Miracle-dz/UniFAR-FTUs huggingface dataset:
Physicochemical modifications and applications of carbon nano-onions for electrochemical energy storage

OF DISSERTATION PHYSICOCHEMICAL MODIFICATIONS AND APPLICATIONS OF CARBON NANO-ONIONS FOR ELECTROCHEMICAL ENERGY STORAGE Carbon nano-onions (CNOs), concentrically multilayered fullerenes, are prepared by several different methods. We are studying the properties of two specific CNOs: ACNOs and N-CNOs. A-CNOs are synthesized by underwater arc discharge, and N-CNOs are synthesized by high-temperature graphitization of commercial nanodiamond. In this study the synthesis of A-CNOs are optimized by designing an arc discharge aparatus to control the arc plasma. Moreover other synthesis parameters such as arc power, duty cycles, temperature, graphitic and metal impurities are controlled for optimum production of A-CNOs. Also, a very efficient purification method is developed to screen out ACNOs from carboneseous and metal impurities. In general, A-CNOs are larger than NCNOs (ca. 30 nm vs. 7 nm diameter). The high surface area, appropriate mesoporosity, high thermal stability and high electrical conductivity of CNOs make them a promising material for various applications. These hydrophobic materials are functionalized with organic groups on their outer layers to study their surface chemistry and to decorate with metal oxide nanoparticles. Both CNOs and CNO nanocomposites are investigated for application in electrochemical capacitors (ECs). The influences of pH, concentration and additives on the performance of the composites are studied. Electrochemical measurements demonstrate high specific capacitance and high cycling stability with high energy and power density of the composite materials in aqueous electrolyte.
Antioxidant Efficacy of Black Tea and Green Tea Equally Modulates Vasculogenic Factors in Preeclamptic Placental Trophoblast: A Comparative Study

Aim: Preeclampsia is hypertensive disorder of human pregnancy. Trophoblast, a prime cell of the placenta, is affected during preeclampsia due to the imbalance between oxidant and antioxidants resulting in aberrant cellular vascularization. Vasculogenesis is regulated by the endothelial nitric oxide synthase (eNOS), a potent vasodilator, regulating the expression of growth factors. Vascular endothelial growth factor (VEGF) is a prime regulator of vasculogenesis. Placental growth factor (PLGF) plays a crucial role in placental development during pregnancy. Synthetic drugs can hardly be used under complicated pregnancy. The requirement for herbal remedies renders essential regulatory mechanism to ensure adequate protection from preeclampsia. Methodology: In the current study, black tea and green tea were used to assess the stress markers (LPO and TAC) and vasculogenic factors (ADMA, eNOS, VEGF-C, and PLGF) in normotensive and preeclamptic placental trophoblast. Results: The increased expression of LPO, ADMA and decreased TAC, eNOS, VEGF-C, PLGF were observed in preeclamptic placental trophoblast. On tea incubation, vasculogenic proteins were significantly altered in preeclamptic placental trophoblast when compared with their respective subjects. Discussion: Our present study results reveal that protective effect of black tea is equal to the green tea. This may be due to the tea polyphenols produces a beneficiary effect in the case of the preeclamptic placenta. Conclusion: The present study concludes that tea with or without fermentation process has a significant impact on crucial vasculogenic factors. This effect can be suitably exploited to avoid further complications in preeclamptic pregnancy.
Enhancing prostaglandin-based estrus synchronization protocol for artificial insemination in water buffaloes.

Estrus synchronization (ES) in tandem with artificial insemination (AI) is a breeding technique which expands the use of male germplasm for genetic propagation. However, in buffalo reproduction in general, the difficulty in estrus detection does not permit the accurate timing of AI leading to low reproductive efficiency. The present study was conducted to evaluate pregnancy rates following four ES protocols aimed at improving reproductive efficiencies of water buffaloes. Post-partum water buffaloes (n=262) with corpus luteum, with body condition score of ≥3, and with ovary size of ≥2 cm were used in this study. The animals were randomly allocated into four treatment groups: T1, control - ES with single injection of prostaglandin (PGF2α, 25 mg i.m.) and inseminated after 3 days; T2 - the same as T1 except that the administration of gonadotropin releasing hormone (GnRH; 100 μg i.m.) was done a day before AI; T3 - same as T2 but with the administration of GnRH on the day of AI; and T4 - same as T3 but with the administration of human chorionic gonadotropin (hCG; 1500 IU i.m.) at AI. Determination and confirmation of pregnancy through rectal palpation was done at day 60 post AI. Results of the present study revealed a significant difference (P<0.05) between the control and the treatment groups; however, no significant difference was observed among the three groups of ovulatory hormones. These findings suggest that the administration of ovulatory hormones improved pregnancy rate in water buffaloes and the use of GnRH or hCG at the time of AI is advantageous and cost-effective approach to conduct AI activities in the field.
The effect of aerobic training with silymarin consumption on some cardiovascular risk factors in men with type 2 diabetes

DOI: 10.29252/jorjanibiomedj.8. 1.41 Abstract Background and objective: Type 2 diabetes (T2D) is a metabolic disease that leads to increased levels of lipids, therefore the present study aimed to investigate the effect of eight weeks of aerobic training(AT) with silymarin (S)consumption on lipid profile in men with type 2 diabetes. Methods: 60 middle-aged male volunteers were randomly divided into 4 groups, including: (1) control(C) + placebo, (2) AT + placebo, (3) S consumption and (4) AT+S consumption. The AT groups performed for eight weeks, three sessions per week and 20-45 minutes per session at an intensity of 60 to 85% of the reserve heart rate, and the S groups of consumed 140 mg / kg of S daily (in two meals). Serum levels of Low Density Lipoprotein (LDL), High Density Lipoprotein (HDL), Cholesterol (CHO), and Triglyceride (TG) were measured before and after the test. Data were analyzed using one-way ANOVA and Bonferroni’s test, and P value less than 0.05 was considered significant. Results: AT reduced serum levels of LDL, CHO, TG and increased HDL in men with T2D(P ≥ 0.05). Consumption of S reduced LDL, CHO, TG and increased HDL in men with T2D(P ≥ 0.05). AT and S consumption reduced LDL, CHO, TG and increased HDL; also, decrease in LDL, CHO, TG and increase in HDL in the AT and S consumption group was more favorable than the effect of S alone (P ≥ 0.05). Conclusion: It seems that AT and S consumption simultaneously have interactive effects on reducing LDL, CHO, TG and increasing HDL in men with T2D.
BioSAILs: versatile workflow management for high-throughput data analysis

Motivation High-throughput analysis in the current era of systems biology encompasses a range of analysis workflows for different applications, such as transcriptomics, epigenetics, variant discovery, de novo genome assembly, etc. Many research institutes house a genomics core facility that is responsible for generating high-throughput sequencing data and often includes a core bioinformatics team that carries out data analysis. Core teams must both keep track of data and maintain numerous software packages and databases – which must be scalable according to ever-changing research needs – and they must allocate computational resources to them. Typical data analysis pipelines involve multiple software packages and require the ability to install, execute, and maintain software stacks on a variety of hardware/operating system configurations, including high-performance computing (HPC) facilities, stand-alone servers, and Cloud services. At the same time, individual researchers need to analyze their data and share their analysis steps with collaborators. Having to rely on ad hoc scripts and rigid internally developed pipelines is inefficient, difficult to track and maintain, and ultimately, limits the ability to adapt and evolve as research methods progress. Results Here, we present BioSAILs (Bioinformatics Standardized Analysis Information Layers), a scientific workflow management system (WMS) developed by the Core Bioinformatics team at NYU Abu Dhabi. BioSAILs comprises two central components, BioX command and HPCRunner command, supported by BioStacks software stacks. BioX structures executable workflows that may be either run directly on a desktop or lab server, or submitted by HPCRunner to HPC infrastructure or the Cloud. BioSAILs is supported by a range of pre-configured, customizable BioStacks software stacks for various applications (e.g. RNA-seq, de novo genome/transcriptome assembly, variant discovery, etc.) Software stacks are built using Conda and BioConda (6), have been pre-packaged into modules using EasyBuild, and can be deployed with or without BioSAILs. Within the BioSAILs WMS, users can also invoke commands that take advantage of containerized software in Docker (10) and Singularity (8). Finally, the BioSAILs web resource provides documentation, blog posts related to various BioSAILs analysis tasks, forums, knowledge base & FAQs, as well as an interactive web-based workflow editor/creator. BioSAILs is production-level software that has been in use as the main WMS at NYU Abu Dhabi for the past 2 years and is continuously developed and maintained by the core bioinformatics team. Availability BioSAILs is open source software, available under the GNU license. Online documentation, support and guides can be found at biosails.abudhabi. nyu.edu. The public Github project is available at Github – BioSAILs. HPC-Runner and BioX-Workflow can be installed through Conda using the BioConda channel.
icaA/D Genes and Biofilm Formation of Methicillin-Resistant Staphylococcus aureus in Dr. Soetomo Hospital, Surabaya

Methicillin-resistant Staphylococcus aureus (MRSA) is a global health concern. One of the factors causing hospital infection is related to the ability of MRSA bacteria to form biofilms. Polysaccharide intercellular adhesin (PIA), encoded by ica gene, have an important role in S. aureus intracellular accumulation and aggregation. The aims of this study was to analyze the relationship between icaA, icaD genes and biofilm production in MRSA carrier and clinical isolate in Dr. Soetomo Hospital Surabaya. This study was an observational study using cross sectional approach. The sample was 47 MRSA isolates is as follow 28 isolates from carrier and 19 were clinical isolates. All of MRSA isolates carried mecA gene. PCR was performed to detect icaA and icaD genes. Biofilm formation was detected using microtiter plate assay (MTP). icaA gene was detected in all isolates whereas icaD gene in 96,4% carrier isolates and all (100%) of clinical isolates. Positive MTP results showed in all (100%) of carrier isolates and 57,9% of clinical isolates. Statistic result was significantly different in biofilm formation between carrier and clinical MRSA isolates. The proportion of positive biofilm formation in isolate with positive icaA/D genes was 82.6%. There was not any association between icaA and icaD gene with biofilm production.
SapM mutation to improve the BCG vaccine: genomic, transcriptomic and preclinical safety characterization

The Mycobacterium bovis Bacille Calmette Guérin (BCG) vaccine shows variable efficacy in protection against adult tuberculosis (TB). Earlier, we have described a BCG mutant vaccine with a transposon insertion in the gene coding for the secreted acid phosphatase SapM, which led to enhanced long-term survival of vaccinated mice challenged with TB infection. To facilitate development of this mutation as part of a future improved live attenuated TB vaccine, we have now characterized the genome and transcriptome of this sapM::Tn mutant versus parental BCG Pasteur. Furthermore, we show that the sapM::Tn mutant had an equal low pathogenicity as WT BCG upon intravenous administration to immunocompromised SCID mice, passing this important safety test. Subsequently, we investigated the clearance of this improved vaccine strain following vaccination and found a more effective innate immune control over the sapM::Tn vaccine bacteria as compared to WT BCG. This leads to a fast contraction of IFNγ producing Th1 and Tc1 cells after sapM::Tn BCG vaccination. These findings corroborate that a live attenuated vaccine that affords improved long-term survival upon TB infection can be obtained by a mutation that further attenuates BCG. These findings suggest that an analysis of the effectiveness of innate immune control of the vaccine bacteria could be instructive also for other live attenuated TB vaccines that are currently under development, and encourage further studies of SapM mutation as a strategy in developing a more protective live attenuated TB vaccine.
A Molecular Dynamics Study to Assess the Positive Ion Distribution and the Effects of Protonation on the N-terminus Region of a Xylanase

Xylanase enzyme families play an important role in many industries due to its ability to digest the hemicellulose within plant cell walls. Developing the enzyme that can withstand a highly acidic environment in a stomach requires an extended information in molecular scale for further protein engineering. In this study, an atomistic molecular dynamics simulation was performed to assess the positive ion distribution pattern on the N-terminus region of a Xylanase enzyme molecule. Then, another series of simulations were performed for the enzyme protonated at the aspartate residues 11 and/or 32 identified by the previous calculation. Conformational analysis showed that ASP32 protonation caused a significant disruption at the N-terminus region, as the nearby arginine residue 31 (ARG31) became free from the Coulomb interaction with the negatively charged ASP32 sidechain and cause the N-terminus region to misfold.
De novo mutations across 1,465 diverse genomes reveal novel mutational insights and reductions in the Amish founder population

de novo Mutations (DNMs), or mutations that appear in an individual despite not being seen in their parents, are an important source of genetic variation whose impact is relevant to studies of human evolution, genetics, and disease. Utilizing high-coverage whole genome sequencing data as part of the Trans-Omics for Precision Medicine (TOPMed) program, we directly estimate and analyze DNM counts, rates, and spectra from 1,465 trios across an array of diverse human populations. Using the resulting call set of 86,865 single nucleotide DNMs, we find a significant positive correlation between local recombination rate and local DNM rate, which together can explain up to 35.5% of the genome-wide variation in population level rare genetic variation from 41K unrelated TOPMed samples. While genome-wide heterozygosity does correlate weakly with DNM count, we do not find significant differences in DNM rate between individuals of European, African, and Latino ancestry, nor across ancestrally distinct segments within admixed individuals. However, interestingly, we do find significantly fewer DNMs in Amish individuals compared with other Europeans, even after accounting for parental age and sequencing center. Specifically, we find significant reductions in the number of T→C mutations in the Amish, which seems to underpin their overall reduction in DNMs. Finally, we calculate near-zero estimates of narrow sense heritability (h2), which suggest that variation in DNM rate is significantly shaped by non-additive genetic effects and/or the environment, and that a less mutagenic environment may be responsible for the reduced DNM rate in the Amish. Significance Here we provide one of the largest and most diverse human de novo mutation (DNM) call sets to date, and use it to quantify the genome-wide relationship between local mutation rate and population-level rare genetic variation. While we demonstrate that the human single nucleotide mutation rate is similar across numerous human ancestries and populations, we also discover a reduced mutation rate in the Amish founder population, which shows that mutation rates can shift rapidly. Finally, we find that variation in mutation rates is not heritable, which suggests that the environment may influence mutation rates more significantly than previously realized.
The effects of omega-3 polyunsaturated fatty acids on AMPK activation and lipid metabolism in skeletal muscle

The Effects of Omega-3 Polyunsaturated Fatty Acids on AMPK Activation and Lipid Metabolism in Skeletal Muscle Myra Woodworth-Hobbs Intramyocellular lipid accumulation and low lipid oxidative capacity contribute to the formation of insulin resistance, but omega-3 polyunsaturated fatty acids (n-3 PUFA) are shown to attenuate insulin resistance caused by high levels of saturated fats. The AMP-activated protein kinase (AMPK) promotes lipid oxidation and oxidative gene expression, highlighting its possible role in promoting insulin sensitivity by reducing lipid content and improving oxidative capacity. This study evaluated the effects of n-3 PUFA on the AMPK pathway and alterations to lipid content, oxidative markers, and insulin signaling proteins in a muscle cell culture model, with the hypothesis that n-3 PUFA would attenuate the saturated fatty acid-induced increase in intramyocellular lipids and detriments to the AMPK pathway, oxidative markers, and insulin signaling. The findings confirm that n-3 PUFA both attenuate saturated fatty acid-induced increases in intramyocellular lipid content and normalize insulin signaling and oxidative metabolic markers, though independently of the AMPK signaling pathway.
Ovitrap survey and serotype identification of dengue virus on Aedes sp mosquito in Potorono, Banguntapan, Bantul, Indonesia

Dengue fever is caused by DENV transmitted by Aedes sp. Ovitrap is used to survey the density of Aedes sp population. The aim of the study was to survey the adult p of Aedes sp and to identify DENV serotype. Ovitraps were used to collect the eggs of Aedes sp in indoor and outdoor of randomly selected houses. Total of 100 ovitraps was provided in 4 areas, 95 ovitraps were collected after nine days. Dengue virus serotypes were determined by RT-PCR. Ovitrap index in RT 7, RT 13, RT 1, and RT 3 were 42,9%, 64%, 54.2%, and 20%, respectively. The results of RT-PCR in 4 areas showed negative DENV 1-4. Ovitrap index in 4 areas of Potorono, Banguntapan, Bantul is high with the most abundant mosquitoes was Aedes aegypti. Surveillance of adult Aedes sp mosquitos is necessary for vector management control of DENV transmission.
Use of Organo-Mineral Fertilizers in Grain Sorghum as Reverse Logistics of Organic Residues

Organo-mineral fertilizers are an opportunity for technological innovation, because allow the correct disposal of waste from various agroindustrial sectors, which is a global problem, in order to add value to the by-product generated, as prioritized in reverse logistics. In this sense, the objective of this work was to evaluate the effect of organic matter sources on the composition of organo-mineral fertilizers in relation to the exclusive use of mineral fertilizers in cultivation of grain sorghum. The experiment was carried out at the Experimental Farm of the Federal Institute of the Triângulo Mineiro, located in the municipality of Campina Verde, State of Minas Gerais, Brazil. The experimental design was a randomized block with eight treatments and four replications arranged in a 4 × 2 + 2 factorial scheme, corresponding to: four levels of organo-mineral fertilizers (70, 100, 130 and 160% of the recommended dose of phosphorus), two sources of organo-mineral fertilizers (sewage sludge and filter cake), and two controls (without and with recommended mineral fertilization). The evaluations were: height of stem, number of leaves and stem diameter at 30, 60, and 90 days after sowing (DAS); total plant height; dry mass of plant shoot at 90 DAS, in vitro digestibility of organic matter at 90 DAS; the relationship of leaf area/ leaf and leaf area/ plant at 90 DAS. All parameters obtained a significant effect for the levels of organo-mineral fertilizer, independent of organic source, except to number of leaves and stem diameter. However, the relationship between the two organic sources was not significant just to plant height at 60 DAS. Interaction between fertilizer levels and organic source occurred to plant height at 90 DAS, dry mass per plant at 90 DAS and in vitro digestibility of organic matter. There was good adjustment in the quadratic regression equation for sorghum growth.
Development of a single uredinium inoculation method for Puccinia kuehnii, the causal agent of sugarcane orange rust

ABSTRACT The use of resistant varieties is the ideal method to control rusts. Nevertheless, knowing the pathogen’s diversity is fundamental to the success of this measure. Diversity can be analyzed phenotypically and/or genotypically. For phenotypic diversity, the reaction of genotypes is assessed by means of inoculations of the pathogen generally obtained from several uredinia. One handicap of this technique is its impossibility to detect diversity among these uredinia, assuming that they are all homogenous. Therefore, the aim of the present study was to develop a single uredinium technique for Puccinia kuehnii to be used in studies of rust diversity in sugarcane. The comparison between the two inoculation methods was done by employing urediniospores from SP89-1115 on the varieties SP89-1115 (susceptible) and RB975201 (resistant). The adopted design was completely randomized with five and seven replicates, respectively, examining incubation, latency, disease score, and injured area at 14 and 21 days. The two inoculation techniques were significantly equal for the susceptible variety, considering all evaluated parameters. For the resistant genotype, a significant difference was identified in the injured area and such difference did not interfere in the classification of the reaction of the material since values were below 1%. The single uredinium technique developed in this study showed to be reliable since the genotypic profile of the inoculated fungus was similar to that of pathogens from the produced lesions.
Partial sequence characterization and ontogenetic expression of genes involved in lipid metabolism in the tropical gar (
 Atractosteus tropicus
 )

Laboratorio de Acuicultura Tropical, DACBIOL‐UJAT, Villahermosa, Mexico Laboratorio de Investigación Bases Bioquímicas y Moleculares de Patologías Metabólicas e Infecciosas, DAMC‐UJAT, Ranchería Sur Cuarta Sección, Comalcalco, Mexico Laboratorio de Fisiología Comparada y Genómica Funcional, Centro de Investigaciones Biológicas del Noroeste, Instituto Politécnico Nacional 195, La Paz, Mexico Facultad de Ciencias Marinas, Universidad Autónoma de Baja California (UABC), Ensenada, Mexico Consejo Nacional de Ciencia y Tecnología, Ciudad de México, Mexico
Incidence and ultramicroscopic characterization of Cerotelium fici (castagne) rust in Ficus carica L.

The aim of the research was to identify the emerging rust disease in fig cultivation. In commercial orchards in the Western Ghats of Tamil Nadu, India, trees infected with rust exhibited reddish-brown angular leaf spots on their upper surfaces while their lower leaf surfaces contained numerous orange to reddish, rust pustules. An intensive survey was conducted to determine the incidence and severity of rust in fig orchards of the different districts of the Western Ghats and found that the incidence was very severe (100 %) in Pannaikadu, Dindigul district. To confirm the pathogen and its infection module, scanning electron microscopy was used to analyze these rust pustules and their anatomy. Based on the microscopy study, the subjected pathogen was identified as Cerotelium fici, this is the first detailed report of C. fici infection on fig plants in India.