Miracle-dz/UniFAR-FTUs huggingface dataset:
Long-term shifts in the species composition of a coastal fish community

To study decadal shifts in a coastal nekton community, we analyzed data on 25 fish and invertebrate species collected from 1959 to 2005 by the University of Rhode Island, Graduate School of Oceanography (Narragansett, Rhode Island, USA). This weekly trawl survey samples two locations: inside Narragansett Bay and in Rhode Island Sound. Over four decades, the community has shifted progressively from vertebrates to invertebrates and, especially since 1980, from benthic to pelagic species. Demersal species that declined include winter flounder (Pseudopleuronectes americanus), silver hake (Merluccius bilinearis), and red hake (Urophycis chuss); meanwhile warm-water fish (butterfish, Peprilus triacanthus; scup, Stenotomus chrysops) and invertebrates (lobster, crab, squid) increased with time. Total numbers reached a maximum in the 1990s, while mean body size decreased. Taxonomic diversity increased over time, as the community shifted from fish to invertebrates of several phyla. The shifts in species composition.
Substrate Controlled Fed‐Batch Production of l‐Lysine with Corynebacterium glutamicum

A fed‐batch process for the production of l‐lysine with Corynebacterium glutamicum in a stirred tank reactor was developed up to a 150‐L scale applying the general approach of reaction engineering: Experimental optimization of medium composition (13 components: mineral salts and biotin) in parallel shake‐flask experiments using a Genetic Algorithm and the study of l‐leucine, ammonia, and phosphate supply in glucose controlled fed‐batch fermentations resulted in a volumetric l‐lysine productivity of 8.3 mol/(m3·h), a l‐lysine yield of 32% (mol/mol), and a l‐lysine concentration of 500 mM. The glucose concentration was controlled to 50 mM using on‐line HPLC and semicontinuous extended Kalman‐filter with a minimum variance controller. Nitrogen accumulation of the C. glutamicum cells in the early process phase for subsequent l‐lysine formation was identified by means of a reaction engineering analysis. Glucose limitation in the inoculum (1–2 h) results in growth linked l‐lysine production with a differential l‐lysine selectivity of 38% (mol/mol) and a maximum cell specific l‐lysine production rate of 1.1 mmol/(g·h) . l‐Lysine was not growth linked produced, if the inoculum was transferred at the exponential state.
Camelina sativa affects the fatty acid contents in M. longissimus muscle of lambs

Practicalapplications:The results ofthis studyshowedfavorable changesintheUFAcontentsinlongissimus dorsi muscle of lambs. The changes were obtained by supplementing the diets of the lambs with C. sativa cake, the plant cultivated as a biodiesel source. Inclusion of C. sativa cake in the concentrate dry matter for lambs may allow animal products to obtain the nutritionally desired fatty acids. Consumption of enriched products may act as chemopreventive agents and counteract the development of some human diseases.
Plasmid profile and antimicrobial resistance ratings of enterococci isolates from pigs and poultry birds in Abia state, Nigeria

Our aim was to isolate and investigate the resistance ratings of enterococci poultry and pig isolates to various antimicrobial agents as well as to determine their plasmid profiles. Antimicrobial resistance ratings and the plasmid profiles of Enterococci isolated from poultry birds and pigs were analyzed. Three hundred and thirty enterococci isolates from poultry birds and pigs were obtained from the three zones in Abia State. Antimicrobial resistance ratings, transformation, curing and plasmid extraction for enterococci were done. The result showed that in both animal species multi-resistance to antimicrobials occurred in more than 40% of enterococci isolates. The enterococci isolates were resistant to floxapen (90%), ceprofloxacin (70%) and norfloxacin (80%). It also showed that the organisms were sensitive to lincocin (100%), chloramphenicol (85%) and gentamicin (75%). There were significant differences (P 0.05). There was significant difference (P 0,05). Il y avait une difference significative (P<0,05) parmi les isolats lors de la pre- transformation et post-transformation. L'analyse du profil plasmidique d 'Enterococcus spp. a revele les bandes d'ADN plasmidique allant de la taille de 800 a 2. 000 bp qui semblait bandes brillantes. Les grands ont ete perdus lors de stockage de cellules,, certains etaient moins plasmide. Pas de correlation entre schemas de plasmides et la resistance aux antimicrobiens. Les recherches montrent de bonnes perspectives pour des recherches plus approfondies dans la meme domaine d'explorer et d'attribuer la cause precise pour la resistance. Aux antimicrobiens et la multiresistance. Mots- cles: Enterococcus spp. , Plasmide, Volailles, Porcs, la resistance aux antimicrobiens.
The role of fire disturbance for global vegetation dynamics: coupling fire into a Dynamic Global Vegetation Model

Disturbances from fire, wind-throw, insects and other herbivores are, besides climate, CO 2 , and soils, critical factors for composition, structure and dynamics of most vegetation. To simulate the influence of fire on the dynamic equilibrium, as well as on potential change, of vegetation at the global scale, we have developed a fire model, running inside the modular framework of the Lund-Potsdam-Jena Dynamic Global Vegetation Model (LPJ-DGVM). 2 Estimated litter moisture is the main driver of day-to-day fire probability. The length of the fire season is used to estimate the fractional area of a grid cell which is burnt in a given year. This affected area is converted into an average fire return interval which can be compared to observations. 3 When driven by observed climate for the 20th century (at a 0.5 ° longitude/latitude resolution), the model yielded fire return intervals in good agreement with observations for many regions (except parts of semiarid Africa and boreal Siberia). We suggest that further improvement for these regions must involve additional process descriptions such as permafrost and fuel/fire dynamics.
Purification and Identification of p68 RNA Helicase Acting as a Transcriptional Coactivator Specific for the Activation Function 1 of Human Estrogen Receptor α

ABSTRACT The estrogen receptor (ER) regulates the expression of target genes in a ligand-dependent manner. The ligand-dependent activation function AF-2 of the ER is located in the ligand binding domain (LBD), while the N-terminal A/B domain (AF-1) functions in a ligand-independent manner when isolated from the LBD. AF-1 and AF-2 exhibit cell type and promoter context specificity. Furthermore, the AF-1 activity of the human ERα (hERα) is enhanced through phosphorylation of the Ser118 residue by mitogen-activated protein kinase (MAPK). From MCF-7 cells, we purified and cloned a 68-kDa protein (p68) which interacted with the A/B domain but not with the LBD of hERα. Phosphorylation of hERα Ser118 potentiated the interaction with p68. We demonstrate that p68 enhanced the activity of AF-1 but not AF-2 and the estrogen-induced as well as the anti-estrogen-induced transcriptional activity of the full-length ERα in a cell-type-specific manner. However, it did not potentiate AF-1 or AF-2 of ERβ, androgen receptor, retinoic acid receptor alpha, or mineralocorticoid receptor. We also show that the RNA helicase activity previously ascribed to p68 is dispensable for the ERα AF-1 coactivator activity and that p68 binds to CBP in vitro. Furthermore, the interaction region for p68 in the ERα A/B domain was essential for the full activity of hERα AF-1. Taken together, these findings show that p68 acts as a coactivator specific for the ERα AF-1 and strongly suggest that the interaction between p68 and the hERα A/B domain is regulated by MAPK-induced phosphorylation of Ser118.
Rapid identification and characterization of peroxisomal assembly mutants in Yarrowia lipolytica

We describe the isolation and characterization of peroxisomal assembly mutants in the genetically manipulable yeast Yarrowia lipolytica (pay mutants). These mutants were initially identified as oleic acid‐non‐utilizers by their inability to grow on oleic acid, the utilization of which requires peroxisomal β‐oxidation enzymes. Identification of a subset of oleic acid‐non‐utilizers as pay mutants was obtained by a rapid immunofluorescence procedure using antibodies to the peroxisomal targeting signal Ser‐Lys‐Leu‐CO2H. Punctate structures characteristic of peroxisomes were not detected in pay mutants using this technique. This rapid identification by immunofluorescence should be generally applicable to the selection of peroxisomal assembly mutants in other yeasts. To take advantage of the pay mutant system, we constructed a genomic library in the autonomously replicating vector pINA445 and developed an efficient and rapid electroporation procedure for the functional complementation of these mutants. We have been successful in functionally complementing two independent pay mutants. Molecular analysis of these and other complementing genes will allow for characterization of some of the cellular elements involved in peroxisomal assembly.
In vitro flowering and micropropagation of Lisianthus (Eustoma grandiflorum) in response to plant growth regulators (NAA and BA)

In vitro flowering and micropropagation are useful for plant breeding programs and commercial production of important ornamental plants. In vitro conditions including media components, kind, concentration and ratio of plant growth regulators and culture conditions significantly affect in vitro flowering and micropropagation. There is no any report dealing with the in vitro flowering of Lisianthus (Eustoma grandiflorum). Here, a protocol was developed for flowering and high frequency in vitro micropropagation of E. grandiflorum, an ornamental plant. Micropropagation is an effective tools for propaga- tion of ornamental plants in large scale. The aim of the present study was to evaluate the effect of different concentrations of NAA and BA on micropropagation and flowering of Lisianthus, in vitro. Used culture medium was MS enriched with 0, 0.1, 0.2 and 2 mg L -1 of NAA and BA. In establishment process of explants, the most shoot length (2.07 cm per plant) was obtained on medium supplemented with 0.1 mg L -1 BA (without NAA). Maximum shoot number (5.80 per plant) was produced in medium containing 0.1 mg L -1 BA along with 0.2 mg L -1 NAA. Bud explants in culture media containing 0.2 mg L -1 NAA (without BA) and 0.1 mg L -1 NAA along with 2 mg L -1 BA produced maximum node number (3.20 per plant). The largest number of root (14.53 per plant) and root length (3.87 cm per plant) were produced on 0.2 mg L -1 NAA without BA, also 0.2 mg L -1 BA plus 0.2 mg L -1 NAA and 0.2 mg L -1 BA without NAA. Explants produced flower on me- dium containing 0.1 mg L -1 BA along with 0.1 mg L -1 NAA without transition of callus formation. Flower was produced from callus in medium containing 0.1 mg L -1 BA along with 2 mg L -1 NAA. Regenerated plants showed 98% survival in greenhouse during ac-
Sequence analysis and over-expression of ribosomal protein S28 gene (RPS28) from the Giant Panda

RPS28 is a component of the 40S small ribosomal subunit encoded by RPS28 gene, which is specific to eukaryotes. The cDNA and the genomic sequence of RPS28 were cloned successfully from the Giant Panda using RT-PCR technology and Touchdown-PCR, respectively. Both sequences were analyzed preliminarily and the cDNA of the RPS28 gene was also overexpressed in Escherichia coli ER2566 and immunoblotted. The cDNA of the RPS28 cloned from Giant Panda is 216 bp in size, containing an open reading frame of 210 bp encoding 69 amino acids. The length of the genomic sequence is 790 bp, which was found to possess three exons and two introns. Alignment analysis indicated that the nucleotide sequence of the coding sequence shows a high homology to those of Homo sapiens, Bos Taurus, Mus musculus, Rattus norvegicus and Sus scrofa (92.4, 92.4, 87.1, 86.7 and 89.5%, respectively) as determined by Blast analysis. The amino acid sequence encoded by RPS28 gene of the Giant Panda shared a high homology (100%) with those of Homo sapiens, B. Taurus, M. musculus, R. norvegicus and S. scrofa. Primary structure analysis revealed that the molecular weight of the putative RPS28 protein is 7.841 kD with a theoretical pI 10.70. Topology prediction showed there is one ribosomal protein S28e signature site, three protein kinase C phosphorylation site and two casein kinase II phosphorylation site in the RPS28 protein of the Giant Panda. The RPS28 gene can be really expressed in Escherichia coli and the RPS28 protein fusioned with the N-terminally GST -tagged protein gave rise to the accumulation of an expected 34 KDa polypeptide. The expression product obtained could be used for purification and study of its function further.
Inactivation or removal of the budded particles of a nuclear polyhedrosis virus of a silkworm, Bombyx mori L. (Lep., Bombycidae)

Effective methods to inactivate or remove budded particles of a nuclear polyhedrosis virus of Bombyx mori (BmNPV) from a cell‐cultured media or from host haemolymph that is infected by this virus have been developed. Two types of suspensions containing BmNPV budded virus particles, TC‐100 media that cultured BmN4 cells infected by this virus and haemolymph of B. mori larvae infected by this virus, were treated by 6% (w/v) polyethylene glycol (PEG), 0.01% (w/v) chitosan, 0.05% (v/v) linoleic acid (an emulsion), and/or diethylether. Treatment by linoleic acid followed by PEG‐precipitation and treatment by diethylether followed by PEG‐precipitation were so effective that these treatments suppressed the viral titre of BmNPV‐infected larval haemolymph from an original titre (> 109 TCID50 units/ml) to below a detectable limit. These methods are suggested as being potentially useful in an insect factory system; that is, a protein production system utilizing a baculovirus vector and its insect host or cultured cells on a large scale.
A Preliminary Analysis of Self-incompatibility in Sour Cherry

Self-incompatibility was investigated in sour cherry (Prunus cerasus L.) by examining pollen growth in the pistil by use of ultraviolet fluorescence microscopy following self- and cross-pollination. The sour cherry cultivars Tschernokorka and Crisana exhibit pollen tube inhibition in the style characteristic of gametophytic self- incompatibility. 'Meteor' and 'Montmorency' appear to be partially self-incompatible, with few self-pollen tubes reaching the ovary. Several hybrid seedlings from crosses between self-compatible cultivars were self-incompatible, suggesting that these self- compatible parental cultivars carry self-incompatibility alleles.
The European barley powdery mildew virulence survey and disease nursery 1993-1999.

Les suivis nationaux de virulences chez l'oidium de l'orge ont ete coordonnes a l'echelle europeenne de 1993 a 1999 dans le cadre de l'action COST817. L'objectif etait de comparer les resultats au-dela des frontieres nationales. Les frequences de virulences correspondant aux genes de resistance Mla1, Mla3, Mla6, Mla7, Mla9, Mlal2, Mla13, Mlk, MlLa et Mlg etaient moderees a fortes pour la plupart des annees et des pays. Pour plusieurs sources de resistance supplementaires, les frequences de virulences etaient inferieures a 5 %. En general, aucune augmentation d'agressivite vis-a-vis de la resistance Mlo n'a ete detectee, mais des changements pourraient etre en cours puisque des isolats particuliers d'origine britannique inocules sur des varietes possedant la resistance Mlo ont presente des niveaux d'infection plus eleves que d'autres groupes d'isolats. Par consequent, il est important dans le futur d'etudier avec attention les virulences correspondant aux nouvelles sources de resistance et a la resistance Mlo. Des essais au champ multilocaux ont ete mis en place en 1998 et 1999 pour etudier la resistance a l'oidium des genotypes d'orge dans differents environnements. Ces essais ont montre de grandes interactions entre lieu et expression phenotypique de la resistance. Il est primordial de poursuivre les echanges d'idees, de methodologie et de materiel vegetal entre programmes de suivis nationaux, et de distribuer rapidement les resultats aux agriculteurs et aux selectionneurs a travers l'Europe.
Conversion of Neopullulanase-α-Amylase from Thermoactinomyces vulgaris R-47 into an Amylopullulanase-Type Enzyme

TVA I, an alpha-amylase from Thermoactinomyces vulgaris R-47, is a versatile enzyme which hydrolyzes the alpha-(1-->4)-glucosidic linkages of pullulan to produce panose, known as neopullulanase activity, and the alpha-(1-->6)-glucosidic linkages of certain oligosaccharides. We modified the Ala-357, Gln-359, and Tyr-360 residues located in region II, one of the four regions conserved in alpha-amylase family enzymes, and deleted 11 consecutive amino acid residues located after the C-terminus of region II of the TVA I sequence by means of site-directed mutagenesis. The action pattern of the mutated enzyme for pullulan was greatly altered and it hydrolyzed mainly the alpha-(1-->6)-glucosidic linkages of pullulan to produce maltotriose, while the action patterns for starch and maltooligosaccharides were almost identical to those of the wild-type enzyme. This means that the mutated TVA I has lost the neopullulanase activity, and thus can be designated as an amylopullulanase-type enzyme. The kcat/Km value of the mutated enzyme for alpha-(1-->6)-glucosidic linkages was virtually unaltered, while that for alpha-(1-->4)-glucosidic linkages was about 100 times smaller than that of the wild-type enzyme.
A Morphometric Approach for Addressing Tooth-Based Species Delimitation in Fossil Mako Sharks, Isurus (Elasmobranchii: Lamniformes)

ABSTRACT Morphological studies of fossil and extant shark teeth have typically been qualitative in nature, with resulting taxonomic problems due to the complicated forms of heterodonty exhibited by many sharks. This is apparent in the designation of fossil species assigned to Isurus (Lamniformes), where the status of the putative Neogene fossil species Isurus xiphodon and I. hastalis is solely based upon supposed differences in tooth morphology. Here we apply the geometric morphometric techniques of Procrustes superimposition, resampling-based Goodall's F-test, and canonical variates analysis to extant Isurus teeth, with the goal of assessing whether these quantitative analytical techniques provide a more objective basis for taxonomic decisions than do traditional qualitative morphological descriptions. These quantitative techniques are then applied to I. hastalis and I. xiphodon to examine whether I. xiphodon should be considered a junior synonym of I. hastalis or a separate species. Results show that geometric morphometric techniques can differentiate between the two extant species as well as the two extinct species, supporting I. xiphodon as a valid taxon. We suggest that this type of analysis is applicable for examining tooth-based species delimitations of sharks with both extant and extinct members, and has the potential to be applied to other fossil shark species as well.
CONSERVATION GENETICS OF THE SONOMA TREE VOLE (ARBORIMUS POMO) BASED ON MITOCHONDRIAL AND AMPLIFIED FRAGMENT LENGTH POLYMORPHISM MARKERS

Abstract We used a comparative, multimarker approach to investigate the conservation genetics of an arboreal vole (the Sonoma tree vole [Arborimus pomo]) in the Pacific Northwest of North America. We compared geographic patterns and overall levels of genetic diversity based on 55 amplified fragment length polymorphism (AFLP) loci with those based on a single, commonly used mitochondrial locus, the control region. Although examination of the control region data revealed the presence of 2 distinct mitochondrial DNA (mtDNA) clades within A. pomo (1 in the north and 1 in the south of the species' range), the nuclear perspective provided by AFLP did not reveal a similar geographic division within the species, supporting instead that A. pomo consists of a single panmictic population. Genetic diversity estimates based on the mtDNA data (gene diversity = 0.79 and 0.80 for the 2 clades) were much greater than those based on AFLP (gene diversity = 0.31 and 0.19 for the 2 clades). These contrasting results reflect inherent differences between mitochondrial and nuclear loci in mutation rate, effective population size, expected time to monophyly, and mode of inheritance, and highlight the utility of using the combination of AFLP and mtDNA when assessing the genetic status of wild populations and species of mammals, especially those of conservation concern. In the case of A. pomo, our combined AFLP and mtDNA data support the recognition of the southern Sonoma tree voles as a distinct management unit within the species.
Scaling limit of the Stein variational gradient descent part I: the mean field regime

We study an interacting particle system in $\mathbf{R}^d$ motivated by Stein variational gradient descent [Q. Liu and D. Wang, NIPS 2016], a deterministic algorithm for sampling from a given probability density with unknown normalization. We prove that in the large particle limit the empirical measure converges to a solution of a non-local and nonlinear PDE. We also prove global well-posedness and uniqueness of the solution to the limiting PDE. Finally, we prove that the solution to the PDE converges to the unique invariant solution in large time limit.
Net-entrapment of great cormorants Phalacrocorax carbo sinensis in relation to individual age and population size

Abstract Population control of great cormorants Phalacrocorax carbo sinensis has been suggested as a tool to mitigate fish losses by cormorants foraging in pound nets, gill nets and fykes. The objective of our study was to quantify the difference between first-year birds and older birds in the risk of drowning in fishing gear, and to explore the influence of population size on the proportion of individuals drowning. An index of the proportion of first-year birds and older birds that drowned was obtained for cormorants ringed in the Danish Vorsø colony using resightings of colour-ringed individuals and ring recoveries of individuals found dead. First-year birds were approximately 10 times more likely to drown than older birds. We used ring recoveries of cormorants ringed in Denmark and found dead in Denmark, North Germany and South Sweden (i.e. in the main post-breeding area) to reveal changes over a 25-year period in the proportion drowned among those recovered. Among first-year birds the proportion drowned declined from 66% in 1978–1984 to 24% in 2000–2002, and among older birds the proportion declined from 46% in 1978–1984 to 26% in 1999–2002. During 1978–2000, breeding numbers in Denmark increased from 1,400 to 42,500 nests, and the proportion of cormorants drowned among those recovered was significantly negatively correlated with population size. This suggests that the proportion of the population foraging in nets declined as the population increased. The damage caused by cormorants foraging in pound nets is, therefore, unlikely to decrease in proportion to reductions in population size reached through population control.