounder (Paralichthys olivaceus) pituitary cDNA library. The nucleotide sequence of the a subunit was 619 bp long, encoding 124 amino acids, and that of the GTH-IIβ subunit was 538 bp long, encoding 145 amino acids. GTH subunits had well conserved cysteines, when aligned with other members of the glycoprotein family. The β subunit of gonadotropin II (GTH-IIβ) had a different N-linked glycosylation site. RT-PCR analysis showed an increase of GTH II mRNA levels in association with gonadal development, and also showed that the mRNA expression of the a subunit was detected only in tissues from pituitary glands.
Behavioural responses of deltamethrin- and permethrin-resistant strains of Aedes aegypti when exposed to permethrin in an excito-repellency test system

This study compared the behavioural avoidance responses of the permethrin-resistant and deltamethrinresistant strains of Aedes aegypti, a primary vector of dengue haemorrhagic fever (DHF) in Thailand. The background of biochemical-based resistance mechanism assay of these two strains revealed a significant increase of esterase activity and monooxygenase levels when compared with a laboratory-susceptible strain. Glutathione-S-transferase activity was found to increase only in the permethrin-resistant strain. The DNA sequence of knockdown resistance (kdr) mutation in the voltage-gated sodium channel (IIS6 region) was determined but the leucine to phenylalanine amino acid substitution, which is commonly associated with resistance to pyrethroids in many insect species, was not found in either strain. The behavioural escape response of both contact irritancy and non-contact repellency when exposed to permethrin at standard field dose (0.25 g/m 2 ) was observed by using an excito-repellency test chamber. The results showed that in contact trials, the permethrin-resistant strain showed a lower irritancy response when compared with the deltamethrin-resistant strain. This was probably due to the higher levels of resistance to this insecticide for the permethrin resistance strain. For the repellency test by noncontact trials, the response was not significantly different between the two strains. This may be because the repellency effect was much weaker than that of the irritancy effect. This study indicated that the behavioural response of mosquitoes differs according to different pyrethroid compounds and to the physiological resistance mechanism of the mosquitoes. However, further work is necessary to understand how these responses are mediated.
Structural and biophysical characterization of membrane-coating proteins from the nuclear pore and the primary cilium

A hallmark of eukaryotes is an endomembrane system that spatially separates cellular processes into discrete compartments. Macromolecular transport between these compartments canonically involves the fission and fusion of membrane-bound vesicles. Transport to and from the nucleus is a notable exception to this vesicular pathway. Additionally, transport to the primary cilium is not well characterized and is therefore of interest. The nuclear envelope comprises a double membrane that fuses at points to produce pores, which link the nucleoplasm with the cytoplasm. Coating these openings are nuclear pore complexes (NPCs), which regulate all nucleocytoplasmic trafficking by anchoring barrier forming FG-repeat proteins. At 60-120 MDa, the NPC is the largest macromolecular complex in the cell. However, it is a modular assembly formed by -30 different nucleoporins (Nups) arranged into stable subassemblies. One such module is the -600 kDa Y complex, which forms a Y shape and is the best characterized NPC subcomplex with crystal structures accounting for -90% of its total mass. The molecular details of how the short arms of the Y contact the long stem, in a region called the 'hub', were not known. We solved the structure of this last major missing piece of the Y complex to 4.1 A. This hub structure revealed unexpected curvature, allowed us to build the first atomic resolution composite of the mostly complete Y, and led to a novel higher order assembly model of the Y complex in the intact NPC. The ciliary membrane is topologically contiguous with the plasma membrane yet functionally distinct, due to a unique complement of integral membrane proteins. The Bardet- Biedl syndrome protein complex (BBSome) functions in the establishment or maintenance of this unique composition. The BBSome is -500 kDa octamer comprising BBS1, 2, 4, 5, 7, 8, 9, and BBIP10. To date, only the N-terminal domain of BBS1 had been structurally determined. In order to more completely characterize this complex, we have solved the structure of the BBS9 N-terminal [beta]-propeller to 1.8 A and determined its oligomeric state in solution. This structure has allowed us to identify a putative interaction site and characterized a disease relevant mutation on BBS9.
Habitat selection and diet of juvenile red porgy, Pagrus pagrus (Linnaeus, 1758)

Spatial and temporal variation in population attributes, size and age structure, abundance and distribution, generally reflect life history properties of a species. Changes in diet or habitat (or both) during ontogeny are extremely common in fishes (Werner and Gilliam, 1984). Fish partition food resources between species as well as between size classes within a species. Similar mechanisms such as differences in morphological features, foraging behavior, period of activity and habitat use, affect segregation of resource use in both cases (Werner, 1979; Mittelbach, 1981; Ross, 1986; Norton, 1991). However, different ecological processes have been emphasized in interpreting the adaptive value of resource partitioning in these two situations. Partitioning among species has been argued to reduce interspecific competition (Sale, 1979; Osenberg et al., 1992; Schluter, 1994). By contrast, differential vulnerability to predators or the ability to exploit prey (or both) may lead to de facto partitioning of prey among age classes within a species, with the consequence that intraspecific competition is reduced (Werner et al., 1983). Many fish unHabitat selection and diet of juvenile red porgy, Pagrus pagrus (Linnaeus, 1758)
Gastropod radulae and the assessment of form in evolutionary paleontology

Evolutionary paleontologists seek explanations of form and pattern in a diversity of contexts. A review of this diversity is presented to underscore the difficulty of producing a general model of the factors controlling the morphology of real organisms. A model specific to the marine prosobranch gastropod radula identifies seven factors contributing to form and pattern: (1) phylogenetic, (2) mechanical, (3) ecological, (4) programmatic, (5) maturational, (6) degenerative, and (7) constructional. Aspects of radular morphology attributable to each factor are illustrated in scanning electron micrographs of radulae of marine prosobranch gastropods. Applications of and extrapolations from the radular model are made to promote recognition of a broader range of interacting factors in other systems. Some aspects of form and pattern convey important information about non-evolutionary processes and phenomena and are best examined outside of the evolutionary framework.
Basic Asymptotic Theory, M-Estimation and ML Estimation

Convergence in Probability The scalar an converges in probability to a constant α if, for all positive and δ and for a sufficiently large n, Prob(|an − α| > ) < δ α is called the probability limit, or plim, of an. Consistency If an is an estimator of α, and plim an = α, then an is a (weakly) consistent estimator of α. Convergence in Distribution an converges in distribution to a random variable y (an → y) if, as n → ∞, Prob(an ≤ b) = Prob(y ≤ b) for all b. In other words, the distribution of an becomes the same as the distribution of y.