Miracle-dz/UniFAR-FTUs huggingface dataset:
Soil microorganisms as controllers of atmospheric trace gases (H2, CO, CH4, OCS, N2O, and NO)

Production and consumption processes in soils contribute to the global cycles of many trace gases (CH4, CO, OCS, H2, N2O, and NO) that are relevant for atmospheric chemistry and climate. Soil microbial processes contribute substantially to the budgets of atmospheric trace gases. The flux of trace gases between soil and atmosphere is usually the result of simultaneously operating production and consumption processes in soil: The relevant processes are not yet proven with absolute certainty, but the following are likely for trace gas consumption: H2 oxidation by abiontic soil enzymes; CO cooxidation by the ammonium monooxygenase of nitrifying bacteria; CH4 oxidation by unknown methanotrophic bacteria that utilize CH4 for growth; OCS hydrolysis by bacteria containing carbonic anhydrase; N2O reduction to N2 by denitrifying bacteria; NO consumption by either reduction to N2O in denitrifiers or oxidation to nitrate in heterotrophic bacteria. Wetland soils, in contrast to upland soils are generally anoxic and thus support the production of trace gases (H2, CO, CH4, N2O, and NO) by anaerobic bacteria such as fermenters, methanogens, acetogens, sulfate reducers, and denitrifiers. Methane is the dominant gaseous product of anaerobic degradation of organic matter and is released into the atmosphere, whereas the other trace gases are only intermediates, which are mostly cycled within the anoxic habitat. A significant percentage of the produced methane is oxidized by methanotrophic bacteria at anoxic-oxic interfaces such as the soil surface and the root surface of aquatic plants that serve as conduits for O2 transport into and CH4 transport out of the wetland soils. The dominant production processes in upland soils are different from those in wetland soils and include H2 production by biological N2 fixation, CO production by chemical decomposition of soil organic matter, and NO and N2O production by nitrification and denitrification. The processes responsible for CH4 production in upland soils are completely unclear, as are the OCS production processes in general. A problem for future research is the attribution of trace gas metabolic processes not only to functional groups of microorganisms but also to particular taxa. Thus, it is completely unclear how important microbial diversity is for the control of trace gas flux at the ecosystem level. However, different microbial communities may be part of the reason for differences in trace gas metabolism, e.g., effects of nitrogen fertilizers on CH4 uptake by soil; decrease of CH4 production with decreasing temperature; or different rates and modes of NO and N2O production in different soils and under different conditions.
Maintenance of the Rumen Microbial Population in Continuous Culture

The design and use of an apparatus for continuous in vitro cultivation of the mixed bovine rumen microbial population are described. Data relative to the concentrations and proportions of volatile fatty acids produced, methanogenesis, carbon dioxide production, and survival of bacteria and protozoa indicated that an essentially normal in vivo fermentation pattern was maintained in vitro for experimental periods of from 3 to 10 days. The continuous cultures were responsive to major changes in type of feed intake. A change from grain to hay resulted in increased acetate and decreased propionate production, whereas decreased acetate and increased propionate resulted when feed intake was changed from hay to grain. Methanogenesis, volatile fatty acid production, and the numbers of microorganisms in the cultures were proportional to the amount of feed materials added up to levels calculated to approximate the in vivo maintenance requirement of the adult bovine.
Transcriptional control of delta-crystallin gene expression in the chicken embryo lens: demonstration by a new method for measuring mRNA metabolism

Crystallins are proteins that accumulate to very high concentrations in the fiber cells of the lens of the eye. Crystallins are responsible for the transparency and high refractive index that are essential for lens function. In the chicken embryo, delta-crystallin accounts for more than 70% of the newly synthesized lens proteins. We used density labeling and gene-specific polymerase chain reaction (PCR) to determine the mechanism regulating the expression of the two very similar delta-crystallin genes. Newly synthesized RNA was separated from preexisting RNA by incubating the lenses with 15N- and 13C-labeled ribonucleosides and then separating newly synthesized, density-labeled RNA from the bulk of light RNA by equilibrium density centrifugation in NaI-KI gradients. The relative abundances of the two crystallin mRNAs in the separated fractions were then determined by PCR. This method permitted the quantitation of newly synthesized processed and unprocessed delta-crystallin mRNAs. Additional studies used intron- and gene-specific PCR primers to determine the relative expression of the two delta-crystallin genes in processed RNA and unprocessed RNA extracted from different regions of the embryonic lens. Results of these tests indicated that the differential expression of the delta-crystallin genes was regulated primarily at the level of transcription. This outcome was not expected on the basis of the results of previous studies, which used in vitro transcription and transfection methods to evaluate the relative strengths of delta-crystallin promoter and enhancer sequences. Our data suggest that the cultured cells used in these earlier studies may not have provided an accurate view of delta-crystallin regulation in the intact lens.
Sulfate-reducing bacteria in anaerobic bioprocesses: basic properties of pure isolates, molecular quantification, and controlling strategies

ABSTRACT Anaerobic bioprocesses of wastewater, agricultural waste, or excess sludge are desirable as these provide the prospect of energy recovery via methane gas generated. However, hydrogen sulfide (H2S) generated from reduction of sulfate by sulfate-reducing bacteria (SRBs) during the process is inhibitory to the methane-producing bacteria (MPBs); meanwhile the SRBs and MPBs also compete for utilization of a key substrate in methanogenesis, volatile fatty acids. Therefore, it is quite important to mitigate the adverse impacts of SRBs on methanogenesis. The main objective of this review is to find potential controlling strategies for SRBs. With this in mind, properties of isolated pure SRBs from different sources were firstly summarized, in which 45 isolated pure SRBs belonging to seven phylogenetic lineages that can grow under versatile environments were included; then the state of the art on molecular quantification of SRBs through quantitative polymerase chain reaction was presented, in which related studies focusing on anaerobic bioprocesses were collated. Finally, potential effective controlling strategies of SRBs were outlined and discussed, which include enhancement/inhibition of H2S production as well as onsite elimination of H2S formed.
Recognize Arabic Handwritten using CNN Model

One of the most challenges that face machine learning is handwritten recognition, especially Arabic scripts, because many styles found for Arabic font. In this paper, an investigation model is proposed to make recognition for Arabic handwritten scripts utilizing Convolutional Neural Network (CNN), with multi layers of Normalization and Regularization to reduce training time and increase overall accuracy, with validation accuracy 98% for Kaggle dataset for Arabic handwritten characters and digits using Python.
Both products of the fosB gene, FosB and its short form, FosB/SF, are transcriptional activators in fibroblasts

We demonstrate that a member of the fos family, the fosB gene, gives rise to two transcripts by alternative splicing of exon 4, generating two proteins, FosB of 338 amino acids and a short form, FosB/SF, which contains the DNA binding and dimerization domains but not the 101 amino acids of the C terminus. FosB/SF activates an AP-1-chloramphenicol acetyltransferase construct in NIH 3T3 cells, as determined by transient and stable transfections, although more weakly than does FosB. In contrast to FosB, FosB/SF has lost its ability to repress the dyad symmetry element of the c-fos gene. FosB/SF when expressed in excess to FosB can downmodulate the activity of FosB. Constitutive expression of high levels of FosB/SF in NIH 3T3 cells has no significant inhibitory effect in the induction of cell proliferation or cell cycle progression, indicating that FosB/SF is not a negative regulator of cell growth. This conclusion is further confirmed by the observation that the majority of the Jun molecules are complexed with FosB/SF in the FosB/SF-overexpressing cells.
The Saccharomyces cerevisiae Cdc68 transcription activator is antagonized by San1, a protein implicated in transcriptional silencing

The CDC68 gene (also called SPT16) encodes a transcription factor for the expression of a diverse set of genes in the budding yeast Saccharomyces cerevisiae. To identify other proteins that are functionally related to the Cdc68 protein, we searched for genetic suppressors of a cdc68 mutation. Four suppressor genes in which mutations reverse the temperature sensitivity imposed by the cdc68-1 mutation were found. We show here that one of the suppressor genes is the previously reported SAN1 gene; san1 mutations were originally identified as suppressors of a sir4 mutation, implicated in the chromatin-mediated transcriptional silencing of the two mating-type loci HML and HMR. Each san1 mutation, including a san1 null allele, reversed all aspects of the cdc68 mutant phenotype. Conversely, increased copy number of the wild-type SAN1 gene lowered the restrictive temperature for the cdc68-1 mutation. Our findings suggest that the San1 protein antagonizes the transcriptional activator function of the Cdc68 protein. The identification of san1 mutations as suppressors of cdc68 mutations suggests a role for Cdc68 in chromatin structure.
Synthesis and mesomorphism behaviour of chalcones and pyrazoles type compounds as photo-luminescent materials

ABSTRACT The following organic and organic–inorganic hybrid compounds were prepared as photo-luminescent materials following efficient and practical synthetic methods: 1,3-bis[4-(n-alkoxy)phenyl]-2-propen-1-one (where, n-alkoxy: O(CH2)nH, n = 6,7,8,9 or 10); 3,5-bis[4-(n-alkoxy)phenyl]-1H-pyrazole (where, n-alkoxy: O(CH2)nH, n = 6,7,8,9 or 10) (in case of n = 7, a mixture of 3,5-bis(4-heptyloxyphenyl)-1H-pyrazole and 3,5-bis(4-heptyloxyphenyl)-4H-pyrazole was detected) and bis(3,5-bis [4-(n-alkoxy) phenyl]-1H-pyrazole) silver(I) nitrate (where, n-alkoxy: O(CH2)nH, n = 6,7,8,9 or 10). The prepared compounds have been characterised and their structures were elucidated depending upon (FTIR, UV-Vis, 1HNMR, 13CNMR, 2D 1H-1H-COSY, 2D 1H-13C-HSQC and mass spectra) in addition to molar conductivity measurements for silver(I) complexes. The mesomorphism behaviour of the prepared compounds was studied using polarised light optical microscopy and confirmed with differential scanning calorimetry and X-ray powder diffraction techniques. The studies showed that among all of these compounds only the pyrazole derivatives are liquid crystal materials. The luminescent properties of all the prepared compounds were also investigated which confirmed that all of these compounds are photo-luminescent in the crystalline solid state and in the mesophase. Graphical Abstract
Homogeneous Bacterial Aerosols Produced with a Spinning-Disc Generator

Aerosols composed of viable particles of a uniform size were produced with a commercial spinning-disc generator from aqueous suspensions of Bacillus subtilis var. niger spores containing various amounts of an inert material, dextran, to regulate aerosol particle size. Aerosols composed of single naked spores having an equivalent spherical diameter of 0.87 μm were produced from spore suspensions without dextran, whereas aerosols produced from suspensions containing 0.001, 0.01, 0.1, and 1% dextran had median diameters of 0.90, 1.04, 1.80, and 3.62 μm, respectively. Such aerosols, both homogeneous and viable, would be useful for calibrating air sampling devices, evaluating air filter systems, or for employment wherever aerosol behavior may be size-dependent.
Electrochemical Deposition of ZnO Buffer Layer for CIGS Solar Cell

In this study, ZnO thin films were deposited on ITO (Indium tin oxide) conductive glass by electrochemical deposition. The experiment's electrochemical deposition used zinc chloride (ZnCl2) electrolyte with current density of 0.01-0.15 amp, working voltage of 0.95-3 V, and deposition time of 30-120 s. The test chip was oxidized by thermal annealing treatment. The properties of ZnO films were analyzed by Field Emission Scanning Electron Microscopy (FESEM), X-ray diffraction (XRD), Ultraviolet-Visible Spectrophotometry (UV-VIS), and Hall Effect Analysis. The ZnO film with 0.03 amp, 1.55 V, and 120 s of deposition time had the best quality. Its transmittance was up to 91%, and its resistance was 1.79×104Ω/cm2.
Microbial flora of Pacific hake (Merluccius productus)

The commercial significance of hake has been recognized in recent years as a potential raw material for fish protein concentrate (FPC). Studies conducted on hake, however, are limited to the technological development of FPC (5), and little information is available on the microorganisms associated with this species. In this study, microbial flora of Pacific hake was examined, and the shift in microbial population during 5 C storage was determined. Fresh hake were received from a commercial vessel and to differentiate Acinetobacter from Moraxella by cytochrome oxidase or penicillin sensitivity, the former being oxidase-negative and resistant to 1 IU of penicillin. Acinetobacter was differentiated from Moraxella by its resistance to 3 IU of penicillin. All those resistant to 1 IU of penicillin were equally resistant to 3 IU, but the latter concentration more clearly differentiated the sensitive species. The microbial counts and the analyses of the flora of Pacific hake stored at 5 C are presented in
Agar Art: a CURE for the Microbiology Laboratory

We previously developed and assessed “The Art of Microbiology,” a course-based undergraduate research experience (CURE) which uses agar art to spur student experimentation, where we found student outcomes related to science persistence. However, these outcomes were not correlated with specific activities and gains were not reported from more than one class. ABSTRACT We previously developed and assessed “The Art of Microbiology,” a course-based undergraduate research experience (CURE) which uses agar art to spur student experimentation, where we found student outcomes related to science persistence. However, these outcomes were not correlated with specific activities and gains were not reported from more than one class. In this study, we explored which of the three major activities in this CURE—agar art, experimental design, or poster presentations—affected student engagement and outcomes associated with improved understanding of the nature of science (NOS). The Art of Microbiology was studied in three microbiology teaching laboratories: at a research university with either the CURE developer (18 students) or a CURE implementer (39 students) and at a community college with a CURE implementer (25 students). Our quasi-experimental mixed methods study used pre/post-NOS surveys and semi-structured class-wide interviews. Community college students had lower baseline NOS responses but had gains in NOS similar to research university students post-CURE. We surveyed research university students following each major activity using the Assessing Student Perspective of Engagement in Class Tool (ASPECT) survey but did not find a correlation between NOS and activity engagement. Of the three activities, we found the highest engagement with agar art, especially in the CURE developer class. Interviewed students in all classes described agar art as a fun, relevant, and low-stakes assignment. This work contributes to the evidence supporting agar art as a curricular tool, especially in ways that can add research to classrooms in and beyond the research university.
Plasma and floating potentials in magnetron discharges

This letter reports on great differences in values of the plasma Up and floating Ufl potentials in sputtering discharges generated by single and dual magnetrons. It is shown that (i) the differences in Up and Ufl result in strongly different properties of films sputtered by single and dual magnetrons at the same power delivered to the magnetron discharge, (ii) in the direct current single and dual magnetron discharges, the values of Up and Ufl strongly depend on the electric conductivity of the surface of the grounded deposition chamber, and (iii) a pulsed dual magnetron with a closed magnetic B field is the only one sputtering system, which enables us to sputter the films with fully reproducible properties.
Regulation of Predation by Prey Density: the Protozoan-Rhizobium Relationship

Tetramitus rostratus and strains of Hartmanella, Naegleria, and Vahlkampfia consumed large numbers of Rhizobium meliloti cells in a salt solution, but protozoan multiplication and the bacterial decline stopped when the prey density fell to about 106 to 107 cells/ml. At higher prey densities, the maximum numbers of Hartmanella sp. and Naegleria sp. were proportional to the quantity of R. meliloti initially provided to the amoebas. When supplemental rhizobia were supplied to Hartmanella sp. or Naegleria sp. after their active feeding had terminated, presumably because the remaining 106 or 107 bacteria/ml could not be captured, replication of the protozoa was initiated. The rate of elimination of rhizobia present in large populations was proportional to the initial abundance of Naegleria sp. , but the final numbers of amoebas and surviving R. meliloti cells were independent of initial numbers of predators. The surviving bacteria were not intrinsically resistant to attack because 98% of the survivors, when concentrated, were consumed. It is suggested that large populations of bacteria in nature may be reduced in size by predatory protozoa, but many of the prey cells will not be eliminated.
Inactivation of the Bactericidal Activity of Human Serum by Liquoid (Sodium Polyanetholsulfonate

Four serum-sensitive strains of Escherichia coli were exposed to 10, 20, and 50% fresh, heat-inactivated, and fresh human serum to which had been added Liquoid at a final concentration of 0.05, 0.025, 0.0125 and 0.006%. It was found that 50% fresh serum (in nutrient, Mueller-Hinton, thioglycolate, or Trypticase Soy Broth) killed more than 104 organisms/ml within 3 min, whereas 20 and 10% fresh serum required up to 20 and 40 min, respectively, to kill a comparable number of organisms. To neutralize the activity of 50% fresh serum, 0.0125% Liquoid had to be added, whereas an 0.006% final concentration of Liquoid was sufficient to antagonize the activity of 10 and 20% serum. However, when exposing extremely small bacterial inocula to fresh serum, at least 0.025% Liquoid was necessary to abolish the serum-bactericidal activity of 20 and 50% fresh serum. Liquoid had to be added to 50% fresh serum within seconds to prevent the killing of the majority of test organisms derived from small inocula. It is recommended that blood samples drawn from septicemic or bacteremic patients be aseptically added to a suitable broth which contains at least 0.025% Liquoid in order to improve the chances of isolating pathogens present in small numbers.
Antibiotic Disc Susceptibility Tests for Rapid Presumptive Identification of Gram-Negative Anaerobic Bacilli

A method for identification of gram-negative anaerobic bacilli is described. Based on differences in susceptibility to paper discs containing 10 μg of colistin, 60 μg of erythromycin, 1,000 μg of kanamycin, 1,000 μg of neomycin, 2 units of penicillin, and 15 μg of rifampin, these bacteria may be placed into five groups. Other tests such as colony morphology, production of pigment, growth in bile, esculin hydrolysis, and reaction on egg yolk-agar may be used for further identification. The susceptibility tests are rapid and simple to perform and are helpful in characterizing gram-negative anaerobic bacilli. They are not intended for use in predicting clinical effectiveness of the drugs utilized.
Enhancement of Mass Transfer Intensification for Essential Oil Release from Lavandula pubescence Using Integrated Ultrasonic-Microwave Technique and Enzymatic Pretreatment

This work was designed to utilize the integration of ultrasonic-microwave assisted preceded by enzymolysis pretreatment to enhance the extraction efficiency of essential oil (EO) from wild Lavandula pubescens (Lp). Cellulase (C-ase), hemicellulase (H-ase), and mixed enzymes (C-ase/H-ase) were used at 10 mg/100 mL of the liquid phase. Gas chromatography-mass spectrometry (GC-MS) system was used for chemical composition analyses of Lavandula pubescens essential oil (Lp-EO). C-ase pretreatment achieved the highest yield (0.50%) of EO and highest ratio of carvacrol (29.22%) as the main compound in comparison to other treatments. Changes in the morphological structure of Lp tissues were tracked using scanning electron microscopy (SEM). Free radical-scavenging activity was assessed using DPPH•-SA and ABTS•+-SA assays. The optimal extraction conditions were enzyme concentration of 14.82 mg/100 mL, sonication time of 38.18 min, and microwave power at 333 W. At these conditions, the maximum % yield, % DPPH•-SA, an.
Optical coherence tomography of lymphatic vessel endothelial hyaluronan receptors in vivo

Optical Coherence Tomography (OCT) imaging of living subjects offers millimeters depth of penetration into tissue while maintaining high spatial resolution. However, because most molecular biomarkers do not produce inherent OCT contrast signals, exogenous contrast agents must be employed to achieve molecular imaging. Here we demonstrate that microbeads (μBs) can be used as effective contrast agents to target cellular biomarkers in lymphatic vessels and can be detected by OCT using a phase variance algorithm. We applied this technique to image the molecular dynamics of lymphatic vessel endothelial hyaluronan receptor 1 (LYVE-1) in vivo, which showed significant down-regulation during tissue inflammation.
Biological Factors Influencing the Effectiveness of Wood Preservatives against Decay

The commonest wood preservatives are the natural toxicants that are mainly responsible for the varying amounts of decay resistance in untreated heartwood. There are volatile materials in some woods that are effective against fungi and green plants while they last (Sowder, 1929; Weintraub and Price, 1948), as well as water-soluble materials that favor fungi (Findlay, 1956). It is true that the correlation between decay resistance and the amount and toxicity of extractable material has not been good even within the same species (Scheffer et al., 1944), but this is also true for extracts from preservative-treated wood. The tree is therefore logically the first biological variable to consider. The differences between the most important tree species both in their natural decay resistance and in their ability to absorb artificial preservatives are fairly well known as a result of practical experience. Analysis of the differences within species to determine the contributions to natural resistance of such factors as age and size of tree, position in tree, and genetic differences between trees has been made particularly in the classical statistical studies by Scheffer et al. (1949) and Scheffer and Hopp (1949) on locust and white oak. Correspondingly thorough studies on variation wvithin species in relation to treatability have not been encountered. For use in boats and ships, the natural preservatives in the wood have continued to be more important than artificial preservatives. It is true that most of the practical interest in industry is undoubtedly in the factors that influence success of artificial preserva-