Miracle-dz/UniFAR-FTUs huggingface dataset:
Evaluation of different feeding options on growth response and carcass characteristic of yearling Kereyu-Bulls to attain local/export market weight

The study was conducted at Adami Tulu agricultural research center on growth performance and carcass characteristics evaluation of one year old 24 Kereyu bulls. The objectives of the fattening trial were: to evaluate different feeds options on one year aged Kereyu bulls for them to attain 300kg export market weight gain, to evaluate the carcass characteristics of the animals under fattening and to identify the most economical feeding options to obtain the targeted export market weight gain.
Regulation of mitochondrial function by Myocardin during cardiac development and disease

ii Dedication . iv Acknowledgements . vi List of Figures . xv List of Tables . xvii List of Abbreviations . xviii CHAPTER I: Literature Review . 1 1.1 Mammalian Cardiac Development . 1 1.1.1 Cardiac development . 1 1.1.2 Cardiac Transcription Factors . 3 1.1.3 Cardiac Reprogramming . 4 1.2 Myocardin Biology . 5 1.2. 1 Discovery . 5 1.2. 2 Characterization of a Co-Activator . 6 1.2. 3 Alternatively Spliced Isoforms . 8 1.2. 4 Functional role of Myocardin during development . 9 1.3 Myocardin Family . 11 1.3. 1 Myocardin Related Transcription Factors (MRTFs) . 11 1.3. 2 MASTR . 13 1.4 Myocardin: An Essential Cofactor for Cardiac Development . 14 1.4. 1 Cre-Lox Recombinase Animal Models. 14 1.5 Myocardin Domains . 17 1.5. 1 Functional Domains . 17 1.5. 2 Transcription Factor Binding Domains. 17 1.6 Regulators of Myocardin Activity & Expression . 19 1.6. 1 Transcriptional Regulators . 19 1.6. 2 Epigenetic Regulators . 20 1.6. 2A DNA Methylation . 21 1.6. 2B Histone Modification: Acetylation . 22 1.6. 2C Histone Modification: Methylation . 25 1.6. 3 Post-Translational Modification of Myocardin in Smooth Muscle . 26 1.6. 4 Post-Translational Modification of Myocardin in Cardiac Muscle . 30 1.7 Myocardin in Heart Disease . 32
Observing the Cooperation of Varroa Destructor and DNA Virus AmFV in the Onset of Colony Collapse Disorder in Emerging Apis mellifera

The honey bee population is declining from the onset of a disorder known as Colony Collapse Disorder (CCD) which has been associated with climate change, increase use of insecticides, and parasite/viral communication. Much focus has been directed towards the communication between RNA viruses with the honey bee parasite Varroa destructor and their relationship to haemolymph levels in emerging worker bees, but their association with DNA viruses has been neglected. The study proposed is to closely observe whether parasite burden in combination with reduced haemolymph levels could increase viral replication of DNA virus AmFV in emerging honey worker bees. Since, haemolymph houses the cells and proteins needed for proper immune response, the predicted outcome is that a significant increase of viral replication will be present in the emerging workers despite the virus mechanisms for replication are DNA based instead of RNA based.
PREDICTION OF FOREX TREND MOVEMENT USING LINEAR REGRESSION LINE, TWO-STAGE OF MULTI-LAYER PERCEPTRON AND DYNAMIC TIME WARPING ALGORITHMS

Foreign Exchange Currency prediction has become a challengÂ­ing task since the late 1970s due to uncertainty movement of exchange rates. However, most researchers in this area were neglecting to analyse trend patterns from historical Forex data as input features. Thus, this motivates us to investigate possiÂ­bility of repeated trend patterns from historical Forex data. This paper aims to investigate the repeated trend patterns as features from historical Forex data, which proposes new combination techniques - Linear Regression Line, two-stage of Multi-Layer Perceptron and Dynamic Time Warping algorithms in order to improve the performance of prediction significantly, thus achievÂ­ing greater accuracy.
Antimicrobial Activities of a Novel Marine Streptomyces sp. MMM2 Isolated from El- Arish coast, Egypt

isolated from the Red Sea (Berenice and Safaga) and Mediterranean Sea (Arish and Abou Quir), and screened for their ability to produce antimicrobial agents (s) against Staphylococcus aureus , E.coli , Pseudomonas aeruginosa , Enterococcus faecalis , Bacillus subtilis , Klebsiella pneumoniae and Edwardsiella tarda using agar well diffusion. The most potent isolate identified as Streptomyces sp. MMM2 by the 16S rRNA sequence gene. Optimization of the antimicrobial products was performed by Plackett–Burman experimental design. Ethyl acetate, hexane, and acetone extracts were used for the screening. Antifungal activity of Streptomyces sp. MMM2 was also estimated. Chemical characterization of the ethyl acetate extract of Streptomyces sp. MMM2 was performed using GC-MS spectrophotometry, FTIR, Raman, and NMR. This analysis showed that effective compounds that had antimicrobial activities were hexadecanoic acid methyl ester, 9-octadecadienoic, octadecadienoic acid methyl ester, hexadecanoic acid, 2-hydroxy-1-(hydroxymethyl) ethyl ester, 9,12-octadecadienoyl chloride.
A Deep Learning Segmentation Approach in Free-Breathing Real-Time Cardiac Magnetic Resonance Imaging

Objectives The purpose of this study was to segment the left ventricle (LV) blood pool, LV myocardium, and right ventricle (RV) blood pool of end-diastole and end-systole frames in free-breathing cardiac magnetic resonance (CMR) imaging. Automatic and accurate segmentation of cardiac structures could reduce the postprocessing time of cardiac function analysis. Method We proposed a novel deep learning network using a residual block for the segmentation of the heart and a random data augmentation strategy to reduce the training time and the problem of overfitting. Automated cardiac diagnosis challenge (ACDC) data were used for training, and the free-breathing CMR data were used for validation and testing. Results The average Dice was 0.919 (LV), 0.806 (myocardium), and 0.818 (RV). The average IoU was 0.860 (LV), 0.699 (myocardium), and 0.761 (RV). Conclusions The proposed method may aid in the segmentation of cardiac images and improves the postprocessing efficiency of cardiac function analysis.
Polyploidy increases overall diversity despite higher turnover than diploids in the Brassicaceae

Although polyploidy, or whole-genome duplication, is widespread across the Plant Tree of Life, its long-term evolutionary significance is still poorly understood. Here we examine the effects of polyploidy in driving macroevolutionary patterns within the angiosperm family Brassicaceae, a speciose clade exhibiting extensive inter-specific variation in chromosome numbers. We inferred ploidal levels from haploid chromosome numbers for 80% of species in the most comprehensive species-level chronogram for the Brassicaceae published to date. After evaluating a total of 54 phylogenetic models of diversification, we found that ploidy drives diversification rates across the Brassicaceae, with polyploids experiencing faster rates of speciation and extinction, but relatively slower rates of diversification. Nevertheless, diversification rates are, on average, positive for both polyploids and diploids. We also found that despite diversifying significantly slower than diploids, polyploids have played a significant role in driving present-day differences in species richness among clades. Overall, although most polyploids go extinct before sustainable populations are established, rare successful polyploids persist and significantly contribute to the long-term evolution of lineages. Our findings suggest that polyploidy has played a major role in shaping the long-term evolution of the Brassicaceae and highlight the importance of polyploidy in shaping present-day diversity patterns across the plant Tree of Life. Significance statement Although polyploidy is a source of innovation, its long-term evolutionary significance is still debated. Here we analyze the evolutionary role of polyploidy within the Brassicaceae, a diverse clade exhibiting extensive variation in chromosome numbers among species. We found that, although polyploids diversify slower than diploids, polyploids have faster extinction and speciation rates. Our results also suggest that polyploidy has played an important role in shaping present-day differences in species richness within the Brassicaceae, with potential implications in explaining diversity patterns across the plant Tree of Life.
Feeding strategies alter gene expression of the calpain system and meat quality in the longissimus muscle of Braford steers

Objective The aim of the present study was to determine the effect of supplementing pasture-finished steers with corn silage on the expression level of the calpain system proteins and beef tenderization. Methods Thirty Braford steers grazing on summer pasture were used for the study. For 120 days fifteen animals were supplemented with corn silage at 1% of body weight per head per day (Suppl) whereas the remaining 15 steers only received pasture (Contr). Carcass and meat traits were evaluated and compared between groups. Gene expression and activities of proteases (calpain 1 and calpain 2) and inhibitor (calpastatin) were measured using real-time polymerase chain reaction and casein zymography. Results Carcass and meat traits were significantly different between feeding systems. Supplemented steers showed higher hot carcass weight (p<0.01), fat content (p = 0.02), and Warner-Bratzler shear force (p = 0.03). Furthermore, the control group showed higher protease:inhibitor ratios, at mRNA (p = 0.01) and protein levels (p<0.10). Warner-Bratzler shear force and mRNA calpains:calpastatin ratio were associated in both feeding systems (p<0.01). Conclusion Based on the results obtained in the study, beef tenderness differences among finishing strategies could be modulated through differential expression of the calpain system proteins.
Quality Changes of Fish Burger From Rainbow Trout During Refrigerated Storage

: Physical, chemical, microbiological and sensory changes of fish burgers prepared from fresh rainbow trout fillets (Group A) and frozen-thawed rainbow trout fillets (Group B) were determined during the storage at 4°C for 21 days. There were significant differences (p<0.05) between pH and TBA values of two groups but there were no significant differences (p>0.05) between sensory attributes except texture properties at l st day of the storage. Although fish burgers were found in good quality limits at the end of the storage due to the results of physical, chemical and sensory analysis, according to microbiological analysis results, Group A is not in good quality limits and Group B should consume before 9 days of the storage.
Influence of nano-silica and humic acid on physiological characteristics of Bermuda grass (Cynodon dactylon L.) under salinity stress

This research was conducted to evaluate the effects of water salinity and nano-silica (NS) and humic acid (HA) on Bermuda grass. The study was carried out under greenhouse and exterior space conditions in a completely randomized design with factorial arrangements. Treatments included 4 water salinity levels (0, 5, 7 and 9 dS/m) and 4 level of NS (0, 1, 2 and 3 mm/l) as well as 4 level of HA (0, 50, 100 and 150 mg/l). Results indicated a decrease in chlorophyll content, and increase in proline, malondialdehyde (MDA), catalase (CAT), superoxide dismutase (SOD) and electrolyte leakage (EL) with increasing levels of salinity. The chlorophyll content in greenhouse and exterior space also increased with increasing levels of NS and HA, while proline in two environments, with increasing levels of NS and HA decreased. EL with increasing levels of NS fluctuated, but with increasing levels of HA, it decreased in two environments. With increasing levels of NS, CAT in both environments was eventually decreased after the oscillation, but there was no particular trend in HA levels. With increasing levels of NS and HA, MDA in the greenhouse decreased and in the exterior space – it increased. Finally, by increasing levels of NS and HA, SOD did not show any change in the greenhouse condition, but in the exterior space, the SOD was decreased.
Antibiotic resistance profiles of vancomycin resistant enterococci in chicken meat samples

Antibiotic resistance is one of the serious threats to global public health and food safety today. Acquired antibiotic resistance in microorganisms arises from prevalent use of antibiotics for human and animal medicine. Owing to the fact that Vancomycin Resistant Enteroccocci (VRE) is a vital problem for public health, determination of the antibiotic resistance profiles of Enterococcus spp. isolates have crucial importance as a part of the farm to fork food safety. In the study, 120 retail chicken meat samples were analyzed, and 36 (30%) of the samples were detected as Enterococcus spp. positive. According to the results, the most prevalent species was E. faecalis with a rate of 44.4% (16/36), followed by 27.8% (10/36) E. faecium , 11.1% (4/36) E. durans , 2.8% (1/36) E. gallinarum and 2.8% (1/36) E. casseliflavus. Antibiotic resistance profiles of the verified Enterococcus spp. isolates were determined with disc diffusion method in terms of eight different antibiotics. Among the Enterococcus spp. isolates, 20 (55.5%) isolates were phenotypically resistant to vancomycin, 6 isolates (16.7%) were detected as vanA positive, 3 isolates (8.3%) were detected as vanB positive, and one isolate (5%) showed high resistance to vancomycin (MIC >256 µg/ml). Even though the observed percentages are low, the observed resistance patterns are still of concern for public health.
Effects of Drying Condition on Physico-chemical Properties of Foam-mat Dried Shrimp Powder

ABSTRACT The effects of drying parameters on moisture content, water activity, bulk density, water binding capacity (WBC), oil absorption, and color parameters (L*,a*, b*) of foam-mat dried shrimp powders were investigated. Shrimp purees were dried as a foam mat at different drying temperatures (50ºC, 60ºC, and 70ºC) and thicknesses of the foam layer (4 and 8 mm). The experimental results showed that as the temperature increased, the moisture content, water activity, and oil absorption of the samples decreased. However, their solubility increased significantly (P ˂0.05). Bulk density of shrimp powder increased with increasing the thickness of the foam layer. Increasing temperature led to increased and decreased WBC with 4 and 8 mm thickness, respectively. Furthermore, the a*, b*, and L* (at 8 mm thickness) decreased with increasing temperature; however, L* increased at 4 mm thickness. Fourier transform infrared (FTIR) spectra showed some major shifts, such as in the region of 1000–1700 cm−1, related to C–O, C–O–C, and C–H band stretching. The differential scanning calorimetry thermograms showed a large peak with a denaturation peak around 72ºC for shrimp proteins.
Amino acid release patterns of growing pig diets formulated with different dietary protein sources

ABSTRACT This study elucidated the dynamics of AA release in low-protein growing pig diets formulated with different protein sources. Four protein sources including soybean meal (SM), corn gluten meal (CGM), fish meal (FM) and fermented soybean meal (FSM) were used to formulate growing pig diets and subjected to in vitro digestion for 4, 8, 12, 16, 20, 24, and 28 h at 39°C. The AA contents were measured by ultra-high performance liquid chromatography (UPLC). FSM group recorded the highest AA release rate at 4-12 h digestion while the CGM group recorded the lowest at 8-20 h digestion (p < 0.05). AA release in the SM group was significantly higher than that in the FM group at 8, 12 and 20 h digestion (p < 0.05). Lysine, methionine and phenylalanine contents in the dietary groups showed significant variations within the first 8 h of digestion due to synthetic AA supplementation. However, after 8 h, the essential AA (EAA) release rate in the FSM group was consistently higher while those in the CGM group were consistently lower (p < 0.05). Based on the results, the AA release patterns of diets can be effectively regulated to meet animal demand by adjusting the structure of the dietary protein source.
Assessment of human diploid genome assembly with 10x Linked-Reads data

Background Producing cost-effective haplotype-resolved personal genomes remains challenging. 10x Linked-Read sequencing, with its high base quality and long-range information, has been demonstrated to facilitate de novo assembly of human genomes and variant detection. In this study, we investigate in depth how the parameter space of 10x library preparation and sequencing affects assembly quality, on the basis of both simulated and real libraries. Findings We prepared and sequenced eight 10x libraries with a diverse set of parameters from standard cell lines NA12878 and NA24385 and performed whole genome assembly on the data. We also developed the simulator LRTK-SIM to follow the workflow of 10x data generation and produce realistic simulated Linked-Read data sets. We found that assembly quality could be improved by increasing the total sequencing coverage (C) and keeping physical coverage of DNA fragments (CF) or read coverage per fragment (CR) within broad ranges. The optimal physical coverage was between 332X and 823X and assembly quality worsened if it increased to greater than 1,000X for a given C. Long DNA fragments could significantly extend phase blocks, but decreased contig contiguity. The optimal length-weighted fragment length (WμFL) was around 50 – 150kb. When broadly optimal parameters were used for library preparation and sequencing, ca. 80% of the genome was assembled in a diploid state. Conclusion The Linked-Read libraries we generated and the parameter space we identified provide theoretical considerations and practical guidelines for personal genome assemblies based on 10x Linked-Read sequencing.
Competition Among Gardnerella Subgroups From the Human Vaginal Microbiome

Gardnerella spp. are hallmarks of bacterial vaginosis, a clinically significant dysbiosis of the vaginal microbiome. Gardnerella has four subgroups (A, B, C and D) based on cpn60 sequences. Multiple subgroups are often detected in individual women, and interactions between these subgroups are expected to influence their population dynamics and associated signs and symptoms of bacterial vaginosis. In the present study, contact-independent and contact-dependent interactions between the four Gardnerella subgroups were investigated in vitro. The cell free supernatants of mono- and co-cultures had no effect on growth rates of the Gardnerella subgroups suggesting that there are no contact-independent interactions (and no contest competition). For contact-dependent interactions, mixed communities of 2, 3 or 4 subgroups were created and the initial (0 h) and final population sizes (48 h) were quantified using subgroup-specific PCR. Compared to the null hypothesis of additive interactions, most (69.3%) of the mixed communities exhibited competition (p < 0.0001). Competition reduced the growth rates of subgroups A, B and C. In contrast, the growth rate of subgroup D increased in the presence of the other subgroups (p < 0.0001). All subgroups were able to form biofilm alone and in mixed communities. Our study suggests that there is scramble competition among Gardnerella subgroups, which likely contributes to the observed distributions of Gardnerella spp. in vaginal microbiomes and the formation of the multispecies biofilms characteristic of bacterial vaginosis.
Anastrozole mediated modulation of mitochondrial activity by inhibition of mitochondrial permeability transition pore opening: An initial perspective

Background Mitochondrial permeability transmembrane pore [mPTP] plays a vital role in alteration of the structure and function of mitochondria. Cyclophillin D is a mitochondrial protein that regulates mPTP function and a known drug target for therapeutic studies involving mitochondria. While aromatase inhibitor’s role on mPTP has been previously studied, the role of anastrazole on mPTP is not completely elucidated. Methods The role of anastrozole in modulating the mPTP was evaluated by docking and molecular dynamics using human cyclophillin D data. Peripheral blood mononuclear cells [PBMCs] of patients with mitochondrial disorders and healthy controls were treated with anastrazole and evaluated for mean fluorescence by flow cytometer. Spectrophotometry was employed for total ATP level estimation. Findings Anastrozole – cyclophillin D complex is more stable when compared to cyclosporine A – cyclophillin D. Anastrozole performed better than cyclosporine in inhibiting mPTP pore. Additional effects included reduction in mitochondrial swelling and mitochondrial membrane depolarization, decreased super oxide generations, caspase 3 intrinsic activity and cellular apoptosis levels and increase in ATP levels. Interpretation These results highlights the potency of anastrozole as a promising agent in ameliorating the phenotype by inhibiting the opening of mPTP pore. However, larger functional studies are required to validate the efficacy of this molecule as a therapeutic agent in mitochondrial disorders.
The role of small GTPases in mammalian cytokinesis

Cytokinesis is the final physical separation of two daughter cells, which occurs at the end of mitosis. Emerging evidence has placed membrane trafficking at the heart of mammalian cytokinesis, as it is clear that the control of membrane traffic into the cleavage furrow created by the ingressed acto-myosin contractile ring is vital for the expansion of surface area and proper separation. These findings also indicated that both the secretory and endocytic recycling pathways could be the potential internal membrane stores contributing to this process. Small GTPases are known to play crucial roles in the regulation of intracellular membrane traffic. Recent studies from diverse model systems highlighted roles for two GTPases Rab11 and Arf6 in Drosophila cellularisation, Caenorabditis elegans and mammalian cytokinesis. These proteins are both involved in endosomal recycling, and disraption of them by expressing mutants and RNAi results in severe cytokinesis defects. In a previous study, our group have identified Ai-fophilin2/Rab11-FIP4 as a dual Rab11/Arf binding protein. Immunofluorescence data revealed that FIP4 strikingly localises to the cleavage furrow and the midbody in mammalian cells during cell division. With this information in mind, it is proposed that the interaction of Rab11/Arf6 with Rab11-FIP3/4 may serve to regulate delivery of recycling endosomes (RE) to the furrow/midbody during cytokinesis in mammalian cells. In this thesis, studies were earned out to investigate the function of Rab11 and Arf6 in mitosis. Firstly, the localisation of Rab11 and Arf6 throughout mitosis was examined. Both of the proteins were concentrated at the furrow/midbody region similar to Rab11-FIP4. Using GTP-deficient mutants and RNAi approaches, it was shown that Rab11 and Ajrf6 are both required for mammalian cytokinesis. Furthermore, time-lapse microscopy revealed that these two proteins both function in the late stage of cytokinesis, possibly midbody abscission but not furrow ingression. Many Rab proteins have overlapping endosomal distributions, and therefore the second part of this study examined whether other endosomal Rabs also localise to the dividing site and contribute to membrane delivery to the furrow/midbody. Although none of the Rabs investigated showed characteristic distribution at the cleavage site, interference with one of the Rab GTPases, Rab4, did result in a minor defect in cytokinesis, implicating a role in this process. Finally, preliminary study of regulation mechanism of FIP3 and FIP4 in mitosis was carried out. Bioinformatics and immunoflurorescence experiments implicated that the FIPs may be regulated by cell-cycle dependent kinases. Hence the possibility of FIP3 and FIP4 being phosphorylated by mitotic kinases, such as Aurora B and Polo-like kinase (Plk) was examined. This will provide more leads to elucidate FIP3 and FIP4's function in cell division and better our understanding of the membrane trafficking pathway during cytokinesis.