Miracle-dz/UniFAR-FTUs huggingface dataset:
Reinstatement of Xanthomonas citri (ex Hasse) and X. phaseoli (ex Smith) to Species and Reclassification of All X. campestris pv. citri Strains

A recent epiphytotic disease on citrus in Florida nurseries was caused by strains of Xanthomonas campestris with different host specificity and lower pathogenic capacities than those of previously described strains of X. campestris pv. citri. The new strains were classified as X. campestris pv. citri because they were isolated from rutaceous hosts and despite the fact that they caused a different disease than strains previously described in that pathovar. Restriction fragment length polymorphism analyses revealed that the Florida strains comprised a heterogeneous (E) group, interrelated with X. campestris pv. alfalfae, X. campestris pv. cyamopsidis, and X. campestris pv. dieffenbachiae. In contrast, the previously described strains of X. campestris pv. citri formed two highly distinct, homogeneous (A and B/C/D) groups. Furthermore, the strains of X. campestris pv. campestris, X. campestris pv. glycines, X. campestris pv. malvacearum, X. campestris pv. phaseoli, X. campestris pv. pisi, and X. campestris pv. vignicola tested were also distinctive and appeared to be only distantly related to one another and to all X. campestris pv. citri strains. We concluded (i) that some pathovars are sufficiently distinct from the type strain of the species X. campestris to be considered as separate species, (ii) that X. campestris pv. citri group A and X. campestris pv. phaseoli (not including X. campestris pv. phaseoli var. fuscans) represent distinctly separate subbranches of the genus and should be respectively reinstated to species as X. citri (ex Hasse) nom. rev. 3213 and X. phaseoli (ex Smith) nom. rev. G27, and (iii) that the X. campestris pv. citri B/C/D strains and the heterogeneous E strains should be respectively renamed X. campestris pv. aurantifolii pv. nov. and X. campestris pv. citrumelo pv. nov.
Inter-specific relationships among two Tunisian Thymus taxa: Thymus capitatus Hoffm. et Link. and Thymus algeriensis Boiss. et Reut. using molecular markers

Genetic relationships between two sympatric species Thymus capitatus Hoffm. et Link. and Thymus algeriensis Boiss. et Reut. ( Thymus hirtus Willd. subsp. algeriensis Boiss. et Reut.) were assessed using random amplified polymorphic DNA (RAPD) markers. Eighteen natural populations from different geographical and bioclimatic zones were evaluated. The seven selected primers generated 121 RAPD markers for T. capitatus (103 polymorphic; P = 85.12%) and 154 for T. algeriensis (141 polymorphic; P = 91.56%). The genetic diversity within T. capitatus and T. algeriensis populations based on Shannon’s index was high (H’ pop = 0.303 and 0.307, respectively). A high genetic differentiation was revealed (G ST = 0.359 and Φ ST = 0.284 for T. capitatus , G ST = 0.335 and Φ ST = 0.296 for T. algeriensis ). The large proportions of the genetic variation were observed within populations for the two studied taxa. A high genetic population’s structure was also estimated by a principal component analysis (PCA). Unweighted pair-group method using arithmetic average (UPGMA) cluster analysis based on Nei and Li's coefficient among populations identified that T. algeriensis and T. capitatus populations were clustered into two distinct groups. The high genetic divergence between the two species corroborates their taxonomic status. Keywords: Genetic diversity, inter-specific relationships, molecular markers, Thymus capitatus , Thymus algeriensis
Predicting harvest of non-native signal crayfish in lakes —a role for changing climate?

The signal crayfish (Pacifastacus leniusculus) was introduced to Sweden in 1960, and it has a high commercial and recreational value, but it may also have negative effects on native ecosystems. To better predict how climate warming will affect population dynamics of this cool-water crayfish, we explored the role of temperature and density dependence as explanatory factors of the subsequent years’ catch rates of commercially sized signal crayfish in four Swedish lakes. We found air temperatures to be good proxies for water temperatures in all lakes, except during winter. We could only obtain water temperature data for Lake Vattern, and winter temperature data were therefore only included in the analysis of catch-per-unit-effort patterns in this lake. Our results indicate that increasing mean air temperatures will potentially affect the population dynamics of cool-water freshwater crayfish species such as the signal crayfish. Based on data from four lakes, it seems that the population dynamics of signal cra.
Ultrastructure of the primary gill lamellae of Scomber australasicus

The ultrastructure of the primary epithelium, and the efferent half of the subepithelium, of the primary gill lamellae of slimy mackerel (Scomber australasicus) is described. The following cells are identified and described: light nucleated epithelial cells (surface and basal), dark nucleated cells, mucous cells, acidophilic cells, type 1 cells, type 2 cells, type 3 cells and chloride cells in the epithelial region, and subepithelial cells A and B, fibroblasts, chondrocytes, cells of the wall of efferent blood vessel and some blood cells in the subepithelium.
IFN‐α promotes definitive maturation of dendritic cells generated by short‐term culture of monocytes with GM‐CSF and IL‐4

Dendritic cells (DC) generated in vitro have to be viable and phenotypically mature to be capable of inducing T cell‐mediated immunity after in vivo administration. To facilitate optimization of DC‐based vaccination protocols, we investigated whether the cytokine environment and the mode of activation affect maturation and survival of DC derived from monocytes by a short‐term protocol. Monocytes cultured for 24 h with granulocyte macrophage‐colony stimulating factor and interleukin‐4 were stimulated with proinflammatory mediators for another 36 h to generate mature DC. Additional activation with CD40 ligand and interferon (IFN)‐γ increased viability of DC and promoted definitive maturation as defined by maintenance of a mature phenotype after withdrawal of cytokines. Addition of IFN‐α to DC cultures prior to stimulation further enhanced definitive maturation: IFN‐α‐primed DC expressed high levels of costimulatory molecules and CC chemokine receptor 7 (CCR7) up to 5 days after cytokine withdrawal. Compared with unprimed DC, IFN‐α‐primed DC displayed equal capacity to migrate upon CCR7 ligation and to prime antigen‐specific T helper cell as well as cytolytic T cell responses. In conclusion, we show that optimal maturation and survival of monocyte‐derived DC require multiple activation signals. Furthermore, we identified a novel role for IFN‐α in DC development: IFN‐α priming of monocytes promotes definitive maturation of DC upon activation.
Diversity of the Poroid Hymenochaetaceae (Basidiomycota) from the Atlantic Forest and Pampa in Southern Brazil

Abstract A synopsis of the current knowledge about the poroid Hymenochaetaceae from Southern Brazil (States Paraná, Santa Catarina and Rio Grande do Sul) is presented. Fortytwo species belonging to nine genera are reported from the areas surveyed. An annotated, partly illustrated, checklist and identification keys are provided. The new combinations Fomitiporia bambusarum and Fulvifomes rhytiphloeus are also proposed. Atlantic Forest / Hymenochaetales / Neotropics / Taxonomy
Evaluation of the agronomical and biochemical characteristics of new lines of bread wheat in Turkey.

Sixteen new lines of bread wheat obtained from the CIMMYT/ICARDA and a standard cultivar were evaluated during three successive years (2003, 2004 and 2005). The experiments were conducted at the experimental farm of the Faculty of Agriculture of the Uluda? University in Bursa. The lines and the standard cultivar showed significant differences in plant height, number of seeds/spike, seed weight/spike, seed yield and a 1000-kernel weight. The lines numbered 4, 6, 7, 9, 11, 14 and 15 produced significantly higher seed yields than the standard cultivar. Therefore, they formed the highest group (a) of seed yield. Similarly, these lines had a higher number of seeds/spike value than the standard cultivar. However, lines 6 and 11 produced higher seed yields than lines 4, 7, 9, 14 and 15. In particular, the gluten composition and the zeleny sedimentation test values of whole flours revealed that lines 6 and 11 could be suitable for high-quality pasta production with good sensory characteristics. To summarize, there were significant differences between the lines with respect to agronomic and biochemical characteristics. In particular, lines 6 and 11 had better performance than both the other lines and the standard cultivar because of their seed yield and quality.
Peroxisome Proliferator-Activated Receptor γ-Independent Ablation of Cyclin D1 by Thiazolidinediones and Their Derivatives in Breast Cancer Cells

In light of the clinical relevance of targeting cyclin D1 in breast cancer, we have investigated the mechanism underlying the effect of the peroxisome proliferator-activated receptor-γ (PPARγ) agonists troglitazone and ciglitazone on cyclin D1 repression. We obtain evidence that the ability of high doses of troglitazone and ciglitazone to repress cyclin D1 is independent of PPARγ activation. PPARγ-inactive troglitazone and ciglitazone analogs 5-[4-(6-hydroxy-2,5,7,8-tetramethyl-chroman-2-yl-methoxy)-benzylidene]-2,4-thiazolidinedione (Δ2-TG) and 5-[4-(1-methyl-cyclohexylmethoxy)-benzylidene]-thiazolidine-2,4-dione are able to facilitate cyclin D1 ablation with potency similar to that of troglitazone and ciglitazone in MCF-7 cells. Reverse transcription-polymerase chain reaction shows that the mRNA level of cyclin D1 remains unaltered in drug-treated cells, indicating the repression is mediated at the post-transcriptional level. Moreover, the ablative effect of these agents is specific to cyclin D1, in that the expression levels of many other cyclins and cyclin-dependent kinases examined remain unchanged after drug treatment. Our data indicate that troglitazone- and Δ2-TG-induced cyclin D1 repression is mediated via proteasome-facilitated proteolysis because it is inhibited by different proteasome inhibitors, including N-carbobenzoxy-l-leucinyl-l-leucinyl-l-norleucinal (MG132), lactacystin, and epoxomicin, and is preceded by increased ubiquitination. The dissociation of these two pharmacological activities (i.e., PPARγ activation and cyclin D1 ablation) provides a molecular basis to use Δ2-TG as a scaffold to develop a novel class of cyclin D1-ablative agents. Therefore, a series of Δ2-TG derivatives have been synthesized. Among them, 5-[4-(6-allyoxy-2,5,7,8-tetramethyl-chroman-2-yl-methoxy)-benzylidene]-2,4-thiazolidinedione represents a structurally optimized agent with potency that is an order of magnitude higher than that of Δ2-TG in cyclin D1 repression and MCF-7 cell growth inhibition.
Effect of organic farming on yield and quality of potato tubers in Ardabil

In order to study the possibility of replacing current potato cropping system in Ardabil province of Iran, which seriously depends on chemical inputs, with organic farming methods, an experiment was conducted in the years 2004 and 2005. The experimental design in each year was split plot based on randomized complete blocks with three replications. Main plots were three fertilizer types as 40 Mg ha ¹ well–composted dairy manure (A1), 250 kg ha ¹ nitrogen plus 180 kg ha ¹ P 2 O 5 as chemical fertilizers (A2), and 20 Mg ha ¹ dairy manure plus 125 kg ha ¹ nitrogen and 90 kg ha-¹ P 2 O 5 as the chemical fertilizers (A3). Sub-plots were four types of pesticide against Colorado potato beetle (Leptinotarsa decemlineata Say.): lemon skin extract as an organic pesticide (B1), hot pepper extract as an organic pesticide (B2), endosulfan (Tiodan 35 EC) as a chemical pesticide (B3) and control (without any pesticide application) (B4). Several characteristics, such as potato yield, percent of dry matter of tuber, tuber weight and tuber nitrate content, were measured. Results showed that the yields of plots in which manure was used (A1 and A3) were about 0.4 kg m ² higher than in the plots that received only chemical fertilizers, however, no significant difference was observed between A1 and A3. The percent of dry matter of tuber of A1 was also higher than in the other treatments. Although endosulfan-treated (B3) had highest tuber yield and dry matter among pesticide treatments, it was not significantly different from the lemon skin extract-treated (B1). Different fertilizers and pesticides did not affect the tuber nitrate content.
Geographic variation in Crowea exalata (Rutaceae) and the recognition of two new subspecies

Crowea exalata F.Muell. was sampled throughout its morphological and geographical range to test the validity of the current circumscription of the species and subspecies. Through numerical analysis of morphological and chemical (leaf flavonoids and volatile oils) data four taxa are recognised, subsp. exalata, subsp. revoluta Paul G.Wilson, subsp. magnifolia Gebert subsp. nov. and subsp. obcordata Gebert subsp. nov. Descriptions and a key to all taxa are provided.
Ontogenetic variation in light requirements of juvenile rainforest evergreens

Summary 1. Although shade tolerance is often assumed to be a fixed trait of species, recent work has reported size-related changes in the relative and absolute light requirements of woody taxa. We hypothesized that, in evergreen forests, light requirements of shade-tolerant species that accumulate multiple foliage cohorts will be more stable during juvenile ontogeny than those of intolerant species with short leaf lifetimes. 2. We quantified the light environments occupied by three size classes of 13 coexisting evergreens in a temperate rainforest, to determine how size influenced their relative shade tolerance. Minimum light requirements (MLRs) of species were estimated by computing the 10th percentile of the distribution of juveniles in relation to percentage canopy openness, for each size class. Leaf life span in low light (2%‐5% canopy openness) was estimated by recording survival of marked leaves over 12 months, or retrospectively on species with clearly discernible foliage cohorts. 3. Agreement of ranks of species’ MLR across size classes was significant, although not strong (Kendall’s W = 0·159, P = 0·02). MLRs of the most shade-tolerant species changed little between size-classes, whereas those of most of the less-tolerant species rose with increasing size. 4. Shift in MLR across size-classes was negatively correlated with leaf life span, possibly because of the effects of leaf life span on biomass distribution and whole-plant carbon balance. Survival of light-demanding species with short leaf lifetimes may thus depend on their encountering increasing light levels as they grow taller, whereas progressive accumulation of an extensive leaf area by late-successional taxa enables them to continue to tolerate low light despite increasing size. 5. Results suggest that shade-tolerance differences between evergreens become increasingly apparent with increasing size. In identifying a relationship with leaf life span, this work also provides a basis for predicting changes in species’ light requirements during juvenile ontogeny.
Relationship between west African rainfall and the survival of central European sand martins Riparia riparia

The aim of this study was to investigate the effects of Sahelian rainfall on the central European Sand Martin Riparia riparia population for the period 1986–1992. The studied population breeds along the River Tisza in Hungary and is one of the largest in central Europe. The changes in the population size did not show a significant relationship to Sahelian rainfall, but a large decrease in 1991 coincided with the drought in three Sahelian areas. The survival rates of adults had a significant relationship to the rainfall of the southern Sahel but not to the other two studied areas (northern Sahel, central Sudan). The model selection included this relationship and raised the possibility of predicting the adult survival rate in autumn for the following wintering season, using African rainfall data. The analysis showed a significant difference in the survival rates between the sexes, with that of the female being lower. Differences in the changes of the population size and adult survival rate showed the importance of the recruitment of adults, and this may depend mainly on the survival of juveniles.
Group size effect on vigilance and daytime activity budgets of the Equus kiang (Equidae, Perissodactyla) in Arjinshan National Nature Reserve, Xinjiang, China

Abstract. Vigilance is recognized as the response to potential predation threats. Many factors influence vigilance behaviour, and the effect of group size has had a great deal of attention in recent years. The group size effect hypothesis proposes that there is a negative relationship between group size and vigilance, which has been proven ture for many birds and mammal species. However this relationship has not been investigated for a number of other species including the Equus kiang. The E. kiang is the largest wild ass in the world, and endemic to the Tibetan Plateau. Previous studies have reported its distribution and reproduction, but information about their behaviour especially their daytime activity budgets is still very limited. Also unknown is if the distinctive habitat of the Tibetan Plateau makes their behaviour different from other Equidae species. So in this paper, we discuss our behavioural observations of the daytime activity budgets and the group size effect on vigilance for the E. kiang population in the Arjinshan National Nature Reserve, Xinjiang, China. The results indicate that group size has a significant effect on the vigilance levels: with an increase in group size, both the group scan level decreased and group scan frequency increased. Our results also showed that E. kiang spent most of their time feeding (51.41 ± 2.74 %), followed by moving (22.49 ± 1.40 %), standing (19.62 ± 6.74 %), resting (18.41 ± 2.13 %), and other activities (8.64 ± 0.72 %). Their feeding behaviour showed three distinct activity peaks during the day: early morning (8:00–11:00), midday (14:30–15:30), and around sunset (18:00–19:30). During the peaks of activity, E. kiang spent most of their time feeding, and during the period of inactivity, E. kiang spent most of their time resting and standing. So the group size effect was supported for E. kiang by this study, and our results are consistent with research on other Equidae species.
Inheritance of some fertility traits in three successive generations of Holstein-Friesian cattle

aim of the paper was to establish reproductive traits and their heritability during the three successive generations of Holstein-Friesian cattle. Research was conducted on the duration of pregnancy, service period and fertility intensity. In each generation there were 135 first calved cows. Service period and fertility intensity refers to the following calving. Significant differences were established (P < 0.05) regarding duration of pregnancy between I and II generation. Significant (P < 0.05) influence of season on duration of pregnancy and service period was established in I generation (1991), on duration of service period and fertility intensity in II generation (1996) and on duration of pregnancy and service period in III generation (2000). Season effect (summer) was established for all traits of fertility in II generation (P < 0.05). The season (spring) had influence on duration of pregnancy (P < 0.05) and summer had an influence on duration of service period and fertility intensity, and winter effected the duration of service period (P < 0.05) in III generation. Values of heritability coefficients are pretty low for all generations. Considerably greater values for heritability were established for service period and intensity of fertility of cows per generations.
Foraging behaviour in orb-web spiders (Araneidae): do web decorations increase prey capture success in Argiope keyserlingi Karsch, 1878?

Orb web spiders in the genus Argiope attach highly visible silk bands called decorations or stabilimenta to their webs. Two different hypotheses regarding the function of these structures were investigated in the field using Argiope keyserlingi: prey attraction and anti-predatory device. The first hypothesis suggests that web decorations attract prey to the web, and webs carrying decorations will capture more prey than those without. A field census of prey capture showed that webs adorned with more decorative bands indeed captured more but similarly sized prey per hour compared with webs carrying fewer decorations. Web height or web size, however, were not related to the rate of prey capture. This pattern was confirmed by a paired comparison of prey-capture rates within individuals that increased or decreased the number of decorative bands on consecutive days. Individuals that used more decorations also captured more prey compared with days when they spun fewer decorations. The second hypothesis suggests that these structures function as anti-predatory devices and, consequently, spiders on decorated webs benefit from a lower rate of mortality than spiders on undecorated webs. A census of the mortality rates of spiders over 19 days revealed that spiders did not disappear from undecorated webs more frequently than from decorated webs. Consequently, the idea that web decorations act as anti-predatory devices in A. keyserlingi was not supported.
A Model of Girls’ School Delinquency: School Bonding and Reputation

Using a longitudinal national database, the authors conducted a path analysis of girls’ school delinquency to determine the indirect and direct effects of socioeconomic status, parental involvement, bonding to school, and girls’ self-perception of reputation on school delinquency during middle school and high school. Self-perception of reputation was the most influential factor in girls’ school delinquency, followed by bond to school and socioeconomic status. Implications for school counselors are presented.
IL-8/CXCL8 and Growth-Related Oncogene α/CXCL1 Induce Chondrocyte Hypertrophic Differentiation 1

Foci of chondrocyte hypertrophy that commonly develop in osteoarthritic (OA) cartilage can promote dysregulated matrix repair and pathologic calcification in OA. The closely related chemokines IL-8/CXCL8 and growth-related oncogene α (GROα)/CXCL1 and their receptors are up-regulated in OA cartilage chondrocytes. Because these chemokines regulate leukocyte activation through p38 mitogen-activated protein kinase signaling, a pathway implicated in chondrocyte hypertrophic differentiation, we tested whether IL-8 and GROα promote chondrocyte hypertrophy. We observed that normal human and bovine primary articular chondrocytes expressed both IL-8Rs (CXCR1, CXCR2). IL-8 and the selective CXCR2 ligand GROα (10 ng/ml) induced tissue inhibitor of metalloproteinase-3 expression, markers of hypertrophy (type X collagen and MMP-13 expression, alkaline phosphatase activity), as well as matrix calcification. IL-8 and the selective CXCR2 ligand GROα also induced increased transamidation activity of chondrocyte transglutaminases (TGs), enzymes up-regulated in chondrocyte hypertrophy that have the potential to modulate differentiation and calcification. Under these conditions, p38 mitogen-activated protein kinase pathway signaling mediated induction of both type X collagen and TG activity. Studies using mouse knee chondrocytes lacking one of the two known articular chondrocyte-expressed TG isoenzymes (TG2) demonstrated that TG2 was essential for murine GROα homologue KC-induced TG activity and critically mediated induction by KC of type X collagen, matrix metalloproteinase-13, alkaline phosphatase, and calcification. In conclusion, IL-8 and GROα induce articular chondrocyte hypertrophy and calcification through p38 and TG2. Our results suggest a novel linkage between inflammation and altered differentiation of articular chondrocytes. Furthermore, CXCR2 and TG2 may be sites for intervention in the pathogenesis of OA.