Miracle-dz/UniFAR-FTUs huggingface dataset:
Catch-at-age assessment in the face of time-varying selectivity

Linton, B. C. , and Bence, J. R. 2011. Catch-at-age assessment in the face of time-varying selectivity. – ICES Journal of Marine Science, 68: . Age-based fishery selectivity represents the relative vulnerability of specific ages of fish to a fishery, whereby age classes that are highly selected tend to be overrepresented in the catch compared with their relative abundance in the population. Statistical catch-at-age analysis (SCAA) results can be sensitive to misspecification of selectivity, which can occur when changes in selectivity over time are not accounted for properly in the assessment model. Four approaches for modelling time-varying selectivity were evaluated within SCAA using Monte Carlo simulations: double-logistic functions with one, two, and all four of the function parameters varying over time, and age-specific selectivity parameters that all varied over time. None of these estimation approaches outperformed the others always. In addition, methods of model selection were compared to identify good estimation models, i.e. those accurately matching the true fish population. The degree of retrospectivity, the best selection method, was based on a retrospective analysis of errors in model estimates as the data time-series for estimation is sequentially shortened. This selection method performed about as well as knowing the correct selectivity model and led to substantial benefits over misspecifying the selectivity model.
AMERICAN GERIATRICS

and on the fascinating problems of how these hormones are concerned in the production of both hormonedependent and independent (autonomous) tumours and in tumour inhibition and regression. Excellent papers by Luria and Harris deal thoroughly with recent work on the virus-induced experimental cancers, but it is clear that these studies are still far from producing a rational approach to chemotherapy. In the field of the bifunctional alkylating agents Bergel and co-workers describe a number of peptide derivatives of their " phenylalanine mustard. " This was made in the D and L forms, of which only the latter (melphalan) was a tumour inhibitor; similarly the activity of the peptides seems to depend upon optical configuration, and it is hoped that eventually a peptide may selectively affect tumour tissue. Larionov, working in the same field, has found that the varying activity of the DL phenylalanine mustard (named sarcolysine) in different tumours is related to their different ability to take up phenylalanine and methionine into their protein content. Garattini and Palma report an admirably thorough investigation, with full statistical controls, of the inhibitory effects on the Walker tumour and various tissues of a number of alkylating agents, and antimetabolites. So far the tumour has usually shown less inhibition than normal tissues, but many other agents remain to be examined. The development of 5-fluorouracil and some derivatives is described by Heidelberger, but the clinical results are rather disappointing. Maisin deals with the restorative effect of isologous bone-marrow and of ribonucleic acid on the bone-marrow of rats which has been damaged by alkylating agents; and with the clinical implications. In a stimulating paper on general cell theory and drug design Danielli discusses directions in which research could be rationally pursued. Some of the author's recent experiments are also described. The book can be recommended to those seeking a broad and up-to-date survey of the subject defined by the title. G. M. TIMMIS.
Cys106 Oxidation of High Mobility Group Box 1 (HMGB1) Promotes Self-Oligomerization and Cytokine Release (172.22)

Oxidative stress can induce covalent disulfide bonds to form between protein-protein thiol groups. HMGB1, a DNA chaperon and damage associated molecular pattern molecule, is integral to oxidative stress. As a redox-sensitive protein, HMGB1 contains three cysteines: Cys23, Cys45, and Cys106. In this study, we focused on the oxidative oligomerization and pro-inflammatory cytokine induction by Cys106. HMGB1 oligomerization is positively modulated by copper and hydrogen peroxide. Mutagenesis of the Cys106 residue within HMGB1 blocks the formation of such oligomers. Addition of copper and hydrogen peroxide in HEK293T cell enhanced the oxidative self-oligomerization of HMGB1, while inhibiting it for mutant HMGB1 C106A. Furthermore, we used a bimolecular fluorescence complementation assay to directly visualize the Cys106 oxidation-induced HMGB1 oligomerization in live cells under oxidative stress conditions. And we were able to reproduce the oligomerization effect of HMGB1 using FRET analysis. Interestingly, the oligomerized-HMGB1 binds to TLR4/MD2 complex with higher affinity than monomer HMGB1. Oligomerized HMGB1 transferred nuclear factor-κB signaling at significant levels using HEK293/TLR4 cells, and the cytokine production by oligomerized-HMGB1 is now under investigation. In conclusion, the oligomerized-HMGB1 most likely plays a regulatory role in the secretion of pro-inflammatory cytokines under physiological conditions.
Spacing of the Tadpoles of Hyla versicolor and Rana clamitans

Abstract How individuals are located in space can impact their interactions. We investigated spacing behavior of tadpoles of Gray Treefrogs (Hyla versicolor) and Green Frogs (Rana clamitans) at two densities in the laboratory. Tadpoles of H. versicolor were more dispersed than those of R. clamitans. Spacing (e.g., random, dispersed, or aggregated) of tadpoles was not affected by density; however, dispersion tended to increase during the experiment. Our results suggest that spacing behavior in tadpoles is dynamic over time and may provide some insight into the outcome of intra- and interspecific interactions.
Classification and phylogenetic relationship of microaerophilic actinomycetes

ABSTRACT In consideration of the genera proposed for the family Actinomycetaceae, weighted considerations were given to the factors of morphology, carbon dioxide and oxygen utilization, anaerobic and aerobic fermentation balances, glucose metabolism, presence of catalase and haemoproteins, and cell wall composition. Primarily, on the basis of cell wall composition but strongly supported by metabolic and fermentation characteristics, it was concluded the genus Arachnia belongs in the family Propionibacteriaceae. Similarly, the genus Bacterionema is more suitable within the family Mycobacteriaceae or Corynebacteriaceae. The family Actinomycetaceae would retain Actinomyces israelii, A. bovis, A. naeslundii, A. odontolyticus, A. viscosus, and Rothia dentocariosa.
SPATIAL PATTERN IN AN EPIDEMIC SYSTEM WITH CROSS-DIFFUSION OF THE SUSCEPTIBLE

In this paper, pattern formation of a spatial model with cross diffusion of the susceptible is investigated. We compute Hopf and Turing bifurcations for the model. In particular, the exact Turing domain is delineated in the parameter space. When the parameters are in that domain, a series of numerical simulations reveals that the typical dynamics of the infecteds class typically involves the formation of isolated groups, i.e., striped, spotted or labyrinthine patterns. Furthermore, spatial oscillatory and anti-phase dynamics of different spatial points were also found. These results demonstrate that cross diffusion of susceptibles may have great influence on the spread of the epidemic.
Metabolic Capacities and Immunocompetence of Sea Scallops (Placopecten magellanicus, Gmelin) at Different Ages and Life Stages

ABSTRACT We evaluated the development of metabolic capacities, immunocompetence, and growth patterns according to sex, age, and gametogenesis stages among scallops Placopecten magellanicus from the Magdalen Islands (Québec, Canada). Our 2-y study allowed us to evaluate in detail both seasonality and interannual variability of their physiological state. Enzymes— namely, phosphoglucose isomerase, phosphomannose isomerase, pyruvate kinase, aspartate aminotransferase, citrate synthase, chymotrypsin, and lipase were assessed in muscles and digestive glands of scallops. Immunocompetence was evaluated by measuring hemocyte activity in hemolymph and the efficiency of phagocytic cells. The various reproductive stages were identified with histological examination, and growth was estimated using digestive gland and gonadosomatic indices. Lipase and phagocytosis appeared to be good biomarkers of the physiological state of scallops in relation to their age and reproductive stage: Lipase activity is higher in young scallops (2 y old) as well as during the development and the ripe stages, and is associated with low phagocytic activity. Results suggest that the lipid digestion capacity may increase to improve lipid conversion during the development and ripe stages. After this period, metabolic reserves were presumably used to synthesize hemocytes at a higher rate and to rebuild gonadal tissue. The regulation of the reproductive cycle and immunocompetence was observed to depend directly on the environmental parameters without concomitant changes in the activity of the measured enzymes of the energy metabolism.
Trophic levels of marine consumers from nitrogen stable isotope analysis: estimation and uncertainty

Estimates of trophic levels (TLs) are used to calibrate, parameterize, and validate foodweb models and to calculate metrics and indicators of foodweb structure and human impacts. We develop a method to estimate TL from nitrogen stable isotope data (δ15Nδ15N) and apply it to 5535 individuals from 62 species of marine fish and squids sampled from the Celtic Sea, English Channel, Irish Sea, and North Sea. With this method, uncertainties in δ15Nδ15N at the base of the foodweb (from a marine isoscape generated with environmental data) and in trophic fractionation (from existing fixed and scaled fractionation models) are propagated through the analysis to quantify uncertainty in TL. Higher values of base and consumer δ15N lead to greater uncertainty in TL estimates for individual consumers. Base and consumer δ15Nδ15N are higher in coastal regions with lower salinity, such as the Irish Sea and Channel coasts, so uncertainty in individual TL estimates is relatively high in these regions. Conversely, when base and consumer δ15Nδ15N are low, as in the high salinity waters of the northern North Sea, uncertainty is relatively low. Uncertainty intervals for species' predicted TL at a reference mass (based on ≥10 individuals spanning a range of body sizes) are small compared with estimates for individual consumers, as are estimates of slope of the TL body mass relationship. For ∼50% of region and species combinations showing trends in TL with body mass, there are eight times more positive relationships than negative ones. Our approach can be applied at large spatial scales. It generates estimates of uncertainty that support more rigorous and informed comparisons of the trophic ecology of size classes, species, and species-groups. A data file that includes estimates of TL and associated uncertainty for all sampled individuals accompanies this study.
A note on the antibiotic properties of Bacillus subtilis against Colletotrichum trifolii

On a etudie l'influence et les mecanismes d'action in vitro et in vivoBacillus subtilissur le Colletotrichum trifolii, un champignon causant l'anthracnose de la luzerne (Medicago sativa). Lors d'essais en chambre de culture, l'application du filtrat du bouillon nutritif du B. subtilis a reduit significativement l'incidence et la gravite de la maladie de respectivement 56 a 16% et de 2,0 a 1,2. L'application de cellules lavees du B. subtilis n'a pas entraine une diminution de l'incidence et de la gravite de la maladie. Sur les folioles de la luzerne, le filtrat a cause une reduction de la germination des conidies, la lyse des conidies et une formation reduite d'appressoriums. In vitro, il a reduit la germination des conidies, induit la lyse des conidies et la formation de tubes germinatifs enfles. Un antibiotique de la famille des iturines, l'iturine D, serait l'agent actif dans la suppression du C. trifolii par le B. subtilis.
Evaluation of Essential Oils from Six Aromatic Plants in Togo for Callosobruchus maculatus F. Pest Control

The insecticidal activity of essential oils extracted by steam distillation from six aromatic plants from Togo, Cymbopogon schoenanthus (L.) Spreng. , C. citratus (D.C.) Stapf. , C. nardus (L.) Rendle, Lippia multiflora Moldemke, Eucalyptus citriodora Hook. , Diplolofium africanum Turcz. , was tested against the cowpea weevil, Callosobruchus maculatus F. Concentrations of 6.7; 10.0; 16.7 and 33.3 µl/1 were evaluated. The chemical composition of the essential oils used was established by GC/MS analysis. Only C. schoenanthus oil showed significant insecticidal activity at 6.7 µl/l oil (LC50 2.3 µl/l). At concentrations higher than 33.3 µl/1, all test plants showed similar insecticidal activity; more than 90% of the test insects died within 24 hours of exposure. Oviposition was also reduced significantly by the essential oil treatments. RésuméL’activité insecticide des huiles essentielles extraites par entraînement à la vapeur de six plantes aromatiques du Togo, Cymbopogon schoenanthus (L.) Spreng. , C. citratus (D.C.) Stapf. , C. nardus (L.) Rendle, Lippia multiflora Moldemke, Eucalyptus citriodora Hook. , Diplolofium africanum Turcz. , a été testée contre la bruche du niébé, Callosobruchus maculatus F. Les concentrations de 6,7; 10,0; 16,7 et 33,3 µl/1 ont été appliquées. La composition chimique des huiles essentielles utilisées a été établie par analyses CPG/SM. Seule l’huile de C. schoenanthus a montré une activité insecticide significative à 6,7 µl/1 (LC50 2,3 µl/1). A des concentrations supérieures à 33,3 µl/1 l’activité insecticides est la même pour toutes les plantes étudiées; plus de 90% des insectes traités sont morts en 24 h. L’oviposition est aussi fortement réduite par le traitement aux huiles essentielles.
Tempo de migração dos macrófagos em matrinxã, Brycon amazonicus, por meio da técnica de inoculação de leveduras Saccharomyces cerevisiae

In aquaculture, analysis of activation and increased macrophages migration are used in order to verify the ability of the nonspecific immune fish exposed to a challenge. This study aimed to determine the time of macrophages migration in matrinxa, Brycon amazonicus, through the technique of yeast Saccharomyces cerevisiae inoculation, verifying possible changes in hematological parameters. Thirty animals with average weight of 101.55 ± 24.50 g and average length of 19.75 ± 1.72 cm were employed. The experimental inoculation periods were 2, 4, 8 and 12 hours. Thereafter, animals were anesthetized and blood was withdrawn through a caudal puncture for the determination of total erythrocytes number, differential and total leukocyte counts and total thrombocytes count, hematocrit, hemoglobin concentration and calculation of the erythrocytes index. The results for the phagocytic capacity were not significantly different between experimental periods. In the phagocytic index, the period of 2 hours presented the highest rate of phagocytized cells, indicating that 2 hours of incubation was sufficient for the macrophages migration in B. amazonicus. The number of erythrocyte was the only parameter that presented significant difference among periods.
Tyrosine Mutation in CD3ε–ITAM Blocked T Lymphocyte Apoptosis Mediated by CD3ε

Anti‐CD3ε monoclonal antibody induces programmed cell death of thymocytes and accelerates activation‐induced cell death (AICD) by apoptosis of matured or transformed T lymphocytes. However, the underlying molecular mechanism of this phenomenon is unclear. Therefore, we produced a chimera protein (termed CD8ε by fusing the extracellular and transmembrane domains of human CD8α to the intracellular domain of mouse CD3ε and expressed in CD8−Jurkat T cells. Stable cell lines of mutants expressing the motifs of Y170F, Y181F, and Y170F/Y181F in the CD3ε − ITAM were established. Experiments showed that apoptosis could be induced only in the T Jurkat cells with intact CD3ε intracellular domain, but not in the cells with the mutant CD8ε when stimulated with anti‐CD8α monoclonal antibody. This finding indicated that a single tyrosine mutation in CD3ε − ITAM blocked the signal transduction, causing the cell death by apoptosis when stimulated by CD8ε molecule. During the apoptotic process, we showed that expressions of CD95, CD95L and Nur77 were enhanced in stimulated TJK cells but not in control cells. In addition, the high expression of Nur77 kept pace with the onset of apoptosis of T‐cells mediated by CD8ε. We further showed that 3′‐phosphatidylinositol kinase (PI3K) were not only enhanced during T cell activation, but also in the AICD process. The results suggest that PI3K/Akt is not only a cell proliferation signal, but also a potential apoptosis regulator in T lymphocytes.
Coral mucus release and following particle trapping contribute to rapid nutrient recycling in a Northern Red Sea fringing reef

Mucusreleased bycoralscanfunctionasan importantenergycarrier andparticle trapinreefecosystems with strong tidal currents. In fringing reefs with calm conditions, these processes may occur on smaller spatial scales. Observations of coral mucus dynamics in the Northern Red Sea revealed highly particle-enriched and negatively buoyant mucusstringsattachedto,27%ofcoralcoloniesforupto79min.MucusstringsofthescleractiniancoralgenusAcropora exhibited three orders of magnitude higher particulate organic carbon and nitrogen concentrations when compared with freshly released coral mucus, which confirms efficient particle trapping. After detachment from the coral surface, more than95% ofmucus strings rapidlydescended tothe reef seafloor withinless than 1m. Suchmucus-induced transportmay account for 21-25% of the total sedimentary particulate organic matter supply. In situ and laboratory analyses of planktonic and benthic microbial degradation of mucus strings showed high rates of up to 16 and 26% particulate organic carbon h � 1 , respectively. These findings suggest a newly discovered, tight sediment-water coupling mechanism via coral
The influence of enriched rhizosphere CO2 on N uptake and metabolism in wild‐type and NR‐deficient barley plants

Positive influences of high concentrations of dissolved inorganic carbon (DIC) in the growth medium of salinity-stressed plants are associated with carbon assimilation through phosphoenolpyruvate carboxylase (PEPc) activity in roots ; and also in salinity-stressed tomato plants, enriched CO 2 in the rhizosphere increases NO 3 - uptake. In the present study, wild-type and nitrate reductase-deficient plants of barley (Hordeum vulgare L. cv. Steptoe) were used to determine whether the influence of enriched CO 2 on NO 3 - uptake and metabolism is dependent on the activity of nitrate reductase (NR) in the plant. Plants grown in NH 4 + and aerated with ambient air, were transferred to either NO 3 - or NH 4 + solutions and aerated with air containing between 0 and 6 500 μmol mol -1 CO 2 . Nitrogen uptake and tissue concentrations of NO 3 - and NH 4 + were measured as well as activities of NR and PEPc. The uptake of NO 3 - by the wild-type was increased by increasing CO 2 . This was associated with increased in vitro NR activity, but increased uptake of NO 3 - was found also in the NR-deficient genotype when exposed to high CO 2 concentrations ; so that the influence of CO 2 on NO 3 - uptake was independent of the reduction of NO 3 - and assimilation into amino acids. The increase in uptake of NO 3 - in wild-type plants with enriched CO 2 was the same at pH 7 as at pH 5, indicating that the relative abundance of HCO 3 - or CO 2 in the medium did not influence NO 3 - uptake. Uptake of NH 4 + was decreased by enriched CO 2 in a pH (5 or 7) independent fashion. Thus NO 3 - and NH 4 + uptakes are influenced by the CO 2 component of DIC independently of anaplerotic carbon provision for amino acid synthesis, and CO 2 may directly affect the uptake of NO 3 - and NH 4 + in ways unrelated to the NR activity in the tissue.
Phosphorylation of Human Estrogen Receptor α by Protein Kinase A Regulates Dimerization

ABSTRACT Phosphorylation provides an important mechanism by which transcription factor activity is regulated. Estrogen receptor α (ERα) is phosphorylated on multiple sites, and stimulation of a number of growth factor receptors and/or protein kinases leads to ligand-independent and/or synergistic increase in transcriptional activation by ERα in the presence of estrogen. Here we show that ERα is phosphorylated by protein kinase A (PKA) on serine-236 within the DNA binding domain. Mutation of serine-236 to glutamic acid prevents DNA binding by inhibiting dimerization by ERα, whereas mutation to alanine has little effect on DNA binding or dimerization. Furthermore, PKA overexpression or activation of endogenous PKA inhibits dimerization in the absence of ligand. This inhibition is overcome by the addition of 17β-estradiol or the partial agonist 4-hydroxy tamoxifen. Interestingly, treatment with the complete antagonist ICI 182,780 does not overcome the inhibitory effect of PKA activation. Our results indicate that in the absence of ligand ERα forms dimers through interaction between DNA binding domains and that dimerization mediated by the ligand binding domain only occurs upon ligand binding but that the complete antagonist ICI 182,780 prevents dimerization through the ligand-binding domain. Heterodimer formation between ERα and ERβ is similarly affected by PKA phosphorylation of serine 236 of ERα. However, 4-hydroxytamoxifen is unable to overcome inhibition of dimerization by PKA. Thus, phosphorylation of ERα in the DNA binding domain provides a mechanism by which dimerization and thereby DNA binding by the estrogen receptor is regulated.
Modelling the Dynamical Components of the Sugar Beet Crop

Many models have been constructed to describe the growth of the sugar beet crop up to harvesting. In general, these models have a complex physiological basis, requiring a large number of parameters yet relying on empirical functions with no mechanistic basis to partition assimilates within the crop. An important factor in considering the growth of the crop, both from an economic and environmental point of view, is the response of the crop to varying amounts of available nitrogen in the soil. In this paper, a model is described for crop growth using soil nitrogen content and solar radiation as driving functions. The parsimonious approach to construction resulted in a 14 parameter model, seven of which are associated with the driving variables. This is substantially fewer than for other crop models. The model contains a new dynamical way of describing partitioning of assimilates between shoot, storage root and fibrous roots. The partitioning model is derived from observations on the effect of soil nitrogen on crop growth. Interception of light is determined by foliage cover, which makes the model suitable for use with data collected from satellite imaging. The model fits well to three independent data sets with estimated parameters lying within biologically reasonable bounds. The model is used to test the sensitivity of yield to changes in soil nitrogen.
Phenology of the New Zealand flower thrips, Thrips obscuratus (Crawford) (Thysanoptera: Thripidae), on nectarine and peach flowers

The number and species of thrips (Thysanoptera) infesting flowers and young fruit of unsprayed nectarine and peach trees in Canterbury, New Zealand were determined. Adult thrips (mostly females) were found in similar numbers from pink to shuck fall. Few thrips larvae were found in flowers from pink to full bloom. Larval numbers increased steadily after full bloom, peaked close to petal fall and then gradually declined. Few larvae were found on young fruit at shuck fall. Adults and larvae were almost all Thrips obscuratus (Crawford) (Thysanoptera: Thripidae).