Miracle-dz/UniFAR-FTUs huggingface dataset:
Effects of varying protein and lipid levels and protein‐to‐energy ratios on growth, feed utilization and body composition in juvenile Nibea diacanthus

A two-factor experiment was designed to determine the suitable dietary protein and lipid levels for juvenile Nibea diacanthus. Nine extruded pellet diets were formulated to contain three levels of protein (420, 470 and 520 g kg−1) and three levels of lipid (70, 110 and 150 g kg−1). Each diet was randomly fed to triplicate groups of 25 juvenile N. diacanthus (initial weight 12.12 ± 0.23 g) for 8 weeks in net cages. The results showed that weight gain rate (WGR), specific growth rate, final body weight and energy retention were significantly influenced by the dietary protein and lipid levels-. The highest WGR (982.5g kg−1.) of N. diacanthus was found in the group with dietary protein and lipid of 520 and 150 g kg−1. Feed intake and feed efficiency were significantly impacted by the dietary protein levels. An interactive effect between dietary protein and lipid on the protein retention and protein efficiency ratio was observed. There were no significant differences in condition factor and survival among all treatments. Hepatosomatic index and viscerasomatic index of N. diacanthus were positively related with dietary lipid levels, but negatively with dietary protein levels. Crude protein, crude lipid, ash, moisture and energy contents of the whole body, muscle and liver were influenced by dietary protein and lipid levels. Moreover, total essential amino acid pattern of the muscle was correlated to those of dietary protein. Total protein concentration in the serum was affected by dietary protein and lipid levels. Meanwhile, both serum cholesterol and triglyceride concentrations increased with increasing dietary lipid levels. These results demonstrate that the diet containing 470 g kg−1 protein and 110 g kg−1 lipid is optimal for juvenile N. diacanthus and analysis of WGR by quadratic regression indicated that the estimated optimal protein-to-energy ratio for juvenile N. diacanthus was 24.53 mg protein kJ−1.
Estuarine habitat use by the California sea otter (Enhydra lutris nereis)

ESTUARINE HABITAT USE BY THE CALIFORNIA SEA OTTER (ENHYDRA LUTRIS NEREIS ) by Jacqueline Kimberly Lindsey As the southern sea otter (Enhydra lutris nereis) range expands into northern and southern California, it will encounter estuaries that have been historically occupied by sea otters. Understanding how otters use re-colonized estuarine environments will inform how estuaries might be managed to encourage future sea otter range expansion. This project addressed the question: how do southern sea otters use space in the unique estuarine habitats of Elkhorn Slough? I compared the locations and behaviors of 25 individual sea otters of different status (male, female, and female with pup) among eelgrass, saltmud, saltmarsh, tidal creek, and main channel habitats in Elkhorn Slough. From these data I created a synoptic model to predict space use for resident otters of Elkhorn Slough based on sex, behavior, home range, and habitat distribution. Ninety percent home ranges calculated from the model indicated that females used larger home ranges than males in the slough, but both sexes had smaller home range areas than otters using the rocky outer-coast habitats of the Monterey Peninsula. In Elkhorn Slough, important habitats associated with resting included tidal creeks (for females only) and eelgrass, whereas the main channel was important for foraging behaviors of both sexes. Although using land habitats, sea otters were most likely to be found within 50 m of water. Protection of similar resting and foraging habitats in prey-rich estuaries colonized in the future will promote southern sea otters recovery by allowing them to re-colonize historically important estuarine habitats.
Evaluation of Performance Traits in Brahman Cattle: Blood Parameters, Calf Temperament, Residual Feed Intake, and Bull Reproductive Development

Evaluation of Performance Traits in Brahman Cattle: Blood Parameters, Calf Temperament, Residual Feed Intake, and Bull Reproductive Development. (August 2009) Kara J. Matheney, B.S., Texas A&M University Chair of Advisory Committee: Dr. Ronald D. Randel The objectives of these studies were (1) evaluate the relationship between temperament, blood parameters, and performance in Brahman calves (n = 300); (2) evaluate the relationship between residual feed intake (RFI) and reproductive development in Brahman bulls (n = 41). Serum was collected at 24 h and d 21 to 24, and analyzed for total protein (TP) immunoglobulin G (IgG), and cortisol (CS). Calves were weighed at 24 h, weighed and evaluated for temperament using exit velocity (EV) at d 21 to 24, and at 28 d intervals thereafter. Beginning 28 d prior to weaning, and at 28 d intervals through 56 d post-weaning calves were evaluated for pen score (PS) used to calculate temperament score (TS = (EV+PS)/2). The average TS from 28 d prior to weaning and weaning was used to generate temperament groups; calves 1 SD below the mean being calm, those 1 SD above the mean being temperamental and all remaining classified as intermediate. Calf TS influenced WW (P = 0.04) and ADG from birth to weaning (P = 0.03). Serum TP at 24 h affected (P < 0.05) WW and ADG from birth to
Spectrum of Somatic Hypermutations and Implication on Antibody Function: Case of the anti HIV-1 antibody, b12

Spectrum of Somatic Hypermutations and Implication on Antibody Function: Case of the anti HIV-1 antibody, b12 Mesfin Mulugeta Gewe Chair of the Supervisory Committee: Roland Strong, Full Member Fred Hutchinson Cancer Research Center Sequence diversity, ability to evade immune detection and establishment of human immunodeficiency virus type 1 (HIV-1) latent reservoirs present a formidable challenge to the development of an HIV-1 vaccine. Structure based vaccine design stenciled on infection elicited broadly neutralizing antibodies (bNAbs) is a promising approach, in some measure to circumvent existing challenges. Understanding the antibody maturation process and importance of the high frequency mutations observed in anti-HIV-1 broadly neutralizing antibodies are imperative to the success of structure based vaccine immunogen design. Here we report a biochemical and structural characterization for the affinity maturation of infection elicited neutralizing antibodies IgG1 b12 (b12). We investigated the importance of affinity maturation and mutations accumulated therein in overall antibody function and their potential implications to vaccine development. Using a panel of point
Saturated and Unsaturated Fatty Acids Composition of Olive Oils Obtained from Less Salty Black Table Olives Preserved with Vacuum, MAP and Gamma Irradiation Technologies

In this project assessed the effect of preservation methods on shelf life and quality of table olives which processed two different methods as low salty (2-4%). For this purpose, black olives were processed two kinds of table olive processing techniques, fermented, then packed with Vacuum Pump (VP) and Modified Atmosphere Packaging (MAP), and applied gamma irradiation (1 kGy, 3 kGy, 5 kGy). Then olives stored under normal conditions for 8 months. In this study, gamma irradiation has been applied first time in extending the shelf-life of table olives in the marketing. The Olive oils obtained from less salty black table olives were studied. During storage of table olives, the change of the major fatty acids was determined. Processing methods, salt quantity and storage period have affected almost all the quality parameters of the olive oils which obtained from table olives. The dominating fatty acid of all processing methods was oleic acid with ranged between 70.71-75.59%. Oleic acid quantity wasn’t decreased much during processing and storage. In this context, it is determined that the best preservation was performed by modified atmosphere packaging technology.
Effect of snowpack management on grassland biodiversity and soil properties at a ski resort in the Mediterranean basin (central Italy)

Abstract In the Mediterranean basin, the activity of ski resorts below 2000 m of altitude strongly affects grassland ecosystems because of the increasing use of artificial snow (AS). In a representative ski resort of central Apennines (Italy), we studied soil, vegetation and topographic variables of three adjacent grasslands: undisturbed grassland (UG), ski-runs with natural snow and ski-runs with amassed and AS. The winter temperature at the soil surface was colder in the ski-runs (even more in AS) than in the UG with an increase in dissolved organic matter and a biomass decrease. We identified 21 diagnostic species and 14 functional bioindicators linked to soil indicators like surface temperature and moisture. Conversely to observations made in the Alps and in other sites of the Apennines, we did not record any significant decrease in the floristic diversity between ski-runs and UG. Ski-run management aimed to prolong the snowpack duration-induced higher soil humidity and a short vegetative growth that produced a significant shift of the natural structure and composition of the grassland. To preserve key habitats for biodiversity, the construction and extension of ski resorts below the altitude of 2000 m should be avoided in the climatic belt of the Apennines.
Cytokine and Inflammatory-Related Gene Expression of Melamine Cyanurate on Human Renal Proximal Tubular Cells

Following up with the episode of melamine-contaminated milk formula causing acute urolithiasis disease in children from China, an experimental two-compartment tubular cell model was adopted to investigate the cytotoxicity of melamine cyanurate. Direct cytotoxic effects of melamine cyanurate altered the integrity of tight junction when crystals were physically formed on apical cell surface. This was followed by oxidative DNA damage, in addition to the stimulation of inflammatory cytokines including IL-5, IL-6, IL-8, and MCP-1, which was consistent with the gene expression revealed by the whole human genome 44K gene expression microarray. Cluster analysis of microarray also revealed that genes for calcium-gated channels and zinc finger proteins were affected. Unlike other lithiasis events, long-term impact of melamine seems to be limited at cellular level as melamine induces cell damage merely by physical mean of contact, but has the potential in evoking immune cells recruitment to the site of injury.
Patterns of Participation and Motivation among Saltwater Tournament Anglers

Abstract Tournament anglers and organizations that represent them can be expected to play a greater role in seeking to influence future fisheries policy as tournaments increase in number. In stating management preferences and opinions, tournament anglers may argue they are representative of all anglers. Fisheries managers need to know more about this user segment and how they differ from the general population of anglers. More than 20 studies were reviewed to obtain information on participation patterns and motivations of saltwater tournament anglers. Results were presented for each relevant participation variable where data were available. Since aggregated data were used, no statistical tests of significant differences were possible; comparisons of study results were made by inspection. When saltwater tournament anglers were compared with two control groups of saltwater anglers, the former were more active in terms of all fishing participation indicators considered. Although there was agreement between s.
Characterization of Nucleic Acids and Nucleic Acid Binding Proteins Using NMR

Biological systems are governed by molecular interactions. At the core of all biological systems is the processing of nucleic acids, and preserving the fidelity of the genome is crucial to those systems. This manuscript follows different biological systems interrogated by nuclear magnetic resonance: the structural impact of single ribonucleotide damage in DNA, the formation of oligomeric protein-DNA complexes of an ETS family transcription factor, how methylation affects the charge state of the amino acid arginine and how the base pair opening rates of an oligonucleotide is affected by inosine. INDEX WORDS: Nucleic acids, Nuclear magnetic resonance, Single ribonucleotide damage, Nucleic acid structure, Transcription factors, ETS family protein, PU.1 protein, Biological interactions, Arginine methylation, Base pair opening, Inosine nucleobase CHARACTERIZATION OF NUCLEIC ACIDS AND NUCLEIC ACID BINDING PROTEINS USING NMR
Using ecological theory to inform the restoration and conservation of tallgrass prairie

iii Acknowledgements . v Table of contents . vii List of Figures. viii List of Tables . ix Introduction.1 Chapter1 . 8 Abstract . 9 Introduction . 10 Methods . 15 Results . 20 Discussion . 24 Tables and figures . 32 Chapter 2 . 40 Abstract . 4
Composition and seasonal variations in abundance of Copepod (Crustacea) populations from the northern part of Lake Tanganyika

Copepod has an important ecological role as a main food of several fishes on which commercial fisheries are based in Lake Tanganyika. However, very little multi-annual monitoring programs have been conducted for this group of crustacean zooplankton. This study was conducted in the northern part of Lake Tanganyika by weekly sampling at both pelagic and littoral sites over three consecutive years (2012–2014). The analyzed samples showed that Lake Tanganyika copepod was essentially composed of three suborders including Calanoida (30% by number) with a single endemic species, Cyclopoida (69%) with four dominant species and Harpacticoida (1%). These taxa showed variations in their abundance respectively at pelagic and littoral sampling sites. The average densities of copepods did slightly vary during the sampling period in both areas although higher peaks were observed in 2013. For the post-nauplii stage, Tropocyclops tenellus predominated while the nauplii of T. simplex predominated at both sampling sites. Seasonal fluctuations of copepod densities showed higher peaks in September/October and April/May, respectively, for the three most common species. T. simplex and M. aequatorialis ovigerous females showed higher peaks in the rainy season in 2013. These results can benefit pelagic fisheries research and lake environmental management efforts as the copepod abundance seems to be closely correlated to that of sardines in Lake Tanganyika.
Comparative growth trends of five northern hardwood and montane tree species reveal divergent trajectories and response to climate

In the northeastern United States, tree declines associated with acid deposition induced calcium depletion have been documented, notably for red spruce (Picea rubens Sarg.) and sugar maple (Acer saccharum Marsh.). There is conflicting evidence concerning whether co-occurring tree species capitalized on these declines or suffered similar growth reductions and on how growth has fluctuated relative to environmental variables. We examined five species along three elevational transects on Mt. Mansfield, Vermont: sugar maple, red spruce, red maple (Acer rubrum L.), yellow birch (Betula alleghaniensis Britton), and balsam fir (Abies balsamea (L.) Mill. ). We found baseline differences in growth. Red maple and yellow birch had the highest growth, sugar maple and red spruce had intermediate growth, and balsam fir had the lowest growth. While some year-to-year declines were associated with specific stress events, protracted patterns such as recent increases in red spruce and red maple growth were correlated with inc.
Serum vitamin D and vitamin D receptor gene polymorphism in Moroccan patients with systemic lupus erythematosus

Background: Vitamin D plays an important role in the immunomodulation and could be involved in the development of autoimmune diseases such as systemic lupus erythematous (SLE). The study of the polymorphism of the Vitamin D Receptor (VDR) gene may be of interest in explaining the pathophysiology of SLE. Methods: In this study, we aimed to examine the characteristics of VDR gene BsmI polymorphism for the first time in Moroccan patients with SLE and their relationship with clinical manifestations of the disease. We also measured the serum level of 25-hyroxyvitamin D 3 to assess its relation to such polymorphism. Results: The study included 66 SLE patients and 91 healthy controls. Our results showed that there were no differences observed in VDR genotypes and allelic distribution within the two groups. Both groups were in Hardy-Weinberg equilibrium, with no significant P values for the observed and expected genotype frequencies. 25-hyroxyvitamin D3 serum levels were the same in the two groups. Conclusions: Based on the results of the present study. We cannot verify any association between VDR gene BsmI polymorphism and SLE. This polymorphism could not be regarded as a genetic marker of the SLE. A larger study examining BsmI and other VDR gene polymorphisms is needed.
On the Origins of the Cerebral IVIM Signal

Purpose Intravoxel incoherent motion (IVIM) has been proposed as a means of non-invasive MRI measurement of perfusion parameters such as blood flow and blood volume. Its main competitor in the brain is arterial spin labelling (ASL). In theory, IVIM should not suffer from some of the same limitations as ASL such as poor signal in white matter, and assumptions about arterial arrival times that may be violated in the presence of pathology. Methods In this study we aimed to test IVIM as a viable alternative to ASL for quantitative imaging of perfusion parameters in the brain. First, a direct comparison was performed between IVIM and multi-post label delay pseudo-continuous ASL; second, IVIM images were acquired with and without nulling cerebrospinal fluid; and finally, ultra-high resolution IVIM was performed to minimise partial voluming. Results In all three tests, IVIM failed to disprove the null hypothesis, strongly suggesting that, at least within the brain, the technique does not measure perfusion parameters as proposed. Conclusion Furthermore, the results obtained suggest that the contrast visible in IVIM-derived images is primarily sensitive to cerebrospinal fluid, and not the microvascular blood compartment.
Factors affecting expression of estrus in dairy cows with high milk yields

An increased level of production in dairy cows can lead to reduction of time and intensity of estrus expression (23, 24). Kurykin et al. (22) reported that a delay in the resumption of cycling in cows after calving, weak estrus expression, and low detection rates of estrus have been the major factors limiting reproductive performance on dairy farms. Similarly, Dobson et al. (13) stated that the pattern of estrus expression-standing to be mounted in dairy cows with high milk production has changed over the past half century. Many studies had shown the tendency of the dairy cows with high breeding value for milk yield of a delayed return to a normal ovarian cycle, reduced heat expression, increased silent estrus, poor conception rates, and inappropriate timing of insemination (10, 12, 16, 40). Basically, high yield cows may be better adapted to mobilize body energy reserves to ensure nutrient availability for milk production, which may have a negative effect on fertility (17). At the same time, it was observed that the lactation number has a significant effect on reproduction performance in dairy cows. It is reported that heifers ovulate a little earlier after the onset of estrus than cows (29). In another study it was pointed out that, depending on cattle breed, an atypical P4 cycle was less frequent in older cows (30). P4 is an important regulator of events during the estrus cycle and a key hormone for successful pregnancy in ruminants (2, 11, 18, 38). An increased concentration of P4 on the day of AI was related to the decreased non-return-rate (4, 37, 39), possibly due to a negative effect of elevated P4 on oocyte maturation and ovulation (14). During mid diestrus, the P4 concentration in lactating dairy cows fluctuated between 4.0 and 5.8 ng/mL (34). It was stated that P4 monitoring was an indicator for determining errors in estrus detection and potential silent heats (19, 27). Such a non-invasive method is the measuring of the P4 concentration in milk to obtain detailed information about the fertility status of a cow (7). The purpose of this study was to define the effect of the milk P4 concentration on estrus expression in dairy cows with high milk yield. Another aim was to detect the effect of milk yield and the parity on the milk P4 concentration and a cow’s pregnancy after insemination. Factors affecting expression of estrus in dairy cows with high milk yields
A memory of recent oxygen experience switches pheromone valence in C. elegans

Animals adjust their behavioral priorities according to momentary needs and prior experience. We show that C. elegans changes how it processes sensory information according to the oxygen environment it experienced recently. C.elegans acclimated to 7% O2 are aroused by CO2 and repelled by pheromones that attract animals acclimated to 21% O2. This behavioral plasticity arises from prolonged activity differences in a circuit that continuously signals O2 levels. A sustained change in the activity of O2 sensing neurons reprograms the properties of their post-synaptic partners, the RMG hub interneurons. RMG is gap-junctionally coupled to the ASK and ADL pheromone sensors that respectively drive pheromone attraction and repulsion. Prior O2 experience has opposite effects on the pheromone responsiveness of these neurons. These circuit changes provide a physiological correlate of altered pheromone valence. Our results suggest C. elegans stores a memory of recent O2 experience in the RMG circuit and illustrate how a circuit is flexibly sculpted to guide behavioral decisions in a context-dependent manner.
Sampling roots to capture plant and soil functions

Summary Roots vary in anatomy, morphology and physiology, both spatially (different parts of the same root system) and temporally (plastic changes, root ageing), suggesting that root trait measurements are strongly affected by root sampling categories. In this context, it is urgent to clarify the functional significance of current root sampling categories (e.g. fine roots of the first order, the first three orders, ≤1 mm or ≤2 mm), establish guidelines for choosing between sampling methods and revise root ontology to account for functional differences between traits measured on distinct root categories. Here, we used a worldwide database of fine-root traits to test the hypothesis that distinct fine-root trait values – with link to fine-root functions – were generally affected by different root sampling categories. We observed indeed a clear functional break between first-order roots and roots of all three other sampling categories, and a smaller but substantial break between roots of the three first orders and the ≤2 mm category, demonstrating globally that different sampling methodologies capture different functional parts of roots. Our synthesis suggests that all current root sampling categories present both advantages and pitfalls and that no single method can appropriately tackle the main current challenge of root functional ecology: i.e. linking fine roots to plant and ecosystem functions in a truly comparable way across all plants. We argue instead that a small set of complementary standardized sampling methods is necessary to capture the linkages between root forms and functions. To assist experimenters selecting adequate sampling we developed a decision table following three logical questions: (i) what plant or ecosystem function must be addressed; (ii) what root categories are involved in this function and (iii) what traits should be measured on these root categories. Challenging, strengthening and expending such common reference framework would be a substantial step towards wider comparability of future functional trait datasets. A lay summary is available for this article.