FGA Temperature Control for Incubating Egg

This paper investigates the use of genetic algorithms (GA) in the design and implementation of fuzzy logic controllers (FLC) for incubating egg. What is the best to determine the membership function is the first question that has been tackled. Thus it is important to select the accurate membership functions, but these methods possess one common weakness where conventional FLC use membership function generated by human operators. The membership function selection process is done with trial and error, and it runs step by step which takes too long in solving the problem. This paper develops a system that may help users to determine the membership function of FLC using the GA optimization for the fastest processing in solving the problems. The data collection is based on the simulation results, and the results refer to the transient response specification which is maximum overshoot. From the results presented, we will get a better and exact result; the value of overshot is decreasing from 1.2800 for FLC without GA to 1.0081 with GA (FGA)

The implementation of mamdani’s fuzzy model for controlling the temperature of chicken egg incubator

Today, development of technology is rapidly growing in many fields, including in animal husbandry. This technology could be applied in the process of hatching eggs in chicken farms. Since the process of hatching egg was become an important process that correlated with the failure rate in hatching eggs. In order to get an optimal process of hatching eggs, temperature must be controlled as closely as an ideal temperature, which is around 37-40 Celsius. This study builds the prototype of chicken egg incubator system whose temperature was controlled using a Mamdani logic fuzzy control, so it’s can run optimally. We use DFT11 sensor to get the temperature and humidity of incubator as an input of fuzzy logic. Using a fuzzy logic to control the temperature, the output of this system is the speed of fan (PWM). Furthermore, we use 2 lamps to make the temperature warmer, so that the temperature of this incubator could be control in an ideal temperature. We do software testing and overall system performance testing. Software testing is carried out to see whether the implemented fuzzy logic is in accordance with the expected, by comparing the results obtained from a system built with manual calculations and simulation calculations. Based on the test results, it is found that the fuzzy system has been implemented successfully with 47.36% success. While the results of the overall system performance test show that the system being built has worked well

Monovalent engagement of the BCR activates ovalbumin-specific transnuclear B cells

Valency requirements for B cell activation upon antigen encounter are poorly understood. OB1 transnuclear B cells express an IgG1 B cell receptor (BCR) specific for ovalbumin (OVA), the epitope of which can be mimicked using short synthetic peptides to allow antigen-specific engagement of the BCR. By altering length and valency of epitope-bearing synthetic peptides, we examined the properties of ligands required for optimal OB1 B cell activation. Monovalent engagement of the BCR with an epitope-bearing 17-mer synthetic peptide readily activated OB1 B cells. Dimers of the minimal peptide epitope oriented in an N to N configuration were more stimulatory than their C to C counterparts. Although shorter length correlated with less activation, a monomeric 8-mer peptide epitope behaved as a weak agonist that blocked responses to cell-bound peptide antigen, a blockade which could not be reversed by CD40 ligation. The 8-mer not only delivered a suboptimal signal, which blocked subsequent responses to OVA, anti-IgG, and anti-kappa, but also competed for binding with OVA. Our results show that fine-tuning of BCR-ligand recognition can lead to B cell nonresponsiveness, activation, or inhibition

The effects of commercial cleaning agents on automated DNA extraction efficiency and genetic profile quality.

As forensic DNA analysis has experienced countless advances in the past several decades, it has gained considerable notoriety among the general public, including those that are involved in the commission of crimes, leading to biological evidence that has been contaminated with various cleaning products in an attempt to conceal or destroy DNA evidence. This research examined the effects that three types of cleaning agents have on the ability of the Applied Biosystems® Automate Express™ Forensic DNA Extraction System to efficiently extract high quality DNA free from inhibiting compounds using the Prepfiler Express™ Forensic DNA Extraction Kit. This study further assessed the impact that these chemicals have on the entire forensic DNA analysis process through evaluation of the quality of genetic profiles using a quantitative scale. A dilution series (neat to 1:1000) was prepared from whole human blood, as well as from a bleach product containing sodium hydroxide, a quaternary ammonium-based multi-surface cleaner, and a carpet cleaner with hydrogen peroxide as the active ingredient. Each blood dilution was combined with each dilution of the three cleaning products and each of those samples was analyzed in triplicate. The amount of DNA extracted from bleach-treated samples was reduced compared to corresponding control samples due to destruction of the DNA prior to extraction. The quantification results from samples treated with both the ammonium-based cleaner and the hydrogen peroxide carpet cleaner were similar to controls. The automated system successfully removed inhibitory compounds from samples containing sodium hydroxide and quaternary ammonium compounds, but the blood samples containing the concentrated hydrogen peroxide cleaner showed increased inhibition. The genetic profile quality scores indicated that the ammonium-based cleaner had no effect on profiles regardless of the dilution ratio of the sample, while samples containing at least equal amounts of bleach and blood can be expected to display extensive dropout of alleles. The inhibition previously mentioned due to the hydrogen peroxide carpet cleaner completely inhibited amplification in samples containing 1:100 or 1:1000 diluted blood treated with neat carpet cleaner. These results indicate that crime scene personnel should document any cleaning agents that may have contaminated biological evidence as it could significantly impact the results of DNA analysis depending on the type of product and its concentration in relation to the evidence

Optimizing ODP Device Placement on FTTH Network Using Genetic Algorithms

Currently the problem of Optical Distribution Point (ODP) infrastructure is important in fiber to the home (FTTH) network access because ODP infrastructure development is no longer dependent on demand, so placing ODP manually without a systematic method can cause an increase in the value of optical fiber attenuation. on the length of the cable and cause the cable distribution to be irregular. This study aims to optimize the placement of ODP devices in PT BCV's FTTH network by using the Traveling Salesman Problem (TSP) scheme with the genetic algorithm (GA) approach and using hybrid GA, testing is carried out using Matlab software. Testing with development using Hybrid GA gets the best path with a fitness value of 28.6457 and a computation time of 89.93 seconds

Identification of Genomic, Proteomic, and Metabolomic Signatures Associated with Pulmonary Hypertension Syndrome in Broilers

The present dissertation contains a collection of studies that examine the genomic, proteomic, and metabolomic association to pulmonary hypertension or ascites phenotype in fast-growing broilers. Pulmonary hypertension is a multifactorial metabolic disease influenced by physiological, environmental, and nutritional factors. It is characterized by a number of structural changes including, thrombosis and adverse pulmonary vascular remodeling. Thus, the atrial pressure is increased, and the right ventricle becomes hypertrophied, resulting in heart failure and the death of the bird. Pulmonary hypertension or ascites is a global problem that has negatively impacted the economy. The increased mortality rate of broilers (25%) is estimated to cost $1 billion per year in economic losses. Even though molecular genetic techniques were used in the breeding and selection, they have significantly reduced the occurrence of ascites, but not fully eradicated it. Hence, the main objective of this dissertation was to: measure the expression of the CPQ gene in eight tissues (heart, liver, kidney, thigh, breast, spleen, lung, thymus) to investigate the possible effect of a specific genotype on the gene expression, develop a TaqMan assay for the 125 Kbp chromosomal deletion of CPQ gene to test the potential associations with ascites phenotype, and to identify noninvasive biomarkers for early ascites detection by examining the proteomic and metabolomic changes prior and post ascites development

A Combined Epigenetic and Non-Genetic Approach for Reprogramming Human Somatic Cells

Reprogramming of somatic cells to different extents has been reported using different methods. However, this is normally accompanied by the use of exogenous materials, and the overall reprogramming efficiency has been low. Chemicals and small molecules have been used to improve the reprogramming process during somatic cell nuclear transfer (SCNT) and induced pluripotent stem (iPS) cell generation. We report here the first application of a combined epigenetic and non-genetic approach for reprogramming somatic cells, i.e., DNA methyltransferase (DNMT) and histone deacetylase (HDAC) inhibitors, and human embryonic stem cell (hESC) extracts. When somatic cells were pretreated with these inhibitors before exposure to hESC (MEL1) extracts, morphological analysis revealed a higher rate of hESC-like colony formation than without pretreatment. Quantitative PCR (qPCR) demonstrated that pluripotency genes were upregulated when compared to those of somatic cells or treated with hESC extracts alone. Overall changes in methylation and acetylation levels of pretreated somatic cells suggests that epigenetic states of the cells have an effect on reprogramming efficiency induced by hESC extracts. KnockOutserum replacement (KOSR™) medium (KO-SR) played a positive role in inducing expression of the pluripotency genes. hESC extracts could be an alternative approach to reprogram somatic cells without introducing exogenous materials. The epigenetic pre-treatment of somatic cells could be used to improve the efficiency of reprogramming process. Under differentiation conditions, the reprogrammed cells exhibited differentiation ability into neurons suggesting that, although fully reprogramming was not achieved, the cells could be transdifferentiated after reprogramming

THE FUNCTIONAL PROFILES OF CHICKEN EGGS INCUBATED UNDER MONOCHROMATIC LIGHTING

Poultry production remains susceptible to significant infectious disease threats such as Avian Flu, and Newcastle Disease Virus (NDV), which threaten the supply of poultry production. My dissertation research addresses this challenge by leveraging avian circadian biology to improve responses to vaccines to enhance poultry performance. The central hypothesis is that specific visible light wavelengths would enhance circadian rhythm development in ovo, leading to improved immune responses. I addressed an essential question regarding the effect of providing photoperiods with different wavelengths (Blue, Green, and White) on circadian rhythm development and its interplay with the immune response following the NDV challenge in chick embryos using the RNAseq technology. Our results showed that incubating chicken embryos under blue light 450nm was most efficient in entraining the circadian rhythm in lung tissue, compared to white light or dark treatment. Blue light showed a specific impact on skeletal muscle, regulation of striated muscle contraction, Glycerolipid metabolism, and development of neurons. The white light incubation led to a photo-acceleration stimulant effect on epidermal growth factor receptor signaling pathway, ErbB signaling pathway, MAPK signaling pathway, and Insulin signaling pathway were upregulated in white light non-challenged treatment. The response to NDV challenging showed a distinct transcriptome profile between blue and white light. The blue light showed a potent innate immune response, targeting viral replication, clearly pointing to antiviral response. The white light showed less immune response, but more pronounced cell proliferation and metabolic state, suggesting photo-acceleration as the primary process, particularly T cell development, T cell homeostasis, and T lymphocytes' quantity, suggests a rapid or ongoing transition between innate and adaptive immunity. This observation paves the way to photo-accelerated effect of providing white light during chicken egg incubation on organismal development and immune response. It is noteworthy that unvaccinated white light incubated chicks hatched 6-8 h earlier than other blue or dark incubation at the organism level. In conclusion, this study is the first to generated high-resolution RNASeq evidence demonstrating the effect of lighting color background on the circadian rhythm development and modulation of the innate immune response of chicks’ embryos challenged with NDV

Stalking Flu: Development and Characterization of a Broadly Neutralizing Monoclonal Antibody Targeting the Influenza Hemagglutinin Stem

Seasonal epidemics caused by influenza A viruses (IAV) result in an estimated 290,000- 650,000 deaths worldwide each year (17). While antivirals targeted to influenza exist, resistance to these drugs is increasing and regular vaccination remains the most effective way to prevent infection (26, 73, 99). However due to the persistence of antigenic drift and shift, influenza vaccines must be updated each season and antigenic mismatches can reduce efficacy (24, 118). Immunity to influenza either from vaccination or infection is principally mediated by antibodies generated to one of its major surface proteins, Hemagglutinin (HA). HA is a homotrimer, each monomer HA0 is composed of a globular head and stem (100, 111). Proteases present in the host cleave native HA0 into two subunits, HA1 and HA2. Residues in HA1 form the receptor binding pocket within the head and facilitate interaction with the host cell. The stem is encoded by both HA1 and HA2 and contains the fusion peptide required for cytosolic release (10, 112). Most antibodies isolated from patients following infection or vaccination are targeted to the receptor binding domain of the HA head. These antibodies are efficient neutralizers but highly strain specific, recognizing only antigenically similar strains of the same IAV group and consequently lose relevance rapidly as viruses undergo drift (68, 141). However, patients immunized with heterosubtypic HA can also develop antibodies that target the HA stem domain. These antibodies are often effective against multiple HA subtypes, reflecting strong structural constraints imposed on the HA stem epitope, and are referred to as “broadly neutralizing”. It is because of this strong conservation that there has been an interest in characterizing HA stem antibodies in the development of a universal flu vaccine (22, 115, 123). Since their discovery in 1991, dozens xi of broadly neutralizing stem antibodies have been isolated in humans and even more have been derived using targeted technologies, including hybridoma cell generation (69). We used two immunization protocols that each featured successive injection of influenza with antigenically distinct HA components, H1 then H3, followed by hybridoma cell development to generate candidate monoclonal antibodies (mAbs) targeted to the IAV surface glycoproteins. We screened antibody containing hybridoma supernatant for activity against influenza proteins using ELISA, Neuraminidase Inhibition (NI), and Hemagglutinin Inhibition (HAI) assays. Those antibodies which showed appreciable activity against the immunizing viruses from hybridoma generation were purified for further study. Of 114 antibodies, mAb 1G3 (IgG1) was found by Western blotting to successfully bind the HA protein of H1, H1pdm, and H3 influenza A viruses as well as influenza B viruses of both major lineages (Yamagata and Victoria). Significantly, mAb 1G3 was able to successfully neutralize both influenza A and B viruses in vitro as shown by plaque assay and indirect immunofluorescence of infected cells. 1G3 was also shown to be effective against H1, H3, and an influenza B virus in ovo, delaying onset of positive viral titer and preventing viral expansion overall. Although we believe mAb 1G3 to have a conformational epitope, linear epitope mapping revealed that 1G3 likely binds in the stalk domain near to the fusion peptide and across the C terminus of HA1 and N terminus of HA2. We found this locus to be strongly conserved among heterosubtypic influenza strains, including influenza B. Importantly, only one other antibody known as CR9114 has been identified that can neutralize both influenza A and B viruses in vivo (32). CR9114’s epitope appears to have significant overlap with the proposed epitope of our mAb 1G3, although they are not identical. Where CR9114 xii displayed no activity against B viruses in vitro, 1G3 is the only antibody to date that inhibits both A and B viruses in cells. This previously unseen neutralization profile may suggest the possible presence of an additional inhibition mechanism or mechanisms active in cell culture. While CR9114 prevents the fusogenic conformational change of HA within the host endosome and incites Antibody Dependent Cellular Cytotoxicity (ADCC) in vivo, we have demonstrated through Western blotting and neuraminidase inhibition that our mAb 1G3 likely also prevents extracellular HA cleavage and interferes with virion budding (11, 29, 122). Therefore, mAb 1G3 is a unique and previously uncharacterized antibody that is broadly neutralizing against Group 1 and Group 2 influenza A as well as both lineages of influenza B