Miracle-dz/UniFAR-FTUs huggingface dataset:
Evaluating chemical exposure and effect models for aquatic species with a focus on crude oil constituents

The aim of this PhD thesis is to evaluate a suite of exposure and effect models on their applicability in ecological risk assessment for aquatic species and ecosystems. The focus is on oil constituents, as it is largely unknown whether current ecological models are applicable to crude oil and its constituents. It was concluded that a model for risk assessment of crude oil constituents has to include uptake via water, the biotransformation within organisms, simplified migration processes of individuals within a population, and the interaction between different species (prey and predator). Lisette de Hoop also found out that certain toxicity data on temperate species can be used to predict the sensitivity of polar species to crude oil (constituents). The conclusions of this thesis can lead to improvements of the models, thereby enabling an improved risk assessment of crude oil in the aquatic environment
Sexual dimorphism and foraging behavior of Emerald Toucanets Aulacorhynchus prasinus in Costa Rica

Foraging behavior and diet of male and female Emerald Toucanets were studied at Monteverde, Costa Rica during both wet and dry seasons to determine if sexual dimorphism in bill morphology was related to differences in feeding behaviors between sexes. Based on analysis of museum specimens, bills of males averaged about 20% longer than those of females and the sexes could be reliably distinguished based on differences in bill morphology. Analysis of foraging sequences as first-order Markov chains revealed no differences between sexes or seasons in relative height, relative position in a plant, or foraging substrate. Regardless of season, both male and female toucanets foraged on twigs in outer portions of the mid-canopy. Seasonal differences existed in foraging height above ground, time spent in a single foraging bout, and distance moved between foraging bouts. However, the only within-season difference between sexes was that an average foraging bout during the dry season was longer for females than for males. Toucanets were observed eating fruits, mostly berries, and flowers from 47 species of plants. Fruits consumed in the wet season were larger and heavier than those consumed in the dry season, but no obvious within-season differences existed between sexes in size, color, or type of fruit consumed. We conclude that sexual dimorphism in bill morphology of Emerald Toucanets is not related to differences in foraging behavior or diet. Because of the nature of the resource, foraging-related sexual dimorphism should be rare in frugivorous birds.
Identification of a novel pro-inflammatory human skin-homing V gamma 9V delta 2 T cell subset and its role in the pathogenesis of psoriasis

gd T cells mediate rapid tissue responses in murine skin and participate in cutaneous immune regulation including protection against cancer. The role of human gd cells in cutaneous homeostasis and pathology is characterized poorly. In this study, we show in vivo evidence that human blood contains a distinct subset of proinﬂammatory cutaneous lymphocyte Ag and CCR6-positive V g 9V d 2 T cells, which is rapidly recruited into perturbed human skin. V g 9V d 2 T cells produced an array of proinﬂammatory mediators including IL-17A and activated keratinocytes in a TNF- a – and IFN- g –dependent manner. Examination of the common inﬂammatory skin disease psoriasis revealed a striking reduction of circulating V g 9V d 2 T cells in psoriasis patients compared with healthy controls and atopic dermatitis patients. Decreased numbers of circulating V g 9V d 2 T cells normalized after successful treatment with psoriasis-targeted therapy. Taken together with the increased presence of V g 9V d 2 T cells in psoriatic skin, these data indicate redistribution of V g 9V d 2 T cells from the blood to the skin compartment in psoriasis. In summary, we report a novel human proinﬂammatory gd T cell involved in skin immune surveillance with immediate response characteristics and with potential clinical relevance in inﬂammatory skin disease. The Journal of Immunology , 2011, 187: 2783–2793. and repeated measure one-way ANOVA was used for more than two matched groups. To compare not normally distributed samples, we used Mann–Whitney U test to compare two groups and Kruskal–Wallis test for comparison of three groups. As a nonparametric test for two paired groups, we used Wilcoxon matched pair test. Pearson correlation was used to correlate clinical variables and percentage/absolute numbers of gd T cells, whereas one-way exponential decay was applied for calculation of R 2 . For all statistical tests, we con- sidered p values , 0.05 to be statistically signiﬁcant. Results are expressed as mean 6 SEM.
Optimizing supply and timing of nitrogen application for subirrigated potted chrysanthemums

Abstract: Two disbudded, potted chrysanthemum cultivars were subirrigated with 9.25, 12.3, and 18.5 mM N during vegetative, but not reproductive growth. At commercial harvest, visible symptoms of N deficiency or differences in plant/inflorescence quality were minimal, whereas N uptake efficiency was dramatically improved at 9.25 and 12.3 mM N.
A Note on Comparing Rate of Soil Moisture Loss for Conventional and Conservation Tillage Production methods for Peanut (Arachis hypogaea)

ABSTRACT Soil moisture retention is important for peanut production as well as water conservation in irrigated and non-irrigated fields. One way to increase soil moisture retention of the soil is by increasing soil organic matter. Research was conducted to determine if there is a difference in the rate of soil moisture loss in a field operated under a conservation production system (CPS) method and a conventionally tilled (CT) method, and if there was a time difference between needed wetting events. Experiments were conducted on two different fields with Tifton sandy loam soil. Soil moisture was monitored with Watermark sensors installed at 10, 20 and 30 cm depths. Data was analyzed to determine the rate of soil moisture loss when the soil was wet (below 50 kPa) and dry (above 80 kPa). The rate of soil moisture loss was not significant between CPS and CT when the soil was wet; however, there was a difference in the soil moisture loss rate when soils were dry. When dry, the CT soils lost moisture at a rate.
Biology and Ecology of the Platte Thistle (Cirsium canescens)

Aspects of the life history and population dynamics of the Platte thistle (Cirsium canescens Nutt.), a rangeland weed, were studied in the Nebraska Sandhills from 1977 through 1979. This thistle is a monocarpic perennial, reproducing only by seed production, which typically occurs in small, scattered groups of plants. Seedling mortality at four sites was 75% during the first year, mostly because of dry moisture conditions. In plots with good vegetative cover, thistle rosette plants had a lower mortality rate, but growth rate was slower than that of rosette plants in plots with sparse vegetative cover. Seed heads developed during May and June and gained more than one-half of their dry weight shortly before maturing. Plants averaged 72, 197, and 303 seeds at three sites. Within sites, plants produced seeds in proportion to the number of seed heads per plant. Although naturally occurring biological-control agents have little effect on the vegetative growth phase of the life cycle, they greatly reduce the production of seeds.
Molecular identification and phylogenetic analysis of phytoplasmas associated with alfalfa witches’ broom diseases in the western areas of Iran

During 2014–2015 phytoplasmas associated with alfalfa witches’ broom (AWB) in the western areas of Iran were characterized by molecular analyses studies. Polymerase chain reaction was carried out using direct and nested as says to amplify the 16S ribosomal gene for phytoplasma identification. RFLP analysis of R16F2n/R16R2 amplicons with selected restriction enzymes and phylogenetic studies showed that AWB associated phytoplasma strains from Salafchegan (Qom province), Arak (Markazi province), Tabriz (East Azerbaijan province), Dehgolan and Qhorveh (Kordestan province), Eghlid (Fars province), Mahidasht (Kermanshah province), Dehdasht (Kohgiluyeh and Boyer-Ahmad province), Borujerd (Lorestan province), Chenar-e Mahmudi and Shahrekian (Chaharmahal and Bakhtiari province) belong to 16SrXII-A subgroup (“stolbur”), while AWB associated phytoplasmas from Jowkar (Hamedan province) belong to 16SrII-D subgroup. Disease incidence was variable in the different areas and the highest infection rate (14.7%) was observed in Chenar-e Mahmudi (Chaharmahal and Bakhtiari province). The highly AWB affected areas were generally located in the warmer parts of each region in sparse fields. This is the first report and characterization of 16SrXII-A phytoplasmas associated with alfalfa witches’ broom diseases in Iran and occurrence of 16SrII-D in western areas of Iran.
Acute Effects of N-Acetylcysteine on Total Antioxidant Capacity, Total Oxidant Capacity, Nitric Oxide Level and Gammaglutamyl Transpeptidase Activity in Rabbits

N-acetylcysteine (NAC), acetylated derivative of cysteine amino acid, is widely used mucolytic agent. In this study, it was aimed to investigate the acute effects of NAC on total antioxidant capacity (TAC), total oxidant capacity (TOC), nitric oxide (NO), albumin, globulin, glucose levels and gammaglutamyl transpeptidase (GGT) activity. Eleven New Zealand rabbits were used in the study. Blood samples from the rabbits were taken before the start of the experiment to determine control values. NAC (100 mg/kg) was injected to rabbits as intramuscularly. Blood samples were collected from vena auricularis of rabbits at 3 rd , 6 th and 9 th hours. While TAC levels were found high (P<0.05) at 6 and 9 hours, TOC levels were found low (P<0.05) at 3 rd , 6 th and 9 th hours after NAC injection compared to the values before the experiment. NO levels were found low (P<0.001) at 6 th and 9 th hours, GGT activities were found low (P<0.05) at 3 rd and 6 th hours, total protein and albumin levels were found low (P<0.05) at 3 rd hour after NAC injection compared to values before the experiment. As a result, after intramuscular injection of NAC, plasma TAC levels of rabbits increased, while TOC and NO levels decreased. According to the results, it can be concluded that NAC may show antioxidant effect in a short time. Therefore, NAC could be a good alternative when the antioxidant system needs to be strengthened due to its beneficial properties.
Seed production of Urena lobata in Sierra Leone: effect of harvest date on yield

Seeds of Urena lobata L. cv. 'Ex-Mokwa' and a local type termed 'Indigenous' were sown on 7 May at the start of the rainy season. The 'Ex-Mokwa' crop commenced flowering on 28 August and the 'Indigenous' crop on 6 November. Mature fruit was produced over 14 weeks by 'Ex-Mokwa' and 12 weeks by 'Indigenous', but the bulk of fruit production was confined to a six- to eight-week period commencing 6-8 weeks after the onset of flowering. Seeds maturing early or late within this period were of low viability. Significant viable seed production therefore occurred over a period of only 4-6 weeks. Greatest fruit yields with single harvests were obtained at the end of this period. Lower yields were obtained with later harvests owing to the shedding of fruit. The maximum yield of viable seed was obtained by hand-harvesting fruits at two-weekly intervals over a period of 16 weeks, commencing soon after the appearance of the first ripe fruit. The yield from a single harvest on the optimum date was 69% of this maximum yield. Two, three or four regularly spaced harvests did not significantly increase the yield obtained with this single harvest.
Species composition of the exploratory fisheries with bottom longline off southeastern Brazil

Groundfish resources in areas deeper than 100 m had been exploited in Brazil by few fishing boats only using vertical longlines and handlines until 1994. The first experimental fisheries with bottom longline employing hydraulic winch reel in the country occurred between April 1994 and May 1995. RV Orion have made 20 fishing trips ranging from 19° 30'S to 28° 56' S, from 64 m to 439 m deep, to determine what species are vulnerable to this gear and its feasibility. This paper shows the catch composition of these trips. Bottom longline targets valuable species like groupers (Epinephelus spp and Mycteroperca intersticialis), wreckfish (Polyprion americanus), sandperch (Pseudopercis numida and P semifasciata) and tilefish (Lopholatilus villarii). These species made up 44.68 % of total landings; in addition, 21 other species of teleosts and 3 species of sharks have commercial importance, increasing this number to 86.54% of total catch. These results point to a strong specific gear selectivity. Additionally, 4 species of crustaceans (Stenociops spinosissima, Rochinia crassa, Acanthocarpus alexandrei and Chaceon ramosae) and 6 species of seabirds (Thalassarche chlororhynchus, T. melanophrys, Procellaria aequinoctialis, P. conspicillata and Puffinus gravis) were accidentally caught. Catch composition of commercial longline fleet has been observed to be very alike to RV Orion's, since the fishing areas greatly overlap, and the technological standard and the operational characteristics used at the experimental fisheries has been totally or partially adopted.
Effects of haying on breeding birds in CRP grasslands

The Conservation Reserve Program (CRP) is a voluntary program that is available to agricultural producers to help protect environmentally sensitive or highly erodible land. Management disturbances of CRP grasslands generally are not allowed unless authorized to provide relief to livestock producers during severe drought or a similar natural disaster (i.e., emergency haying and grazing) or to improve the quality and performance of the CRP cover (i.e., managed haying and grazing). Although CRP grasslands may not be hayed or grazed during the primary bird-nesting season, these disturbances may have short-term (1 yr after disturbance) and long-term (≥2 yr after disturbance) effects on grassland bird populations. We assessed the effects of haying on 20 grassland bird species in 483 CRP grasslands in 9 counties of 4 states in the northern Great Plains, USA between 1993 and 2008. We compared breeding bird densities (as determined by total-area counts) in idle and hayed fields to evaluate changes 1, 2, 3, and 4 years after haying. Haying of CRP grasslands had either positive or negative effects on grassland birds, depending on the species, the county, and the number of years after the initial disturbance. Some species (e.g., horned lark [Eremophila alpestris], bobolink [Dolichonyx oryzivorus]) responded positively after haying, and others (e.g., song sparrow [Melospiza melodia]) responded negatively. The responses of some species changed direction as the fields recovered from haying. For example, densities for common yellowthroat (Geothlypis trichas), sedge wren (Cistothorus platensis), and clay-colored sparrow (Spizella pallida) declined the first year after haying but increased in the subsequent 3 years. Ten species showed treatment × county interactions, indicating that the effects of haying varied geographically. This long-term evaluation on the effects of haying on breeding birds provides important information on the strength and direction of changes in bird populations following a disturbance. Results from this study can help guide management of CRP and other grasslands and inform future agricultural programs that address biomass energy production. © 2016 This article is a U.S. Government work and is in the public domain in the USA.
Mesures indirectes de la Biomasse des nématodes du méiobenthos subtidal de la Manche

Plusieurs methodes indirectes destinees a evaluer la biomasse des Nematodes ont ete comparees avec la methode d'evaluation par pesee reelle. Les echantillons etudies proviennent de trois peuplements subtidaux de la Manche: deux stations de sables fins, la station 1, Pierre Noire, et la station 2. Baie de Seine, et une station de sables grossiers, la station 3, Trezen Vraz. La biomasse calculee par la formule de Wieser et celle obtenue par pesee reelle sont similaires uniquement a la station 2. La biomasse moyenne individuelle obtenue par pesee directe (poids sec) est du meme ordre de grandeur aux stations 1 et 3 (0,45 μg et 0,43 μg respectivement) et plus elevee a la station 2 (0,76 μg). Deux morphotypes caracteristiques apparaissent aux deux stations de sables fins et un seul a la station de sables grossiers. Le spectre de taille montre un peuplement compose d'individus de petite taille a la station 1. Il est en revanche deplace vers les classes de grandes tailles a la station 2, et se trouve dans une situation intermediaire a la station 3. La taille et la morphologie des nematodes variant sensiblement selon les stations, il apparait indispensable de determiner la biomasse individuelle moyenne pour chaque type de peuplement
Integrative Network Analysis for Understanding Human Complex Traits

Over the last decade, high throughput biological data, have been accumulating at rapidly increasing rates, providing the opportunity to gain insight into various fundamental biological processes. Such large-scale data have been explored using network representation and graph theory to study biological relationships. Meanwhile, a great amount of effort has also been dedicated to integrate diverse biological data types in order to build networks and apply computational analysis to distill meaningful information for specific biological problems. As a result, network-based analysis has become a powerful paradigm to model and study large-scale biological data. The goal of network-based analysis of human complex traits is to annotate or predict new relationships between biological entities, such as proteins, drugs and phenotypes. Furthermore, such analysis can facilitate the diagnosis and prognosis of common complex diseases. This thesis comprises three contributions. First, heterogeneous biological data are integrated and a novel tool has been developed to easily construct and navigate networks representing the large scale data. In addition the resulting networks can be analyzed using computational methods to solve specific biological problems. Second, an integrative network-based pathway analysis for genome-wide association studies
Influence of seed orientation on seedling emergence in Bauhinia retusa Ham. ex Roxb.

Seedling emergence in B. retusa was influenced by seed orientation in the nursery bed. Earliest and highest seedling emergence was recorded when seeds were sown in an upright position (radicle end up). Emergence was poorer for seeds sown in a horizontal position, and was lowest when seeds were sown with the radicle end down (inverted position). Seedling survival, mean germination time and germination index also followed the same trend but the root growth was best in seed sown with the radicle end down.
Determination of clutch size in Treecreepers Certhia familiaris under food and time constraints

Brood size of Eurasian Treecreepers Certhia familiaris was manipulated in three years that differed in food abundance in order to detect factors that limit clutch size. The Tree-creeper parents were able to successfully raise enlarged broods only in a year with good food availability, but even then, the nestlings were of lower body weight than in reduced broods. Among the enlarged broods, the lowest breeding success was observed in a year with the lowest food abundance. Treecreepers with enlarged broods depleted their food supply in a year with scarce food, but not when food was abundant, and changes in foraging behaviour were observed only when food was scarce. Females and males did not increase their provisioning rates with brood size, but the responses of the sexes differed between years. Our results support Lack's hypothesis of clutch-size regulation: when food was scarce, Treecreepers laid the maximal number of eggs that they were able to raise successfully to fledging. However, trade-offs between current and future reproduction may also be important in clutch size determination of this species. Food abundance and limited foraging time seem to play major roles in limiting the clutch size of Treecreepers, but the importance of these factors differs among years.
Development of 3D Alginate Encapsulation for Better Chondrogenic Differentiation Potential than the 2D Pellet System

Introduction: Articular cartilage damage has reduced potential to regenerate. This is due to lack of blood supply at the site of injury and widely spread chondrocytes in dense extracellular matrix. Alternate strategies to regenerate the damaged tissue require exogenous supply of several chondrocyte implants. There are inherent challenges to optimize an appropriate tissue culture methodology in the enrichment of chondrocytes, thus necessitating the use of alginate hydrogel. Furthermore, human derived adipose stem cells provide an ideal tissue source to treat large focal defects. Objectives: We explored the differentiation potential, expansion and growth kinetics of the human adipose derived stem cells (hADSCs) in 3D alginate microspheres. The growth pattern of articular chondrocytes was also studied in pellet system. Methods: Isolated hADSCs and cartilage derived chondrocytes were cultured and characterized by flow cytometry and scanning electron microscopy (SEM). Cell viability and compatibility was studied using MTT, Annexin V FITC assays. RT-PCR was used to study chondrogenic regulation. Results: Uniformly distributed cells encapsulated in alginate microspheres were imaged by SEM and they expressed multi-potent stem cell phenotype from the third passage. hADSCs were metabolically active within the alginate microspheres. The chondrocyte pellet culture from cartilage demonstrated lower growth potential as compared to alginate encapsulation. Apoptotic assays provided safety profile for the alginate during cell growth. The up regulation of cartilage specific genes like transforming growth factor-beta (TGF-β), collagen type-X, cartilage oligomeric matrix protein (COMP) and collagen type II was observed during the entire period of culture in alginate spheres. Conclusion: The chondrocyte phenotype was conserved in pellet system with rich glycosaminoglycan (GAG) polysaccharides. Moreover, hADSCs could proliferate and differentiate into chondrogenic lineage within alginate matrix. Thus, an enriched chondrocyte requirement in alginate as a scaffold design would aid in the treatment of large focal defects.