Miracle-dz/UniFAR-FTUs huggingface dataset:
Genetic improvement of feed intake and methane emissions of cattle

Feed costs represent half of the total costs of dairy production. One way to increase profitability of dairy production is to reduce feed costs by improving feed efficiency. As DMI is a trait that varies significantly during and across lactations, it is imperative to understand the underlying genetic architecture of DMI across lactation. Moreover, phenotypes of DMI are scarce, due to the difficulty of recording them (expensive and labor-intensive). Some predictor traits have been suggested to predict DMI. Examples of these predictor traits are those related to production (milk yield (MY) or milk content) or to the maintenance of the cow (body weight (BW) or conformation traits). The ability to determine when predictor traits ideally should be measured in order to achieve an accurate prediction of DMI throughout the whole lactation period is thus important. Recently, with the use of information of single nucleotide polymorphism (SNP) markers, together with phenotypic data and pedigree, genomically estimated breeding values (GEBV) of scarcely recorded traits, such as DMI, have become easier to accurately predict. This approach, combined with predictor traits, could contribute to an increased accuracy of predictions of GEBV of DMI. Methane (CH4) is the second important greenhouse gas, and enteric CH4 is the largest source of anthropogenic CH4, representing 17% of global CH4 emissions. Furthermore, methane emissions represent 2-12% of feed energy losses. Selecting for lower CH4 emitting animals and more feed-efficient animals would aid in mitigating global CH4 emissions. To identify the impact on CH4 emissions of selecting for lower DMI animals, it is important to determine the correlations between DMI and CH4 and to identify whether the same genes that control DMI affect CH4. Therefore, the general objectives of this thesis were to (1) explore the genetic architecture of DMI during lactation, (2) study the relationship of DMI to conformation, production and other related traits, (3) investigate the correlations between DMI and methane traits, and determine the SNP in common between DMI and CH4 through a genome-wide association study (GWAS), and (4) investigate the accuracy of predictions of DMI using predictor traits combined with genomic data.
Fermentation of Cassava (Manihot esculenta) and Ripe Plantain Peels (Musa paradisiaca) in the Production of Animal Feed

Aims: To study the effects of fermentation on the nutrient composition of cassava and ripe plantain peels. Study Design: Raw cassava and ripe plantain peel blends were varied at different ratio (100:0, 70:30, 60:40, 50:50 and 0:100) and fermented for 96 h. Place and Duration of Study: Department of Microbiology and Department of Animal Production and Health, Federal University of Akure, Ondo State between October 2015 and July 2016. Methodology: Microbial analysis was carried out using potato dextrose agar, nutrient agar and De man Rogosa agar. pH and total titratable acidity analysis were carried out. Proximate and mineral composition of the blends was also carried out. Results: A total number of fifteen (15) microorganisms were isolated during the fermentation of cassava-plantain blend; these comprise of four molds (Penicillium notatum, Aspergillus niger, Aspergillus flavus, Rhizopus stolonifer), ten bacteria (Bacillus subtilis, Lactobacillus plantarum, Original Research Article Okhonlaye and Foluke; JAMB, 1(2): 1-15, 2016; Article no.JAMB. 30354 2 Lactobacillus fermetum, Pedicoccus acidilactic, Lactobacillus delbrueckii, Micrcoccus luteus, Enterobacter cloacae, Bacillus cereus, Leuconostoc mescenteriodes and Staphylococcus aureus and a yeast (Saccharomyces cerevisae). The pH and TTA values of cassava and plantain peel blends varied as the fermentation day progresses. The proximate composition showed an increase in nutritive value of the fermented sample when compared with raw samples. There was significant increase in the mineral composition of the fermented samples when compared with the raw samples.
Effects of drinking saline water on food and water intake, blood and urine electrolytes and biochemical and haematological parameters in goats: a preliminary study

Drinking-water availability, both of quantity and quality, critically limits animal farming in semiarid and arid areas, but differences among species exist. The aim of the present study was to investigate goat saline-water tolerance. A group of four castrated adult males were used in a 4-week experimental period, which followed a 2-week pre-trial period and preceded a 1-week post-trial period. Animals were offered alfalfa hay and concentrates at about maintenance level and were allowed consecutively the following five levels of water salinity: 0‰, 0.5‰, 5‰, 10‰ and 20‰ NaCl. Feed and water consumption were recorded daily during trial, while blood- and urine-sample collections were performed weekly. Plasma concentrations of aldosterone, sodium (Na), potassium (K), glucose, creatinine, urea and proteins, and haematological parameters were analysed. Furthermore, urine pH, specific weight and concentrations of Na, K and creatinine were measured, as well as plasma and urine osmolality. Water intake increased until 10‰ NaCl (from 2.0 to 3.2 L/day, P < 0.001) and decreased thereafter to reach 2.5 L/day. Feed intake decreased (from 1.4 to 1.1 kg/day, P < 0.001) and urine excretion increased with an increasing salinity (from 1.12 to 1.47 L/day, P < 0.001). Increasing salinity elevated plasma concentrations of Na (from 143 to 150 mmol/L, P < 0.05), glucose (from 67.50 to 80.75 mg/dL, P < 0.05), urea (from 26.5 to 47 mg/dL, P < 0.01), proteins (from 6.3 to 8.3 g/dL, P < 0.001), osmolality (from 284 to 299 mosm/kg, P < 0.01) and creatinine (from 0.8 to 1.0 mg/dL, P < 0.01) whereas, K, aldosterone and bodyweight remained unaffected. Moreover, urine osmolality (from 317 to 1217 mosm/kg, P < 0.001), specific weight (from 1018 to 1040, P < 0.01), Na (from 55 to 377 mmol/L, P < 0.001) and K (from 144 to 329 mmol/L, P < 0.001) increased, whereas, pH and creatinine were unaffected. Observed changes in other haematological parameters are considered of minor physiological importance. The results indicated that goats can subsist on drinking saline water (up to 20‰ NaCl), for at least 2 weeks without harmful effects.
Neural dynamics of real-world object vision that guide behaviour

Vision involves complex neuronal dynamics that link the sensory stream to behaviour. To capture the richness and complexity of the visual world and the behaviour it entails, we used an ecologically valid task with a rich set of real-world object images. We investigated how human brain activity, resolved in space with functional MRI and in time with magnetoencephalography, links the sensory stream to behavioural responses. We found that behaviour-related brain activity emerged rapidly in the ventral visual pathway within 200ms of stimulus onset. The link between stimuli, brain activity, and behaviour could not be accounted for by either category membership or visual features (as provided by an artificial deep neural network model). Our results identify behaviourally-relevant brain activity during object vision, and suggest that object representations guiding behaviour are complex and can neither be explained by visual features or semantic categories alone. Our findings support the view that visual representations in the ventral visual stream need to be understood in terms of their relevance to behaviour, and highlight the importance of complex behavioural assessment for human brain mapping.
Ichthyotoxic Cochlodinium polykrikoides red tides offshore in the South Sea, Korea in 2014: III. Metazooplankton and their grazing impacts on red-tide organisms and heterotrophic protists

Copyright © 2017 The Korean Society of Phycology 285 http://e-algae.org pISSN: 1226-2617 eISSN: 2093-0860 Ichthyotoxic Cochlodinium polykrikoides red tides offshore in the South Sea, Korea in 2014: III. Metazooplankton and their grazing impacts on red-tide organisms and heterotrophic protists Moo Joon Lee, Hae Jin Jeong*, Jae Seong Kim, Keon Kang Jang, Nam Seon Kang, Se Hyeon Jang, Hak Bin Lee, Sang Beom Lee, Hyung Seop Kim and Choong Hyeon Choi Department of Marine Biotechnology, Anyang University, Incheon 23038, Korea School of Earth and Environmental Sciences, College of Natural Sciences, Seoul National University, Seoul 08826, Korea Advanced Institutes of Convergence Technology, Suwon 16229, Korea Water and Eco-Bio Corporation, Kunsan National University, Kunsan 54150, Korea Marine Biodiversity Institute of Korea, Seocheon 33662, Korea School of Marine Life and Applied Sciences, Kunsan National University, Kunsan 54150, Korea
Adding value to ragworms (Hediste diversicolor) through the bioremediation of a super-intensive marine fish farm

The aim of this study was to evaluate the potential added value of Hediste diversicolor, cultured for 5 mo in sand bed tanks supplied with effluent water from a super-intensive marine fish farm, by comparing their fatty acid (FA) profile with that of wild specimens. The polychaetes showed an approximately 35-fold increase in biomass during the experimental period and their FA profile was significantly different from that of wild specimens. In cultivated specimens, the most abundant FA class was that of highly unsaturated FA (HUFA), with eicosapentaenoic acid (EPA, 20:5n-3) being the best represented. Similar percentage (SIMPER) analysis showed an average 20.2% dissimilarity between the FA profile of wild and cultivated specimens, supporting the view that the culture system employed enables the recovery of high value nutrients (e.g. EPA and docosahexaenoic acid [DHA, 22:6n-3]) from fish feeds into the tissues of H. diversicolor that would otherwise be lost from the production environment. While the nutritional value of wild ragworms is well established in marine aquaculture (namely for broodstock maturation diets), the higher level of DHA displayed by the specimens produced under the proposed culture system may grant them a premium market value.
Physiological and production responses when feeding Aspergillus oryzae to dairy cows during short-term, moderate heat stress

Dairy operations located in many temperate climates experience a decline in milk production associated with short-term moderate heat stress during the summer months. The duration and intensity of this heat stress differs dramatically from the sustained, intense heat experienced in many tropical and subtropical countries where the vast majority of heat stress research has been conducted. As such, many of the strategies utilized to ameliorate production losses associated with sustained, intense heat may not be effective in temperate climates. The objective of this research was to characterize the production responses of lactating dairy cows during and after short-term, moderate heat exposure and, to determine if feeding a fungal culture, Aspergillus oryzae , during a 5-day heat stress period, could effectively alleviate the associated production losses. In a two-period, cross-over design, eight mature lactating cows were given a total mixed ration with or without Aspergillus oryzae . Each 15-day period consisted of a 5-day thermoneutral phase, a 5-day heat stress phase and a 5-day thermoneutral recovery phase. When exposed to moderate heat stress for a 5-day period, cows experienced a rise in vaginal temperature and a decline in dry-matter intake. Following the 5-day heat stress phase, milk yield declined by a factor of 0·09. Supplementation with Aspergillus oryzae had no effect on vaginal temperature, dry-matter intake, water intake, milk yield or milk components. These data indicate that short-term, moderate heat stress, which occurs during the spring and summer months in temperate climates, will significantly decrease production in the lactating cow. Addition of fungal cultures to the diet during the period of imposed heat did not ameliorate production losses associated with this type of heat stress.
Algorithms towards haplotype-sharing based association studies of case-control traits on pedigree data

Association studies that attempt to link genes with traits are expected to unearth various genomic roots for various diseases. Recently, haplotype based association studies have become popular due to the inheritance information innate to haplotypes. In this work, we provide a summary of recent works that focus on haplotyping and those focusing on association studies. We show that haplotyping is a very promising technique for case-control association studies on pedigree data. We also present a novel haplotyping algorithm that relaxes the assumption of many previous rule based algorithms. We extend the algorithm to compute and enumerate all possible identity-by-state and identity-by-descent sharings. The algorithm is also able to calculate LOD scores, a metric to measure linkage, for every chromosomal region that is free of breakpoints. Our algorithm is implemented in iBDD, which we believe will be highly useful in downstream case-control association studies on pedigree data.
QUALITY OF ORGANIC BANANA PRODUCED IN THE SEMIARID REGION OF MINAS GERAIS, BRAZIL

A regiao norte de Minas Gerais, semiarida, e importante produtora de banana ‘Prata-Ana’ irrigada, cultura altamente suscetivel ao mal-do-panama. O cultivo orgânico de variedades resistentes pode ser uma alternativa fitossanitaria, alem de agregar valor aos frutos. Objetivou-se caracterizar, em poscolheita, variedades de banana produzidas em sistema orgânico, com base em avaliacoes quimicas e fisicas. As variedades Prata-Ana, BRS Platina, Fhia-18, BRS Conquista e BRS Tropical foram caracterizadas no ponto de colheita (verdes) e maduras (estadio seis de maturacao), por avaliacoes quimicas e fisicas. No ponto de colheita, bananas ‘BRS Conquista’ e ‘BRS Tropical’ tiveram a cor da casca verde mais intensa. A ‘BRS Conquista’ apresentou menor massa fresca, menor comprimento e diâmetro do fruto em relacao as demais variedades. A ‘BRS Platina’ produziu frutos com maior massa fresca, comprimento e diâmetro. Bananas ‘Prata-Ana’, ‘BRS Platina’, ‘Fhia-18’, ‘BRS Conquista’, e ‘BRS Tropical’, maduras, nao apresentaram diferenca no teor de solidos soluveis, pH, acidez titulavel e ratio; a ‘BRS Platina’ obteve a casca com tonalidade amarela mais intensa e menor relacao polpa/casca. Maior resistencia ao despencamento ocorreu em ‘BRS Conquista’, e a ‘BRS Tropical’ foi menos resistente. A banana ‘Prata-Ana’ apresentou maior firmeza. As variedades diferiram mais pelas caracteristicas fisicas (cor da casca, tamanho, resistencia ao despencamento, firmeza e relacao polpa/casca) em relacao as quimicas.
Injury Rates of Red King Crab, Paralithodes camtschaticus,Passing Under Bottom-trawl Footropes

The rate of injuries sustained by red king crab, Paralithodes camtschaticus, during passage under several types of bottom trawl footropes was examined using a modified bottom trawl in Bristol Bay, Alaska. Crabs were recaptured and examined for injuries after passing under each of three trawl footropes representing those commonly used in the bottom trawl fisheries of the eastern Bering Sea. Using the injury rate from tows with a floated footrope which minimized crab contact to account for handling injuries, injury rates of 5, 7, and 10% were estimated for crabs passing under the three commercial trawl footropes.
Utilization of Biodiesel-Derived Crude Glycerol by Fungi for Biomass and Lipid Production

UTILIZATION OF BIODIESEL-DERIVED CRUDE GLYCEROL BY FUNGI FOR BIOMASS AND LIPID PRODUCTION Kimberly A. Marchand Advisors: University of Guelph, 2012 Dr. R. Nicol, Dr. W.D. Lubitz, Dr. H. Lee Rapid expansion of the biodiesel industry has led to a surplus of crude glycerol. This thesis investigates the ability of fungi to utilize crude glycerol as an alternative to conventional carbon substrates for growth and lipid production. Screening revealed that 40 of the 61 isolates tested had increased biomass yield, compared to glucose, when crude glycerol was utilized; 29 of these isolates possessed the ability to completely metabolize 14 g·L of glycerol after 7-14 days. The top four candidates belonged to the genera Galactomyces and Mucor. Overall, Galactomyces sp. proved to be better suited for lipid production. In addition to producing biomass with a high lipid content (up to 45 % w/w), Galactomyces sp. also exhibited high biomass yields (up to 25 g·L). The results obtained in this study compare favourably, and in some cases exceed, other literature reported values for biomass and lipid production using glycerol.
To assess the fresh water algal diversity in relation to water quality from river Panjkora, district Dir lower, Pakistan

Thirty-five species belong to fresh water are taxonomically identified with the quality of water bodies from the remote areas. The samples are collected from the river Panjkora different sites during February 2015 to August 2016. Algae are collected, identified and describe in the area for the first time and exploration of the local species are presented in this article. The total 35 species belongs to 16 Genera, 15 Families, 12 Orders, 9 classes and 5 Phylum’s having phylum Chlorophyta includes 22 (63%) species, Charophyta 6(17%) species, Euglenophyta 4 (11%) Species, Ochrophyta 2 (6%) species and Rhodophyta 1 (3%) species. The most dominant are Genus Euglena 4 species (24%), Genera Ankistrodesmus, Microspora, Spirogyra and Ulothrix has 3 Species (17%), Genera Chaetophora, Chlamydomonas, Cladophora, Nitella, Oocystis, Stigeoclonium and Volvox has 2 species (12%), Asterococcus, Batrachospermum, Chlorochromonas, Synura, Zygogonium each has 1 species (6%). It is the first inclusive taxonomical study in river Panjokora and its surrounding area, the river Panjkora is rich of algal species further investigations were needed. Keywords: Physico-chemical characteristics; Algal diversity; Freshwater; River Panjkora; Dir lower; Pakistan http://dx.doi. org/10.19045/bspab.2017. 60067
Optomotor Response Reduced by Procaine Injection in the Central Complex of the cockroach, Blaberus discoidalis

8 INTRODUCTION . 9 Basic anatomy of the B. discoidalis . 11 External Anatomy . 11 Internal Anatomy . 11 The Head Ganglia in Insects . 12 The Central Complex: Anatomy . 14 Focus of project . 16 Basic Visual Information Flow in Insects . 16 Anatomy . 17 Basic Visual Movement Detection . 18 The Central Complex . 19 Comparative Approach lends Insight into function of Central Complex . 19 Overview of Central Complex Development . 19 The Central Complex's influence on Spatial Orientation . 21 The Central Complex Role in Changing Motor Behavior. 22 The Central Complex and Memory . 25 Motor Behavior . 26 Locomotion . 26 Escape Behavior . 28 Procaine . 30 Significance of Project . 31
Why Phenotypic Drug Susceptibility Testing of Mycobacterium tuberculosis to First-Line Drugs is not Sufficient for Proper Management of Drug-Resistant and Multidrug-Resistant tuberculosis?

Tuberculosis (TB) is a major infectious disease of global proportions inflicting a heavy toll on human populations. Active TB disease is caused mainly by inhalation of droplet nuclei containing few bacilli exhaled by sputum smear-positive pulmonary TB patients (open TB) during close human contact [1]. Primary infection with Mycobacterium tuberculosis, however, leads to clinically active TB disease in only ~10% of the exposed individuals. In the remaining subjects, an effective immune response mounted by the host arrests multiplication of tubercle bacilli, however, complete sterilization is achieved in only a sub-set of individuals [1]. In the remaining subjects, infection is only contained but not eradicated as some bacilli escape killing and persist in granulomatous lesions (latent TB infection). The latent infection may remain dormant for a long-time; however, M. tuberculosis can also resuscitate and cause active TB, typically due to waning of the immune response [1]. Nearly one-third of the human population is latently infected with tubercle bacilli and 5%-10% of the infected individuals will eventually develop active TB disease during their life-time [1].
MYCN, proliferative heterogeneity and treatment responsein neuroblastoma

The amplification of the MYCN oncogene, occurring in 20% of neuroblastomas, a tumor of early childhood, is associated with drug-resistant relapse and poor prognosis. High MYCN expression has paradoxical effects in most cells: it promotes cell cycle progression and sensitizes to cell death. This work aims to characterize, at population and single-cell level, the mechanisms through which amplified MYCN allows tumor regrowth after chemotherapy in neuroblastoma. In MYCN-regulatable neuroblastoma cell line models, MYCN shortens the lengths of cell cycle phases, preferentially in G1, and increases the proportion of cycling cells under exponential growth. Upon DNA-damage induced by the chemotherapeutic agent, doxorubicin (DOX), MYCN delays activation of cell cycle checkpoints and boosts the proportion of transiting cells. During and after chemotherapy MYCN favors cell death and suppresses cellular senescence, shifting p53 downstream effects from cell cycle arrest to apoptosis. However, MYCN also drives clonal regrowth of a small fraction of surviving resister cells after DNA-damage. These resister cells exhibit nearly identical molecular and phenotypic profiles as cells before treatment. Live-cell imaging reveals that resister cells arise exclusively from the G1-phase-arrested subpopulation and rapidly repair DNA-damage-induced double-strand breaks (DSBs). The suppression of DNA repair via ATM inhibition during chemotherapy results in reduction of G1 phase arrest and prevents DNA DSB repair, completely eradicating resister cells. Taken together, these data show that non-genetic tumor heterogeneity and a key oncogenic lesion, MYCN, synergize to resume cellular proliferation after DNA damage and probably cause chemotherapy resistance. This work indicates that improved first-line therapies could specifically target resister cells and help avoid cellular regrowth.
Phenotypic variation of milk fatty acid composition of Pinzgauer cattle breed

Abstract This paper investigated sources of variation of milk fatty acid (FA, g/100 g total FA) profile routinely predicted by mid-infrared spectroscopy in Pinzgauer dual-purpose cattle breed. A total of 19,578 individual milk samples collected from 1232 cows and 77 herds between 2011 and 2014 were available for phenotypic characterisation. Data were analysed using a linear mixed model which included stage of lactation, parity and their interaction as fixed effects, and cow and herd-test-day as random effects. Milk yield averaged 20.87 kg/d, and means for fat, protein and casein were 4.01, 3.44 and 2.72%, respectively. Saturated FA (SFA), monounsaturated FA (MUFA) and polyunsaturated FA (PUFA) averaged 69.20, 25.43 and 3.19 g/100 g total FA, respectively. About half of the SFA were provided by C16:0 (31.24 g/100 g total FA), and almost all MUFA by C18:1 (22.18 g/100 g total FA). Fixed effects were significant in explaining the variation of the studied traits. Milk of first-parity cows had the lowest percentage of SFA, medium-chain FA and C14:0, and the greatest percentage of MUFA, PUFA, trans FA, short- and long-chain FA, and C18:1. Saturated FA, C14:0 and C16:0 increased from calving until 120 days in milk, whereas unsaturated FA, MUFA, PUFA, long-chain FA, C18:0 and C18:1 decreased. Although both parity and stage of lactation affected milk FA, greater variation was observed during lactation than among parities.