Miracle-dz/UniFAR-FTUs huggingface dataset:
Deciphering the complexity of macrophage biology and function with the zebrafish model

Macrophages are present in every tissue of the body. Acting as sentinels of the immune system, they have the ability to engulf apoptotic cells and pathogens and also produce effector signals to mount a proper immune response. In response to tissue injury or microbe invasion, they are rapidly recruited to the injured site and are main key players in the protection of the host. Associated with many diseases, macrophages can have deleterious roles, especially due to their pro-inflammatory function. However, macrophages were discovered to be central during the orchestration of every step of inflammation, from initiation to resolution phases and to participate in tissue development, homeostasis and repair. These plural functions exerted by macrophages support their high plasticity and versatility potential and suggest the existence of macrophage subsets that might be differentially activated and/or recruited during physiological and pathological processes. The study of macrophage behaviour dynamics and functions in their activated states requires tractable in vivo models in which macrophages can be visualized under physiological or stress conditions. Thus, the zebrafish (Danio rerio) has emerged as an excellent vertebrate system to study myeloid development, inflammation and host-pathogen interactions. Conservation of immune cell lineage, optical accessibility of the zebrafish embryo combined with genetic approaches unable us to improve our understanding of macrophage functions. In this review, we discuss recent studies that have used the zebrafish advantages to provide key advances in the field of vertebrate macrophage biology and functions.
Traits association, path analyses and multiple linear regression estimates in rice (Oryza sativa L.).

Screening of segregating breeding lines based on only yield may mislead selection in the breeding programs. So the research objectives were to measure the association existed among yield and yield related traits, measuring the direct and indirect effects of yield associated traits on grain yield and estimate the inﬂuence of secondary traits in determining yield of rice. Forty seven rice genotypes including BINA dhan10, BINA dhan17, NERICA mutant and rest developed genetic materials were planted following randomized complete block design using three replications at BINA complex from July 2015 to December 2016. The statistical program MSTAT-C, BASICA and multiple linear regression analyses model implemented in R were used to analyze the data. Traits association analyses suggested that yield plant − 1 had highly signiﬁcant and positive association existed with plant height ( r p = 0.577, r g = 0.591) followed by active tillers number plant − 1 ( r p = 0.372, r g = 0.364) and tillers number plant − 1 ( r p = 0.337, r g = 0.342) and negative signiﬁcant association with days to ﬁrst ﬂowering ( r p = − 0.095, r g = − 0.094). Plant height had the highest positive direct effect (0.685) and tillers number plant − 1 ( − 0.364) showed maximum negative direct effect towards yield plant − 1 as revealed from path analyses. The multiple linear regression analyses showed that the change of 1 cm of plant height could inﬂuence about 0.19 g rice yield plant − 1 as per Model 1 and 0.16 g rice yield plant − 1 as per Model 2. Measured plant height, active tillers number plant − 1 and days to ﬁrst ﬂowering could be more inﬂuencing traits for selecting breeding lines in segregating generations to develop high yielding of rice genotypes.
Biological activity of extracts from commiphora swynnertonii against microbes of veterinary importance in chickens

Studies were carried out to establish ethno-botanical information and biological activities of crude extracts from Commiphora swynnertonii against selected microbes of veterinary importance in chickens. Initially, a questionnaire survey was conducted to gather information on practices and knowledge on ethno-botanical uses of C. swynnertonii in the study area. Then extracts from different morphological parts of the study plant were tested against selected bacteria and fungi in vitro using agar well diffusion assay. Resin and root bark extracts showed significant activities (P < 0.001) against S. pyogenes, E. coli and B. subtilis compared to other extracts. The fungi, C. albicans and A. niger, were moderately inhibited. Antiviral activity of the resin and root bark extract was tested in ovo using embryonated chicken eggs inoculated with Newcastle disease virus (NDV). Both extracts significantly (P < 0.001) and effectively reduced virus titres. An animal trial was carried out using the resin and chickens experimentally infected with NDV. Results revealed significant reduction (P < 0.05) in clinical signs and mortality rates following administration of the resin before and after the infection. Prophylactic administration of the extract was found to be more effective than the therapeutic approach. HI titres decreased significantly (P < 0.001) in resin and root bark treated groups and in all chickens treated with resin irrespective of dose given and on whether the extract was administered before or after infection suggesting that the plant materials were capable of destroying the NDV before stimulating the developing chick‘s immunity. Another animal trial investigated the effect of the resin against
Zwitterionic Polymer‐Coated Ultrasmall Superparamagnetic Iron Oxide Nanoparticles with Low Protein Interaction and High Biocompatibility

We report the synthesis and detailed in vitro evaluation of zwitterionic ultrasmall superparamagnetic iron oxide NPs (USPIONs) comprised of oleic acid/oleyl alcohol-stabilized magnetite particles (5 nm core diameter) coated with an amphiphilic zwitterionic polymer, poly(maleic anhydride-alt-1-decene) substituted with 3-(dimethylamino)propylamine (PMAL). These particles display a near-neutral zeta potential at pH7 and possess high colloidal stability, maintaining a hydrodynamic diameter of ca. 15-20 nm over a wide range of pHs (4-10) and ionic strength (up to 1 M NaCl). They exhibit very low levels of nonspecific protein binding upon exposure to serum, and negligible uptake by phagocytic and non-phagocytic hepatocarcinoma cells, which suggests that they may be able to resist rapid accumulation in the liver and spleen, a common in vivo fate for NPs. The PMAL-USPIONs exhibit very low cytotoxicity and do not elicit an inflammatory response or display hemolytic activity in vitro. Minimal nonspecific uptake by either cancerous or non-cancerous cell lines was observed, an important precondition to achieve highly selective targeting upon further functionalization with an active targeting agent (e.g., antibody or peptide). Overall, this study establishes the considerable potential of PMAL-USPIONs as a platform for the future development of "stealth" NP-based imaging and/or therapeutic agents.
Creation and Carnivory in the Pitcher Plants of Nepenthaceae and Sarraceniaceae

The morphological adaptations of carnivorous plants and taxonomic distributions of those adaptations are reviewed, as are the conflicting classifications of the plants based on the adaptations, reproductive morphology, and DNA sequences. To begin developing a creationist understanding of the origin of plant carnivory, we here focus specifically on pitcher plants of Nepenthaceae and Sarraceniaceae because their popularity as cultivated curiosities has generated a literature resource amenable to baraminological analysis. Hybridization records were augmented by total nucleotide differences to assess species similarities. Nonhybridizing species falling within the molecular range of hybridizing species were included in the monobaramin of the hybridizing species. The combined data support each of the three genera of the Sarraceniaceae as a monobaramin, but the three could not be combined into a larger monobaramin. With the Nepenthaceae, the data unequivocally place 73% of the species in a single monobaramin, strongly suggesting the whole genus (and, thus, family) is a monobaramin. The lack of variation in the carnivorous habit provides no evidence for the intrabaraminic origin of carnivory from non-carnivorous plants. An array of fascinating symbiotic relationships of pitchers in some species with unusual bacteria, insects, and vertebrates are known and suggest the origin of carnivory from benign functions of the adaptive structures. However, these symbioses still do not account for the apparent complex design for carnivory characteristic of all species in the two families.
Understanding user Emotions Through Interaction with Persuasive Technology

Emotions play a vital role in persuasion; thus, the use of persuasive applications should affect and appeal to the users’ emotions. However, studies in persuasive technology have yet to discover what triggered the users’ emotions. Therefore, the objectives of this study are to examine user emotions and to identify the factors that affect user emotions in using persuasive applications. This study is conducted in three stages; pre-interaction, during-interaction and post-interaction, employed a mixed-method approach using Geneva Emotions Wheel (GEW) and open-ended survey questions that analyzed using thematic analysis. The result shows that most of the emotions that users felt belong to high-control positive valence emotions that consist of interest, joy and pleasure. User, system and interaction are the three factors that triggered the emotions encompasses of elements such as Individual Awareness, Personality, Interface Design, Persuasive Function, Content Presentation, System Quality, Usability, and Tasks. The findings contribute to the body knowledge of Persuasive Technology, where the discovered factors and its elements are the antecedents that should be the concern in constructing an emotion-based trust design framework that could bring emotional impact to users to ensure a successful persuasion.
LC-MS Phytochemical Screening, In Vitro Antioxidant, Antimicrobial and Anticancer Activity of Microalgae Nannochloropsis oculata Extract

Nowadays, marine microalgae are recognized to be a considerably novel and rich origin of bioactive moieties utilized in the sectors of nutraceuticals and pharmaceuticals. In the present study, Nannochloropsis oculata extract (AME) was associated with a wide variety of pharmacological studies such as in vitro antioxidant, antibacterial, and antifungal and anticancer activity (MDA-MB-231) in cancer cells through in vitro models. In the study, the chemical composition and structure of the bioactive compounds found in the AME extract were studied using the LC-MS technique. The results of the anticancer activity showed a decrease in the percentage of cell viability of the MDA-MB-231 cells in a concentration- and time-dependent manner (400 μg/mL at 24 h, 300 μg/mL at 48 h, and 200 μg/mL at 72 h). We have also observed morphological changes in the cells that could be associated with treatment with AME extract. Our observation of the AME extract-treated MDA-MB231 cells under light microscopy showed that when the concentration increased, the number of cells began to decrease. As far as LC-MS analysis is concerned, it showed the presence of the bioactive molecules was terpenoids along with carotenoids, polyphenolic and fatty acids. The result revealed that the AME extract exhibited noteworthy in vitro free radical scavenging potential, with an IC50 value of 52.10 ± 0.85 µg/L in DPPH assay, 122.84 ± 2.32 µg/mL in H2O2 assay and, 96.95 ± 1.68 µg/mL in ABTS assay. The activity was found to be highly significant against bacteria (Gram-positive and negative) and moderately significant against fungal strain with minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC)/minimum fungicidal concentration (MFC) values between 15.63 and 500 µg/mL.
Nitrogen Excretion of Lactating Dairy Cows Fed an Alfalfa Hay- or Birdsfoot Trefoil Hay-Based High-Forage Diet

Nitrogen Excretion of Lactating Dairy Cows Fed an Alfalfa Hayor Birdsfoot Trefoil Hay-Based High-Forage Diet by Mohammad Ghelich Khan Utah State University, 2017 Major Professor: Dr. Jong-Su Eun Department: Animal, Dairy, and Veterinary Sciences Extensive research has been conducted to decrease the environmental impacts of dairy farming by using forages containing condensed tannins (CT). In this study, it was hypothesized that feeding CT-containing birdsfoot trefoil (Lotus corniculatus, BFT) to lactating dairy cows would result in a decrease in N degradation in the rumen, causing a shift in N partitioning into milk and manure outputs, compared with alfalfa hay. Urine N is more volatile and harmful to the environment compared with fecal N. By reducing urine N, overall N utilization efficiency can improve. It was our goal to verify how the changes in N partitioning would affect the overall N utilization efficiency by dairy cows fed BFT hay-based high-forage diet. The results in this report showed that feeding BFThay diet reduced protein degradation in the rumen, decreased N excreted to milk and urine, and increased N excretion into feces, resulting in decreased urinary-N:fecal-N ratio due to feeding BFT-hay diet. However, the change in the N excretion routes was not associated with N utilization efficiency, which may have iv resulted from poor nutritive quality of BFT hay. Although the BFT hay fed in the current study was in a very mature condition and was of poor quality, DM intake and milk yield were similar in both treatments. Therefore, it is implied that BFT hay can replace alfalfa hay in dairy rations, because even poor quality BFT hay compared with alfalfa hay led to similar lactational performance and a beneficial shift in N excretion into environment.
Mechanisms underlying sexual selection and sexual conflict in Drosophila melanogaster.

The revelation that females of many taxa mate with multiple males has broadened perspectives in sexual selection to encompass the study of conflicts of interest between males and females over mating and reproduction. Conflict often exists between the sexes over reproductive decisions such as how often to mate, because the optimum mating rate may often be higher for males than for females. Selection is expected to favour traits in males that manipulate female mating frequency and that confer an advantage over competing males, particularly in relation to post- copulatory competition. A significant fraction of male post-copulatory success in Drosophila melanogaster is determined by the action of accessory gland proteins (Acps) that are transferred by males to females during mating. Acps have significant effects on female behaviour and physiology and have been shown to play a role in mediating sexual conflict. Exploring the role of the male accessory glands and of Acps in moulding evolutionary interactions between the sexes and in determining overall fitness remains an important task and one that will illuminate the mechanisms underlying sexual selection and sexual conflict. In this thesis I use Drosophila melanogaster as a model system to ask how reproductive traits, strategies and morphologies have been shaped by sexual selection and sexual conflict. I show that traits related to ejaculate investment and depletion have evolved in lines of D. melanogaster with an evolutionary history of exposure to high or low levels of sperm competition and mating opportunities. I then describe how I initiated, propagated and analysed lines selected for increased and decreased male accessory gland size. I describe the direct and correlated responses to selection and show that accessory gland size is associated with male post- copulatory success but not with the magnitude of female mating costs. I further probe the nature of female mating costs by analysing the contribution to them of a single Acp, Acp62F. Finally, I summarise my thesis and discuss future directions for investigating the mechanisms of sexual selection and sexual conflict in Drosophila.
ESTUDIO DEL NEJAYOTE COMO MEDIO DE CRECIMIENTO DE PROBI ´ OTICOS Y PRODUCCI ´ ON DE BACTERIOCINAS STUDY OF NEJAYOTE AS CULTURE MEDIUM FOR PROBIOTICS AND PRODUCTION OF BACTERIOCINS

In the present work, the nejayote (nixtamalization residue from maize) as a culture medium for probiotic bacteria and production of bacteriocins was evaluated. Nejayotes obtained from three mills were characterized: reducing sugars 0.166-0.818 g/L, total sugars 23.57-63.41 g/L and protein 5.66-12.92 g/L. The fermentation was performed at 37 C for 48 h by: Lactobacillus casei IMAU60214, Lactobacillus rhamnosus GG and Lactobacillus helveticus IMAU70129. Consumption of reducing sugars from 60-65%, total sugars from 6-30% and protein from 1-15% were observed. Furthermore, bacteriocin production was evaluated with the supernatants of fermentation. The greatest inhibition by the presence of bacteriocins was obtained with the supernatants of fermentation of Lactobacillus casei IMAU60214, and Lactobacillus helveticus IMAU70129. The highest inhibition was 14% for Listeria innocua ATCC33090 and 10% for Escherichia coli K-12. Bacteriocins presence was confirmed with addition of proteinase K. Since bacteriocins produced inhibited to L. innocua (Gram +) and E. coli (Gram -) can be said that they probably have a wide spectrum of inhibition. In conclusion, nejayote can be used for the production of probiotics and bacteriocins but need further investigation to optimize the production of bacteriocins.
Mutation of the SP1 gene is responsible for the small-panicle trait in the rice cultivar Tachisuzuka, but not necessarily for high sugar content in the stem

Abstract Tachisuzuka, a rice cultivar grown for whole-crop silage, is characterized by the small-panicle trait and high-stem sugar content. To investigate the interrelationship between the two features, we attempted to identify the gene responsible for the small-panicle trait in Tachisuzuka, and also to examine the function of the gene using a knockout mutant line. A functionally disruptive deletion of the nucleotide sequence was found in the gene SP1 (Short-Panicle 1; Os11g0235200) in Tachisuzuka, which has been reported as a candidate gene for the small-panicle trait. A gene knockout mutant of SP1 obtained from the cultivar Nipponbare showed a small-panicle phenotype similar to that observed in Tachisuzuka. However, soluble sugar content in the stem did not increase in the knockout line, whereas starch content increased significantly. Overall, disruption of SP1 is responsible for the small-panicle phenotype of Tachisuzuka, but it is only partially associated with the high-stem sugar content.
The reciprocal relationship between competition and intraspecific trait variation

Trait differences among plants are expected to influence the outcome of competition; competition should be strongest between similar species (or individuals) under limiting similarity, and between dissimilar species within competitive hierarchies. These hypotheses are often used to infer competitive dynamics from trait patterns within communities. However, plant traits are frequently plastic in response to competition. This variation is poorly accounted for in trait‐based studies of competition and community assembly. To explore the relationship between trait responses and competitive outcomes, we grew 15 species alone, in monoculture and in mixture. We measured traits relating to leaf and root tissue morphology as well as biomass allocation and related competition‐induced changes in these traits to intra‐ and interspecific competition using multi‐model inference. Additionally, we tested how traits from different competitive environments influenced potential community assembly inferences. The competitive environment had large effects on species’ traits, although many effects were species specific. Differences among species in how competition affected trait expression were linked to both intra‐ and interspecific competition, frequently affecting competitive hierarchies. Intraspecific competition was lower for species that limited competition‐induced increases in root allocation and had less variability in this trait overall. Interspecific competition was lower for species with larger leaves and lower specific leaf area than their neighbours. Switching to more stress‐tolerant strategies by increasing root diameter and leaf tissue density also reduced competition. However, dissimilarity in root tissue density also minimized competition, consistent with limiting similarity affecting competitive outcomes. Moreover, changes in these traits were linked to changes in functional diversity, suggesting that competition affects functional diversity by affecting trait expression. Synthesis. Both trait hierarchies and trait dissimilarity affect the outcome of competition by acting on different traits, although competition‐induced changes in trait expression can alter competitive outcomes. Moreover, the magnitude of these trait changes suggests that the source environment where plant traits are collected can affect the inferences drawn from trait patterns within communities. Combined, our results suggest that considering the effect of competition on trait expression is critical to understanding the relationship between traits and community assembly.