Miracle-dz/UniFAR-FTUs huggingface dataset:
Advanced estimation and mitigation strategies: a cumulative approach to enteric methane abatement from ruminants

Abstract Methane, one of the important greenhouse gas, has a higher global warming potential than that of carbon dioxide. Agriculture, especially livestock, is considered as the biggest sector in producing anthropogenic methane. Among livestock, ruminants are the highest emitters of enteric methane. Methanogenesis, a continuous process in the rumen, carried out by archaea either with a hydrogenotrophic pathway that converts hydrogen and carbon dioxide to methane or with methylotrophic pathway, which the substrate for methanogenesis is methyl groups. For accurate estimation of methane from ruminants, three methods have been successfully used in various experiments under different environmental conditions such as respiration chamber, sulfur hexafluoride tracer technique, and the automated head-chamber or GreenFeed system. Methane production and emission from ruminants are increasing day by day with an increase of ruminants which help to meet up the nutrient demands of the increasing human population throughout the world. Several mitigation strategies have been taken separately for methane abatement from ruminant productions such as animal intervention, diet selection, dietary feed additives, probiotics, defaunation, supplementation of fats, oils, organic acids, plant secondary metabolites, etc. However, sustainable mitigation strategies are not established yet. A cumulative approach of accurate enteric methane measurement and existing mitigation strategies with more focusing on the biological reduction of methane emission by direct-fed microbials could be the sustainable methane mitigation approaches.
Tracking the origin of island diversity: insights from divergence with the continental pool in monocots

At their early age, a large proportion of island pools were a partial sampling of mainland pools whatever islands are oceanic or fragments of the mainland. Through time, colonization, diversification, extinctions, have deeply transformed insular and continental communities and therefore the degree to which they share species. We studied the relative importance of these mechanisms by looking at the shared evolutionary history between species pools on islands and continents. Indeed, most of these mechanisms are not neutral regarding phylogeny but are linked to species evolutionary relationships. We measured the phylogenetic divergence between continental and insular monocot communities through metrics of beta Mean Pairwise Distance and beta Mean Nearest Taxon Distance. We first tested the influence of spatial and environmental distance to the continent, two main factors of divergence, but whose explanatory power in a phylogenetic context was still unclear. We showed that both dispersal and enviromental filtering were important to explain divergence, although species that could pass these filters were not phylogenetically clustered. There was however a clear distinction between oceanic and continental islands: a stable climate in the latters was key to the survival of the original biota leading to a high proportion of shared lineages between the mainland and islands. But distance to the continent was only part of the story, we investigated additionnal mechanisms of phylogenetic divergence through their relation to island features and community structure. This showed that the most divergent islands occurred in the tropics and that processes of persistence of original species, diversification in remote archipelagos, neutral colonization on easy-to-reach islands, turnover, and high speciation rates may have driven phylogenetic divergence at a world scale. This study showed how phylogenetic approaches may explain how divergence, or similarity may have arisen and provide new insights in the continental origin of plant diversity on islands.
H3K9me2 orchestrates inheritance of spatial positioning of peripheral heterochromatin through mitosis

Cell-type-specific 3D organization of the genome is unrecognizable during mitosis. It remains unclear how essential positional information is transmitted through cell division such that a daughter cell recapitulates the spatial genome organization of the parent. Lamina-associated domains (LADs) are regions of repressive heterochromatin positioned at the nuclear periphery that vary by cell type and contribute to cell-specific gene expression and identity. Here we show that histone 3 lysine 9 dimethylation (H3K9me2) is an evolutionarily conserved, specific mark of nuclear peripheral heterochromatin and that it is retained through mitosis. During mitosis, phosphorylation of histone 3 serine 10 temporarily shields the H3K9me2 mark allowing for dissociation of chromatin from the nuclear lamina. Using high-resolution 3D immuno-oligoFISH, we demonstrate that H3K9me2-enriched genomic regions, which are positioned at the nuclear lamina in interphase cells prior to mitosis, re-associate with the forming nuclear lamina before mitotic exit. The H3K9me2 modification of peripheral heterochromatin ensures that positional information is safeguarded through cell division such that individual LADs are re-established at the nuclear periphery in daughter nuclei. Thus, H3K9me2 acts as a 3D architectural mitotic guidepost. Our data establish a mechanism for epigenetic memory and inheritance of spatial organization of the genome.
Quantum chemistry reveals the thermodynamic principles of redox biochemistry

Thermodynamics dictates the structure and function of metabolism. Redox reactions drive cellular energy and material flow. Hence, accurately quantifying the thermodynamics of redox reactions should reveal key design principles that shape cellular metabolism. However, only a limited number of redox potentials have been measured experimentally, and mostly with inconsistent, poorly-reported experimental setups. Here, we develop a quantum chemistry approach for the calculation of redox potentials of biochemical reactions. We demonstrate that our method predicts experimentally measured potentials with unparalleled accuracy. We calculate the reduction potentials of all redox pairs that can be generated from biochemically relevant compounds and highlight fundamental thermodynamic trends that define cellular redox biochemistry. We further use the calculated potentials to address the question of why NAD/NADP are used as the primary cellular electron carriers, demonstrating how their physiological redox range specifically fits the reactions of central metabolism and minimizes the concentration of reactive carbonyls. The use of quantum chemistry tools, as demonstrated in this study, can revolutionize our understanding of key biochemical phenomena by enabling fast and accurate calculation of large datasets of thermodynamic values.
MICROENCAPSULATION OF BIOCOMPOUNDS FROM AVOCADO LEAVES OILY EXTRACTS

Microencapsulation of natural biocompounds is a growing field leading to its incorporation into food formulations. The use of vegetable oils as alternative solvents to extract biocompounds is considered a green process. Although avocado leaves are underexploited they are still rich in naturally-occuring biocompounds. Therefore, we propose the use of edible vegetable oils as green solvents to extract biocompounds from avocado leaves and preserve them by means of spray-drying microencapsulation. Spray drying allowed an encapsulation efficiency of 50% of the avocado leaves pigments extracted with edible oils. The emulsions prepared were heterogeneous and with low cohesiveness which was observed through de polidispersity index (0.52 - 0.87) and the Z-potential (-35.9 to -38.0) respectively. Microcapsules Haussner ratio values (1.49 – 1.61) showed the cohesiveness of the powders, this was confirmed by microscopy techniques, obtaining high particles area values (177.4 – 4460.5 µm2). Corn oil extracts showed higher carotenoids (>10%), chlorophyll a (approximately 5%) and chlorophyll b (>40%) content as compared with safflower oil extracts. However, the higher hygroscopicity values of the corn oil microcapsules (15.70 – 18.34 g water/ 100 g dry capsules) caused changes in their appearance turning its color from white to pale yellow.
A mini-review on the phytochemistry and biological activities of selected Apocynaceae plants

This review aims at studying the phytochemistry and biological activities of some selected Apocynaceae plants. Eleven members of this family were reviewed for their phytochemistry and biological activities. Interestingly, the commonly isolated compounds reported from Mondia whitei (Hook.f.) Skeels, Secondatia floribunda A. DC, Carissa carandas, Tabernaemontana divaricate, Nerium oleander, Wrightia tinctoria, Tabernaemontana divaricate, Alstonia scholaris, Carrisa spinarum Linn, Thevetia peruviana and Caralluma lasiantha were triterpenoids, flavonoids, phytosterols, cardiac glycosides and lignans. All of them exhibited remarkable biological activities, mostly similar to each other. This review provides a detailed insight into the pharmacological activities of these selected members of this family.
Salt Effects on the Thermodynamics of a Frameshifting RNA Pseudoknot under Tension

Because of the potential link between -1 programmed ribosomal frameshifting and response of a pseudoknot (PK) RNA to force, a number of single molecule pulling experiments have been performed on PKs to decipher the mechanism of programmed ribosomal frameshifting. Motivated in part by these experiments, we performed simulations using a coarse-grained model of RNA to describe the response of a PK over a range of mechanical forces (fs) and monovalent salt concentrations (Cs). The coarse-grained simulations quantitatively reproduce the multistep thermal melting observed in experiments, thus validating our model. The free energy changes obtained in simulations are in excellent agreement with experiments. By varying f and C, we calculated the phase diagram that shows a sequence of structural transitions, populating distinct intermediate states. As f and C are changed, the stem-loop tertiary interactions rupture first, followed by unfolding of the 3’-end hairpin (I⇌F). Finally, the 5’-end hairpin unravels, producing an extended state (E⇌I). A theoretical analysis of the phase boundaries shows that the critical force for rupture scales as (log Cm)α with α = 1 (0.5) for E⇌I (I⇌F) transition. This relation is used to obtain the preferential ion-RNA interaction coefficient, which can be quantitatively measured in single-molecule experiments, as done previously for DNA hairpins. A by-product of our work is the suggestion that the frameshift efficiency is likely determined by the stability of the 5’ end hairpin that the ribosome first encounters during translation.
Wide-Coverage CCG Parsing with Quantifier Scope

This dissertation presents the development of a wide-coverage semantic parser capable of handling quantifier scope ambiguities with a novel way. In contrast with traditional approaches that deliver an underspecified representation and focus on enumerating the possible readings “offline” after the end of the syntactic analysis, our parser handles the ambiguities during the derivation using a semantic device known as generalized skolem term. This approach combines most of the benefits of the existing methods and provides solutions to their deficiencies with a natural way. Furthermore, this takes place in the context of the grammar itself, without resorting to ad-hoc complex mechanisms. As a grammar formalism for this work we use Combinatory Categorial Grammar (CCG), exploiting its lexicalized nature and the surface-compositional semantics that provides. The logical forms are represented in first-order logic, using λ-calculus as a “glue” language, in the tradition of Montague. We base our parser on the OpenCCG framework, and we augment it by applying a well-established supertagger and by developing a head-driven probabilistic model. Our model is trained on CCGbank, a CCG version of the Penn Treebank. For the semantic component we develop a Java library capable of representing and unifying λ-calculus expressions, including the necessary support for the new semantic elements of generalized skolem terms. We evaluate the syntactic component of our parser on Section 23 of CCGbank, getting very high lexical accuracy and coverage but less than optimal PARSEVAL and head dependencies measures. For the semantic part, we create a test suite with sentences that exhibit a wide-range of quantifier scope ambiguities, and we test the performance of our parser on this. We also evaluate the semantic component on a small test set derived from the FraCas framework. For almost all cases we get results that conform to the predictions of the theory. Although time did not permit the testing of the semantic component in a wide-coverage setting, we consider these results as a strong indication that this is actually feasible. Finally, we close this dissertation with specific suggestions of what we consider important to be done as a follow-up work.
Covalent linkage of the DNA repair template to the CRISPR/Cas9 complex enhances homology-directed repair

The CRISPR/Cas9 targeted nuclease technology allows the insertion of genetic modifications with single base-pair precision. The preference of mammalian cells to repair Cas9-induced DNA double-strand breaks via non-homologous end joining (NHEJ) rather than via homology-directed repair (HDR) however leads to relatively low rates of correctly edited loci. Here we demonstrate that covalently linking the DNA repair template to Cas9 increases the ratio of HDR over NHEJ up to 23-fold, and therefore provides advantages for clinical applications where high-fidelity repair is needed.
Astrocyte subdomains respond independently in vivo

Astrocytes contact thousands of synapses throughout the territory covered by its fine bushy processes. Astrocytes respond to neuronal activity with an increase in calcium concentration that is in turn linked to their capacity to modulate neuronal activity. It remains unclear whether astrocytes behave as a single functional unit that integrates all of these inputs, or if multiple functional subdomains reside within an individual astrocyte. We utilized the topographic organization of ferret visual cortex to test whether local neuronal activity can elicit spatially restricted events within an individual astrocyte. We monitored calcium activity throughout the extent of astrocytes in ferret visual cortex while presenting visual stimuli that elicit coordinated neuronal activity spatially restricted to functional columns. We found visually-driven calcium responses throughout the entire astrocyte that was largely independent in individual subdomains, often responding to different visual stimulus orientations. A model of the spatial interaction of astrocytes and neuronal orientation maps recapitulated these measurements, consistent with the hypothesis that astrocyte subdomains integrate local neuronal activity. Together, these results suggest that astrocyte responses to neural circuit activity are dominated by functional subdomains that respond locally and independently to neuronal activity.
Distribution and Productivity of Naturalized Alfalfa in Mixed-Grass Prairie

Alfalfa (Medicago sativa L.) is an important forage and conservation crop in North America but occurrences of naturalized alfalfa in rangelands are rare. A naturalized population of yellow-flowered alfalfa in mixed-grass prairie on the Grand River National Grassland in South Dakota has potential agricultural value for the region. Despite this value, the distribution pattern of this alfalfa among and within native plant communities in the northern Great Plains is unknown. Field studies were conducted from 2003 through 2006 along topographic positions at two sites where yellow-flowered alfalfa was naturalized to evaluate the relationships of yellow-flowered alfalfa on biomass production, cover, species diversity, and alfalfa seedbank distribution characteristics. High yellow-flowered alfalfa cover (>50%) was associated with increased total biomass and occurred exclusively in swales and toeslopes that had silty loam soils. However, species diversity and non-alfalfa biomass were reduced when yellow-flowered alfalfa cover was high. Yellow-flowered alfalfa cover was lower and species richness was higher on backslopes and shoulder areas where sandy loam soils were present. A strong positive linear association existed between yellow-flowered alfalfa cover and alfalfa seedbank density (r values ranged from 0.76 to 0.82, P < 0.0001). Greater than 99% of the seeds were viable but germination rate was only 4%, indicating a high percentage of hard seed in this alfalfa population. Naturalized yellow-flowered alfalfa was a dominant component of a stable, low diversity plant community composed of mainly introduced species in rich soils of swales/toeslopes that contributed to forage production and quality in mixed-grass prairie in the northern Great Plains.
Can competitive learning compete? Comparing a connectionist clustering technique to symbolic approaches

A comparison of competitive learning (a neural-network-based approach to data clustering) with established symbolic approaches is presented. Some of the shortcomings of competitive learning are discussed along with attempts at correcting them. The algorithm is extended to handle the performance task of missing feature prediction. Experimental results are compared with similar results of symbolic systems, such as Cluster/2 and Cobweb. In these experiments, competitive learning does not perform as well as its symbolic counterparts. <<ETX>>
The Effect of Herbage Conservation Method on Protein Value and Nitrogen Utilization in Dairy Cows

Ruminant production systems frequently rely on grassland utilization and conservation of herbage as hay or silage. Conservation affects the crude protein (CP) composition and protein value, which is particularly recognized during ensiling. The aim of the current study was to describe the effect of the conservation method on forage protein value and N utilization in dairy cows. Herbage from the same sward was cut and conserved as silage (SI), barn-dried hay (BH), or field-dried hay (FH). Laboratory evaluation indicated differences in CP fractions and ruminal degradability of CP. Conserved forages were fed to six lactating Holstein cows in a replicated 3 × 3 Latin square design, and N balance was assessed. Partitioning of N into milk, feces, and urine was affected only moderately. Lower concentrations of serum, milk, and also urinary urea indicated lower N turnover for FH compared to SI and BH, likely due to lower N intake for FH. However, the use efficiency of feed N for milk N did not differ between the types of forage. Further, high CP concentrations and the unbalanced concentrations of CP and energy in the forages led to excess excretion of N in all treatments and presumably superimposed effects of the conservation method on N utilization.
Manipulation and Resynthesis of Environmental Sounds with Natural Wavelet Grains

A technique is presented to facilitate the creation of constantly changing, randomized audio streams from samples of source material. A core motivation is to make it easier to quickly create soundscapes for virtual environments and other scenarios where long streams of audio are used. While mostly in the background, these streams are vital for the creation of mood and realism in these types of applications. Our approach is to extract the component parts of sampled audio signals, and use them to synthesize a continuous audio stream of indeterminate length. An automatic speech recognition algorithm involving wavelets is used to split up the input signal into syllable-like audio segments. The segments are taken from the original sample and are not transformed in any way. For each segment, a table of similarity between it and all the other segments is constructed. The segments are then output in a continuous stream, with the next segment being chosen from among those other segments which best follow from it. In this way, we can construct an infinite number of variations on the original signal with a minimum amount of interaction. An interface for the manipulation and playback of several of these streams is provided to facilitate building complex audio environments.
Motion Control for Three-Link Brachiation Robot by Using Final-State Control with Error Learning

This paper demonstrates that motion control of a three-link brachiation robot can be performed via final-state control for a linear parameter-varying system with error learning. Since the root joint of the brachiation robot has no drive unit, the control problem is treated as that for an open-chain manipulator possessing nondriven joints in circumstances with gravity. Also, the brachiation robot possesses a nonlinear property in its wide motion area from an initial state to a final desired state. We treat the brachiation robot as a discrete-time linear parameter-varying system by using an extended linearization method and Euler's method. In the experiments, the second and third joints of the brachiation robot are directly driven by AC servo motors installed in each joint. The free vibration of the brachiation robot is coincident with that of the simulation and gives suggestions of the final time to reach a desired state that has to be specified for final-state control. By simulations and experiments, it is demonstrated that the feedforward input obtained by the final-state control method can bring the three-link brachiation robot from an initial state to a desired state in a specific time. Its robustness under a variation of the link mass is also verified.
MATCH SCORE FUSION OF FINGERPRINT AND FACE BIOMETRICS FOR VERIFICATION

In recent years, attacks on password databases have been carried out at an increasing rate, with significant success. Thus, a new approach is needed to prove one's claim to identity instead of relying on a password. In this paper, we investigate the use of biometric match scores for the purpose of verification . Our work was performed using the BSSR1 multimodal match score biometric dataset, which contains match scores from face and fingerprint biometric systems. We investigated the use of match scores as a feature vector, and performed Simple Sum and Product Rule fusion of match scores. The results we obtained demonstrated that the use of match scores for verification purposes can be achieved to give a result that is highly accurate.
Analysis of hepatitis B virus (HBV) drug resistance variations in HBV carriers of Chinese blood donors

Background: To analyze hepatitis B virus (HBV) mutations of nucleoside drug resistance in blood donors of Shantou Central Blood Station. Methods: A total of 22,539 blood donors in Shantou City in 2014 were recruited in the study. Two hundred and one blood samples were detected positive by two types of enzyme-linked immunosorbent assay (ELISA) and 99 cases of HBV positive samples were detected by fluorescence quantitative polymerase chain reaction (PCR). Among them, 45 cases with viral loads greater than 1,000 IU/mL were sequenced by PCR sequencing method. Drug resistance mutation sites of sample DNA sequences were analyzed. Results: All known 10 drug resistant sites of HBV were not detected from these 45 cases of HBV blood donor carriers. Conclusions: The prevalence of HBV strains from blood donors in Shantou were wild-type.