Miracle-dz/UniFAR-FTUs huggingface dataset:
Estudo da combinação de preparações enzimáticas no rendimento de extração aquosa do óleo da polpa de Euterpe oleracea Martius

The oil of the açai palm tree (Euterpe oleracea) fruits has a beneficial lipid profile for health with a high content of mono and polyunsaturated fatty acids, besides antioxidant substances, which provides its appreciation on the industry. The aqueous extraction of vegetable oils supported by enzymes has been widely used because of its benefits compared to the traditional processes. In this context, this work aims to identify the best combination of enzymatic preparations, which would maximize the aqueous extraction yield of the oil of the açai palm tree fruits from the pulp. The açai pulp was obtained from fruits collected in Abaetetuba during the 2015 crop. Four commercial enzymatic preparations (Novozymes) were used: Celluclast 1,5L (cellulase); Viscozyme L (endo 1,3(4) β-glucanase, xylanase, cellulase and hemicellulase); Ultrazym AFP (pectin lyase, cellulase and polygalacturonase); and Shearzyme 500L (endo 1,4-xylanase). The tests of açai oil extraction were performed by a process developed in this work with the following parameters: mean granulometry of the açai pulp of 0,75 cm; global dry matter of the aqueous mixtures of the pulp of 15%; individual enzymatic concentration of 1% (w:w) on pulp basis; constant orbital agitation of 100 rpm and vigorous agitation by hand every 30 minutes; incubation time and temperature of 4 hours and 50°C, respectively. The enzymatic preparations were tested individually (1x1) in quadruplicate, or combined (2x2; 3x3 and 4x4) in triplicate, totaling 89 tests. The negative control presented a mean yield of extraction of 34,91±11,81%, the lowest of all the tests. The tests performed with the isolated enzymatic preparations have enabled an increase of the extraction yield up to 36,66% compared to the negative control, confirming the important role of the enzymes in the aqueous extraction process. The tests performed with the enzymatic preparations combined 3x3 and 4x4 have increased the extraction yield up to 99,05% compared to the negative control, demonstrating the importance of using the combinations of enzymatic preparations. Among the different tests performed, the enzymatic preparations that stood out are Celluclast 1,5 L, Viscozyme L and Ultrazym AFP by facilitating the oil recovery with a reduce standard deviation (±3,01%). Furthermore, the extraction yield using this combination of three enzymatic preparations is statistically equal to the extraction yield using the four enzymatic preparations, which becomes interesting to the industry due to the cost reduction in the process.
Inheritance of Resistance to Temephos in a Laboratory Selected Strain of the Potential Mosquito Vector of West Nile Virus (Culex Pipiens) from Tunisia

The inheritance pattern of resistance was investigated in laboratory-induced temephos resistant and susceptible strains of Culex pipiens. The field population collected in Northwestern Tunisia was subjected to temephos selection and after 6 generations in the laboratory identified as Bou.tem6. Different genetic crosses were carried out between resistant and sensitive strains. The F1 offspring of the reciprocal crosses between the Bou.tem6 and S-Lab strains showed high levels of temephos resistance indicating that the resistant gene is completely dominant. The dose-mortality lines of reciprocal crosses to a sensitive colony showed the same projection and confirmed the autosomal inheritance of the resistance. Dose/mortality data for backcross showed that resistance to temephos is multifactorial. Our results were discussed in relation with previous studies. To cite this article [Tabbabi, A. , & Ben Cheikh, H. (2017). Inheritance of Resistance to Temephos in a Laboratory Selected Strain of the Potential Mosquito Vector of West Nile Virus (Culex pipiens) from Tunisia. The Journal of Middle East and North Africa Sciences, 3(5), 5-9]. (P-ISSN 24129763) (e-ISSN 2412-8937). www.jomenas. org. 2
Novel Microsatellite Markers for Notopterygium oviforme (Apiaceae), an Endangered Herb Endemic to China

Notopterygium oviforme (Apiaceae) is an endangered perennial herb endemic to China. To investigate its population genetics, we characterized 17 novel microsatellite markers based on high throughput Illumina MiSeq sequencing data. The number of observed alleles (N O) per locus varied between 1 and 7 (mean = 3.53). Observed and expected heterozygosities (H O and H E, respectively) ranged from 0.24 to 0.72, and from 0.37 to 0.64, respectively. Fourteen primers were successfully cross-amplified in two congeneric species (N. incisum and N. forbesii). We detected no deviation from the Hardy-Weinberg equilibrium (HWE) and linkage disequilibrium (LD) at any loci. These microsatellite markers are likely to be useful for the study of population genetic diversity and genetic structure of N. oviforme and its congenerics.
Towards Data Distillation for End-to-end Spoken Conversational Question Answering

In spoken question answering, QA systems are designed to answer questions from contiguous text spans within the related speech transcripts. However, the most natural way that human seek or test their knowledge is via human conversations. Therefore, we propose a new Spoken Conversational Question Answering task (SCQA), aiming at enabling QA systems to model complex dialogues flow given the speech utterances and text corpora. In this task, our main objective is to build a QA system to deal with conversational questions both in spoken and text forms, and to explore the plausibility of providing more cues in spoken documents with systems in information gathering. To this end, instead of adopting automatically generated speech transcripts with highly noisy data, we propose a novel unified data distillation approach, DDNet, which directly fuse audio-text features to reduce the misalignment between automatic speech recognition hypotheses and the reference transcriptions. In addition, to evaluate the capacity of QA systems in a dialogue-style interaction, we assemble a Spoken Conversational Question Answering (Spoken-CoQA) dataset with more than 120k question-answer pairs. Experiments demonstrate that our proposed method achieves superior performance in spoken conversational question answering.
High-Throughput Bioinformatics Approaches to Understand Gene Expression Regulation in Head and Neck Tumors.

Cancer is defined as uncontrolled growth of abnormal cells bearing various molecular aberrations. With the aid of massively parallel DNA sequencing technology, we can now comprehensively characterize the genomic, epigenomic and transcriptomic landscapes of cancers. Subtypes of cancer are continually being uncovered, often by clustering expression profiles or determining driver mutations, the identification of which can be very important for prognosis and personalized treatment plans. The goal of this dissertation is to develop and apply bioinformatics algorithms to study subtypes of head and neck tumors. Using computational approaches, we both uncover new subtypes, and investigate the oncogenic mechanisms of driving molecular events in the tumor subtypes. My dissertation consists of three main chapters. In the first chapter, we present a software program (PePr) for conducting the differential binding analysis of replicated ChIP-seq data. PePr estimates the biological variation among samples and reports consistent changes across sample groups. We use PePr to characterize the difference in histone modifications between two human papillomavirus (HPV)-associated cancer cell lines and two non-HPV cell lines. In the second chapter, we identify two robust HPV(+) head and neck squamous cell carcinoma subtypes based on gene expression clustering. One subtype (HPV-KRT) shows more frequent genic viral integration and splicing of E6, and reduced viral oncogenic E6 activity. The HPV-KRT subtype also has more frequent copy number gains of chr3q, fewer losses of chr16q, and more PIK3CA mutations. These genomic changes could potentially lead to the differences in gene expression between the subtypes, including elevated immune response and mesenchymal differentiation in HPV-IMU subtype, and up-regulated keratinocyte differentiation and oxidation-reduction process
Flavonoids as fruit and vegetable intake biomarkers: Development, validation and application of flavonoid biomarkers in nutritional research

To gain better insight into the potential health effects of fruits and vegetables, reliable biomarkers of intake are needed. The main purpose of this study was to investigate the ability of flavonoid excretion in both 24-h and morning urine samples to reflect a low intake and moderate changes in fruit and vegetable consumption. Furthermore, the urinary excretions of 4-pyridoxic acid (4-PA) and potassium were investigated as other potential biomarkers of fruit and vegetable intake. The study was designed as a 5-d randomized, controlled crossover study. On d 1–3, the men (n 12) consumed a self-restricted flavonoid-free diet. On d 4, they were provided a strictly controlled diet containing no fruits or vegetables (basic diet). On d 5, they consumed the basic diet supplemented with 300 or 600 g of fruits and vegetables. The total excretion of flavonoids in 24-h urine samples increased linearly with increasing fruit and vegetable intakes (rs 0.86, P 1 10 ). The total excretion of flavonoids in morning urine also increased, but the association was weaker (rs 0.59, P 0.0001). Urinary 4-PA in 24-h and morning urine samples increased significantly only with the 600-g increase in fruit and vegetable intake, whereas the excretion of potassium in urine did not reflect the changes in fruit and vegetable intake. We conclude that the total excretion of flavonoids in 24-h urine may be used as a new biomarker for fruit and vegetable intake. J. Nutr. 134: 445–451, 2004.
Carprofen compromises the integrity and barrier function of the colonic mucosa of the dog

ix CHAPTER 1. BACKGROUND AND REVIEW OF LITERATURE . 1 1.1 Colon . 1 1.1.1 Macroscopic Anatomy . 1 1.1.2 Microscopic Anatomy . 3 1.1.3 Epithelium of the Mucosa . 4 1.1. 4 Trans-epithelial Ion Transport . 6 1.1. 5 Ussing Chamber System . 9 1.1. 6 Electrophysiology and Permeability in Function of Region of Colon . 12 1.2 Non Steroidal Anti-inflammatory Drugs and Colon . 13 1.2.1 Prostaglandin Synthesis . 13 1.2.2 Prostaglandins and Normal Gastrointestinal Physiology . 14 1.2.3 Prostaglandins and Gastrointestinal Inflammation . 15 1.2.4 Non Steroidal Anti-inflammatory Drugs and Normal Colon . 16 1.2. 5 Non Steroidal Anti-inflammatory Drugs and Inflamed Colon . 17 1.2. 6 Carprofen . 19 1.3 Summary and Hypotheses for Present Studies . 20 CHAPTER 2. MATERIALS AND METHODS . 22 2.1 Objective 1. Control Group . 22 2.1.1 Harvesting and Preparation of Sections of Colonic Mucosa . 22 2.1.2 Ussing Chamber Studies . 22 2.1.2.1 Mounting . 22 2.1.2.2 Solutions . 23 2.1.2.3 Electrical Measurements . 23 2.1.2.4 Mannitol . 24 2.1.3 Histologic Examination . 24 2.2 Objective 2. Carprofen Group . 26 2.2.1 Harvesting and Preparation of Sections of Colonic Mucosa . 26
Genetic Variability and Heritability for Growth and Yield in Cucumber (Cucumis sativus L.)

Quantification of variability is the most essential pre-breeding tool in any crop improvement programme. The present investigation was carried out to assess variability existing in twenty four diverse cucumber genotypes. Results revealed high phenotypic and genotypic coefficient of variation for yield per plant, fruit flesh thickness, number of fruits per plant, number of nodes per plant, number of branches per plant, average fruit weight, internode length and vine length. High heritability, coupled with high genetic advance as per cent mean, was recorded for all the characters studied except days to first female-flower opening, days to 50% flowering and days to first-fruit harvest, indicating a scope for improvement through selection.
Short-term effects of biochar amendment on soil microbial community in humid tropics

ABSTRACT Biochar is known to ameliorate soil fertility and improve crop production but information regarding soil microbiota responses on biochar amendment remains limited. The experiment was conducted to study the effect of biochars from palm kernel (pyrolysed at 400°C) and rice husk (gasified at 800°C) in a sandy loam Acrisol from Peninsular Malaysia. The soil was amended with palm kernel shell biochar (PK), rice husk biochar (RH), palm kernel biochar with fertilizer (FPK), rice husk biochar with fertilizer (FRH), fertilizer and control soil. Soil samples were taken during maize harvesting and were analysed for physico-chemical properties, microbial biomass, microbial abundance and microbial diversity. Increase in pH, moisture content, CEC, organic C, and labile C were recorded in all biochar amended soils. Microbial biomass C was 65% and 36% higher in RH and FRH, respectively, than control. Microbial biomass N was greatest in FPK and FRH with respective increment of 359% and 341% than control. β-glucosidase and xylanase activities were significantly increased in all biochar treated soils than control. A shift in microbial diversity was not detected. The biochar affects the microbial community by altering the soil environment and increasing labile active carbon sources in the short-term amendment.
Docking Sites on MEKs, MAP Kinase Phosphatases, and the Elk-1 Transcription Factor Compete for Binding to ERK2 and are Crucial for Enzymatic Activity

Mitogen-activated protein kinase (MAPK) cascades control gene expression patterns in response to extracellular stimuli. MAPK/ERK kinases (MEKs) activate MAPKs by phosphorylating them; activated MAPKs, in turn, phosphorylate target transcription factors, and are deactivated by phosphatases. One mechanism for maintaining signal specificity and efficiency is the interaction of MAPKs with their substrates and regulators through high-affinity docking sites. In this study, we show that peptides corresponding to the MAPK-docking sites of MEK1, MEK2, Ste7, Elk-1 and MKP-2 potently inhibit MEK2 phosphorylation of ERK2, ERK2 phosphorylation of Elk-1, and MKP-1 dephosphorylation of ERK2. Each peptide inhibited multiple reactions; for example, the MEK2 peptide inhibited not only MEK2, but also ERK2 and MKP-1. In addition, these docking site peptides inhibited MEK2-ERK2 binding. The MAPKdocking site of MEK1 also potently stimulated ERK2-mediated phosphorylation of a target site on the same peptide. Control peptides mutated in conserved basic and hydrophobic residues of the MAPK-docking site consensus lacked biological activity. We conclude that MEKs, MAP kinase phosphatases, and the Elk-1 transcription factor compete for binding to the same region of ERK2 via protein-protein interactions crucial for kinase/phosphatase activity.
A serological report on groundnut bud necrosis virus (GBNV) and tobacco streak virus (TSV) infecting groundnut and parthenium in Guntur and Prakasam districts of A.P.

fields during the survey in Guntur and Prakasam districts during Rabi 2013-14 alone cannot determine the presence of disease and its casual organism. To consolidate, these samples were subjected to a serological test DAC-ELISA. Out of 38 groundnut and parthenium samples of Guntur district tested, 22 samples were positive for GBNV while two were positive to TSV. Out of 24 samples of Prakasam district, 13 were positive to GBNV, two were positive to TSV alone and nine samples were positive to both viruses (mixed infections).
Geochemical constraints on bacteriophage infectivity in terrestrial environments

Lytic phages can be potent and selective inhibitors of microbial growth and can have profound impacts on microbiome composition and function. However, there is uncertainty about the biogeochemical conditions under which phage predation can proceed and modulate microbial ecosystem function, particularly in terrestrial systems. Ionic strength is known to be critical for infection of bacteria by many phages, but there is limited quantitative data on ion thresholds for phage infection that can be compared with environmental ion concentrations. Similarly, while carbon composition varies in terrestrial environments, we know little of which carbon sources favor or disfavor phage infection and how these higher order interactions impact microbiome function. Here, we measured the half-maximal effective concentrations (EC50) of 80 different inorganic ions for the infection of E. coli with two canonical dsDNA and ssRNA phages, T4 and MS2, respectively. We found that many alkaline earth metals and alkali metals enabled successful lytic infection but that the ionic strength thresholds varied for different ions between phages. Additionally, using a freshwater nitrate reducing microbiome, we found that the ability of lytic phage to influence nitrate reduction end-products was dependent on the carbon source as well as the ion concentration. For all phage:host pairs we tested, the ion EC50s for phage infection we measured exceed the ion concentrations found in many terrestrial freshwater systems. Thus, our findings support a model where the influence of phages on terrestrial microbial functional ecology is greatest in hot spots and hot moments such as metazoan guts, drought influenced soils, or biofilms where ion concentration is locally or transiently elevated and carbon source composition is of a sufficiently low complexity to enrich for a dominant phage susceptible population. Significance Viral-prokaryote dynamics greatly influence microbial ecology and the earth’s biogeochemical cycles. Thus, identifying the key environmental controls on phage predation is critical for predictive microbial ecology. Here we conduct laboratory experiments that implicate ionic strength and carbon composition as major controls on phage interactions with bacterial hosts in terrestrial microbiomes. We propose a model in which terrestrial phage predation is most favored in drought impacted soils and in higher ionic strength environments such as metazoan guts or between adjacent cells in biofilms.
Changes in quality and enzymes of Longkong (Aglaia dookkoo Griff.) fruit during storages as affected by maturation, package and methyl jasmonate treatment

The optimum harvesting period of longkong from 13 to 16 weeks of maturation were used to analyse the physiochemical quality changes. Fruit pericarp lightness (L*), yellowness (b*) decreased and redness (a*) increased throughout the maturation. Hue angle (H°) and chroma value (C*) was also decreased. The fruit weight (P<0.05) and diameter was increased throughout the maturation (P≥0.05). Fruit total soluble solids (TSS), pH, total sugar (TS), reducing sugar (RS) and ascorbic acid (AsA) content increased throughout the maturation. Titratable acidity (TA) were decreased at the end of maturation period (P<0.05). Fruit DPPH radical scavenging activity, FRAP activity and total phenolic content (TPC) was increased throughout the maturation. Superoxide dismutase (SOD), catalase (CAT) activity was slightly decreased at the end of maturation (16 week) (P<0.05). Peroxidase (POD) activity was increased at the end of maturation (16 week) (P<0.05). Polygalacturonase (PG) and pectin methylesterase (PME) activities were increased throughout the maturation (P<0.05). Pericarp total phenolic content (pericarp TPC) increased during maturation. The pericarp polyphenol oxidase (PPO) activity increased throughout the maturation (P<0.05). Pericarp peroxidase (POD) and phenylalanine ammonia lyase (PAL) activities were decreased at the end of maturation (16 week). Peel epidermal trichomes losses on the surface and parenchyma cell changes in the cross section were found during the increased stage of maturation. Longkong fruits stored in different OTR packages (PE1, PE2 and PE3) and temperatures (18°C and 25°C) were used to analyses the quality changes. Fruit pericarp L*, b*, H° and C* was continuously decreased, and a* value increased
MECHANISM AND RESEARCH PROGRESS OF ETHANOL FERMENTATION RELATED GENES pdc AND adhII INVOLVED IN FUEL ETHANOL PRODUCTION

ABSTRACT Fuel ethanol is important as one of the perfect energy sources in the replacement of fossil energy which is being used up. The use of biomass to produce fuel ethanol by fermentation are of interest. The product yield from fuel ethanol fermentation depends on high-level expression of the genes (pdc and adhII) which affect the rate and efficiency, key factors in the catabolic pathway of ethanol fermentation. In this paper, we review catabolic pathway of ethanol fermentation, the mechanism of actions of genes pdc and adhII and their applications in ethanol production and the research progress in the metabolic engineering of the genes pdc and adhII .
Investigating the Anti-viral Property of Verotoxin and its Receptor Gb3 in Preventing Primary HIV-1 Infection

Verotoxin produced by Enterohemorrhagic E. coli is comprised of a catalytic A subunit and a receptor Gb3 binding B subunit pentamer. VT causes protein synthesis inhibition by ribosomal inactivation in Gb3 positive cells via receptor mediated endocytosis and retrograde transport to the ER. We propose that verotoxin is a novel inhibitor for HIV-1 infection. Experiments conducted using VT treated Jurkat-C T cells and PHA/IL-2 activated human PBMCs reveal the anti-HIV-1 property of VT is receptor Gb3 independent since the catalytic A subunit alone is sufficient for inhibition. Possible mechanism of action involves mild inhibition of protein synthesis and cell proliferation. Recent findings in our lab suggest Gb3 is a natural resistance factor for HIV-1 infection, which was further investigated by selecting a Gb3 low subpopulation in THP-1 cells using VT treatment. Selected THP-1 cells were completely resistant to HIV-1 infection, however decreased surface CXCR4 expression may be a cause.
GOAT: GPU Outsourcing of Deep Learning Training With Asynchronous Probabilistic Integrity Verification Inside Trusted Execution Environment

Machine learning models based on Deep Neural Networks (DNNs) are increasingly deployed in a wide range of applications ranging from self-driving cars to COVID-19 treatment discovery. To support the computational power necessary to learn a DNN, cloud environments with dedicated hardware support have emerged as critical infrastructure. However, there are many integrity challenges associated with outsourcing computation. Various approaches have been developed to address these challenges, building on trusted execution environments (TEE). Yet, no existing approach scales up to support realistic integrity-preserving DNN model training for heavy workloads (deep architectures and millions of training examples) without sustaining a significant performance hit. To mitigate the time gap between pure TEE (full integrity) and pure GPU (no integrity), we combine random verification of selected computation steps with systematic adjustments of DNN hyper-parameters (e.g., a narrow gradient clipping range), hence limiting the attacker's ability to shift the model parameters significantly provided that the step is not selected for verification during its training phase. Experimental results show the new approach achieves 2X to 20X performance improvement over pure TEE based solution while guaranteeing a very high probability of integrity (e.g., 0.999) with respect to state-of-the-art DNN backdoor attacks.