Miracle-dz/UniFAR-FTUs huggingface dataset:
Biodesulphurisation of dibenzothiophene in hydrophobic media by Rhodococcus sp. strain IGTS8

Rhodococcus sp. strain IGTS8 (ATCC 53968) is capable of removing organic sulphur from various organosulphur compounds such as dibenzothiophene (DBT). Since substrates for this process are invariably hydrophobic, parameters of the biodesulphurisation of DBT in hydrophobic systems were examined. Freeze-dried bacteria, stored for 3 months at -80°C with negligible loss of activity were used primarily as biocatalysts. The most efficacious order of ingredient addition was with oil and water (plus surfactant if used) mixed first and then freeze-dried bacteria added. Various oil/water ratios were examined. The minimum water requirement for desulphurisation was 1·25 cm3 g−1 dry weight. If the minimum water requirement was met, biodesulphurisation at an 90% oil/water (w/w) ratio was still 82% of the maximum at an 80% oil/water ratio. The surfactants, oleic diethanolamine and Triton N101, both stimulated biodesulphurisation in oil/water systems but not in 100% water. The desulphurisation of DBT in oil/water emulsions persisted for 8–16 h, but the rate rapidly declined after 3 h; biodesulphurisation in aqueous media stopped after 3–4 h. © 1997 SCI.
Chemo-enzymatic functionalization of gallic and vanillic acids: synthesis of bio-based epoxy resins prepolymers

The chemo-enzymatic epoxidation of allylated gallic and vanillic acids with lipase B from Candida antarctica and aqueous hydrogen peroxide in the presence of caprylic acid was investigated. The use of 1 molar eq of caprylic acid and 1.8–2 molar eq of H2O2 per allylic double bond led to a high degree of conversion to epoxides (89% yield for allylated gallic acid and 87% yield for allylated vanillic acid) comparatively to the hazardous peracid mCPBA (1.5–3.2 molar eq per double bond allowed 75–85% yield). The epoxidized products obtained could be used in the formulation of novel bio-based epoxy resins.
Developments in optical coherence microscopy

Optical Coherence Microscopy (OCM) utilizes a high NA microscope objective in the sample arm to achieve an axially and laterally high resolution OCT image. An increase in NA, however, leads to a dramatically decreased depth of focus (DOF), and hence shortens the imaging depth range so that high lateral resolution is maintained only within a small depth region around the focal plane. One solution to increase the depth of imaging while keeping a high lateral resolution is dynamic-focusing. Utilizing the voltage controlled refocus capability of a liquid lens, we have recently presented a solution for invariant high resolution imaging using the liquid lens embedded within a fixed optics hand-held custom microscope designed specifically for optical imaging systems using a broadband light source centered at 800 nm with a 120 nm bandwidth. Subsequently, we have developed a Gabor-Domain Optical Coherence Microscopy (GD-OCM) that utilizes the high speed imaging of spectral domain OCT, the high lateral resolution of OCM, and the ability of real time refocusing of our custom design variable focus objective. Finally, key developments in Phase-Resolved Doppler OCT (PR-DOCT) are key enablers to combine high-resolution structural imaging with functional imaging. In this paper we review achievements in GD-OCM and detail how portions of in-focus cross-sectional images can be extracted and fused to form an invariant lateral resolution image with multiple cross-sectional images acquired corresponding to a discrete refocusing step along depth enabled by the varifocal device. We demonstrate sub-cellular resolution imaging of an African frog tadpole (Xenopus Laevis) taken from a 500 μm × 500 μm cross-section as well as cellular imaging in in vivo skin. Finally, A novel dual-detection full-range Fourier-domain optical coherence tomography system was developed that provides 7 μm axial resolution (in air) at about 90 kHz axial scan rate for mirror-image phase resolved Doppler imaging in an African frog tadpole and an in vivo human finger.
A simple technique to convert sitting-drop vapor diffusion into hanging-drop vapor diffusion by solidifying the reservoir solution with agarose

A simple protocol to convert sitting-drop vapor-diffusion plating into a hanging-drop vapor-diffusion experiment in protein crystallization is reported. After making a sitting-drop plate, agarose solution was added to solidify the reservoir solution, and the plates were incubated upside down. Crystallization experiments with hen egg white lysozyme, thaumatin and glucose isomerase showed that the `upside-down sitting-drop' method could produce single crystals with all the benefits of the hanging-drop crystallization method.
Active particles production by pulsed nanosecond discharge in ambient air. Quenching of electronically excited states of nitrogen by O2 molecules and O(3P) atoms

oxygen molecules leads to the dissociation of O2. This conclusion is based on the comparison of calculated dynamics of atomic oxygen in air, excited by pulsed nanosecond discharge, with experimental data. In air plasma at high dissociation degree of oxygen molecules, relaxation of electronic energy of atoms and molecules in reactions with O atoms becomes extremely important. Active production of NO molecules and fast gas heating in the discharge plasma due to the
A highly generalized classifier for osteoporosis radiography based on multiscale fractal, lacunarity, and entropy distributions

Background: Osteoporosis is a common degenerative disease with high incidence among aging populations. However, in regular radiographic diagnostics, asymptomatic osteoporosis is often overlooked and does not include tests for bone mineral density or bone trabecular condition. Therefore, we proposed a highly generalized classifier for osteoporosis radiography based on the multiscale fractal, lacunarity, and entropy distributions. Methods: We collected a total of 104 radiographs (92 for training and 12 for testing) of lumbar spine L4 and divided them into three groups (normal, osteopenia, and osteoporosis). In parallel, 174 radiographs (116 for training and 58 for testing) of calcaneus from health and osteoporotic fracture groups were collected. The texture feature data of all the radiographs were pulled out and analyzed. The Davies–Bouldin index was applied to optimize hyperparameters of feature counting. Neighborhood component analysis was performed to reduce feature dimension and increase generalization. A support vector machine classifier was trained with only the most effective six features for each binary classification scenario. The accuracy and sensitivity performance were estimated by calculating the area under the curve. Results: Interpretable feature trends of osteoporotic pathological changes were depicted. On the spine test dataset, the accuracy and sensitivity of binary classifiers were 0.851 (95% CI: 0.730–0.922), 0.813 (95% CI: 0.718–0.878), and 0.936 (95% CI: 0.826–1) for osteoporosis diagnosis; 0.721 (95% CI: 0.578–0.824), 0.675 (95% CI: 0.563–0.772), and 0.774 (95% CI: 0.635–0.878) for osteopenia diagnosis; and 0.935 (95% CI: 0.830–0.968), 0.928 (95% CI: 0.863–0.963), and 0.910 (95% CI: 0.746–1) for osteoporosis diagnosis from osteopenia. On the calcaneus test dataset, they were 0.767 (95% CI: 0.629–0.879), 0.672 (95% CI: 0.545–0.793), and 0.790 (95% CI: 0.621–0.923) for osteoporosis diagnosis. Conclusion: This method showed the capacity of resisting disturbance on lateral spine radiographs and high generalization on the calcaneus dataset. Pixel-wise texture features not only helped to understand osteoporosis on radiographs better but also shed new light on computer-aided osteopenia and osteoporosis diagnosis.
Gold‐Catalyzed Conversion of Aryl‐ and Alkyl‐Substituted 1‐(o‐Aminophenyl)‐2‐propyn‐1‐ones to the Corresponding 2‐Substituted 4‐Quinolones

Gold-catalyzed cyclization of alkyl- or aryl-substituted 1-(o-aminophenyl)-2-propyn-1-ones to the corresponding 2-substituted 4-quinolones was studied with various gold salts and complexes. Screening of the different catalysts showed highest performance with cationic AuI species. In particular PPh3AuNTf2 complex was the most efficient catalyst. Relative to classic quinolone synthesis that requires harsh cyclocondensation conditions, the current method offers a mild and atom-economic alternative. Mechanistically, DFT studies at TPSS-D3/def2-TZVP level suggest that gold operates in an alkynophilic manner rather than through conjugative carbonyl activation.
Structure and dynamics of protein in the permeation and gating of potassium ion channels : identifying molecular determinants and developing coarse-grained approaches

Ion channels are transmembrane proteins which allow small ions to flow across the membrane downhill along the electrochemical gradient, with high effciency and selectivity over the different ion species, and which play crucial roles in a wide range of vital physiological functions. Research on the channels selective for potassium ions have attracted a great deal of attention over the past decade. This is because of the availability of three dimensional microscopical structures and because they provide a paradigm for the study of the complex superposition of the permeation of the ions and structural rearrangements which is responsible for the regulation of the current in ion channels. In the present work a thorough study of the strong coupling between permeation and the dynamics of the protein in the potassium ion channel KcsA is presented, based on Molecular Dynamics and Metadynamics calculations, which reveals the clear links between the function and the structure of the protein. The molecular determinants for the conformational changes of the pore region have been identified and described in details. The relationship between these rearrangements and the gating process known as "C-type inactivation", found in a variety of potassium ion channels, have been investigated and a mechanism has been proposed for the process. The knowledge acquired from these investigations is finally applied to unveil the driving forces and energetics associated with the permeation and selectivity properties of KcsA channel.
Ulosantoin, a potent insecticide from the sponge Ulosa ruetzleri

Ulosantoin (2), a phosphorylated hydantoin, has been isolated from organic soluble extracts of the sponge Ulosa ruetzleri and found to exhibit marked insecticidal activity against tobacco hornworm larvae and cockroaches. The structure was determined by X-ray diffraction analysis. A structurally related compound, dimethyl N 2 -creatininylphosphate (1), was also isolated from the sponge extracts, but was inactive in the insecticidal screens
Gaussian-3 theory using scaled energies

A modification of Guassian-3 (G3) theory using multiplicative scale factors, instead of the additive higher level correction, is presented. In this method, referred to as G3S, the correlation energy is scaled by five parameters and the Hartree–Fock energy by one parameter. The six parameters are fitted to the G2/97 test set of 299 energies and the resulting mean absolute deviation from experiment is 0.99 kcal/mol compared to 1.01 kcal/mol for G3 theory. The G3S method has the advantage compared to G3 theory in that it can be used for studying potential energy surfaces where the products and reactants have a different number of paired electrons. In addition, versions of the computationally less intensive G3(MP3) and G3(MP2) methods that use scaled energies are also presented. These methods, referred to as G3S(MP3) and G3S(MP2), have mean absolute deviations of 1.16 and 1.35 kcal/mol, respectively.
EFECTO DEL TIPO DE ANTICOAGULANTE UTILIZADO EN LA TOMA DE MUESTRAS, SOBRE LA DETERMINACIÓN DEL PERFIL DE ACILCARNITINAS EN SANGRE Y PLASMA

Background: the collection process for blood sampling is a very important factor that can influence the final results of some laboratory tests. The acylcarnitine determinations in blood are usually used for diagnosis and follow up of patients suffering certain inherited metabolic illnesses. Objective: this study analyzed the possible influence of the type of anticoagulant used in blood sampling on the acylcarnitine profile. Methodology: blood and plasma samples were collected using anticoagulants such as: lithium heparin, potassium EDTA, sodium fluoride-potassium oxalate, and sodium citrate. Samples were also collected without the use of anticoagulants. Acylcarnitine levels were assessed for each sample via tandem mass spectrometry. Results: no significant differences were found among the anticoagulant used. Conclusion: the type of anticoagulant has no effect on the acylcarnitine determination on blood or plasma. For this type of analysis any of the above mentioned anticoagulants can be * Universidad de Caldas, Laboratorio de Bioquimica Clinica y Patologia Molecular, Departamento de Ciencias Basicas de la Salud, Manizales, Colombia. E-mail: jose. osorio_@ucaldas.edu. co
Parametric, equilibrium, and kinetic studies on biosorption of diuron by Anabaena sphaerica and Scenedesmus obliquus

In this study, the bioremoval potential of diuron by the cyanobacterium, Anabaena sphaerica, and the green algae, Scenedesmus obliquus, was investigated under different experimental conditions, including pH, diuron concentrations, contact time, and biomass dosage. Approximately, <80% (40 mg/L) of the analyte was removed by 1 g/L of both species within 80 min at pH = 3. The equilibrium data were well fitted to Langmuir isotherm model, indicating a probable monolayer biosorption of diuron on the biomass surface. Biosorption kinetics was best described by pseudo‐first‐order kinetic model. The biosorption mechanism of diuron over the studied biosorbents was found to be controlled by the external mass transfer. © 2014 American Institute of Chemical Engineers Environ Prog, 34: 504–511, 2015
High aspect ratio sub-micron structuring of transparent materials using non-diffractive ultrafast laser beams : dynamics and interaction regimes

This thesis is focused on the controllability of laser-induced refractive index changes at sub-micron level over long dimensions i.e., with high aspect ratios and sections on the nanoscale. To this end, we explore non-diffractive zerothorder ultrafast Bessel beams and factors contributing to energy confinement beyond the diffraction limit. Laser processing of transparent materials using non-diffracting beams offers a strong advantage for high aspect ratio submicron structures inside the bulk in view of nanophotonics and nanouidics applications. We present the role of various focusing conditions and laser parameters on material modification in bulk fused silica and explore the different interaction regimes. This thesis tackles mostly the moderate focusing conditions as they offer a stable interaction regime backed up dispersion engineering over a large range of laser parameters. The laser pulse duration was found to be key in defining the type of laser induced refractive index or structural modification. For instance, machining using femtosecond laser pulses results in increased refractive index structures whereas picosecond laser pulses result in uniform void i.e., low index structures. To acquire better control over the laser energy deposition and precision, a range of physical mechanisms responsible for the laser induced damage in non-diffractive excitation conditions have been observed experimentally and further interrogated by simulations indicating a critical role of light scattering on carriers. Time-resolved pump-probe microscopy measurements with a sub-picosecond temporal and sub-micron spatial resolution allow access to the instantaneous excitation and relaxation dynamics. Dynamic optical transmission and phase contrast o_er complementary information of either electronic and glass matrix response. Primarily, ultrafast dynamics of free carriers was studied as the electron mediated energy transfer to the lattice is key to the subsequent material transformation. Role of instantaneous excitation at different laser pulse durations and energies is outlined. Then complete carrier dynamics is presented at different laser parameters. Particularly dynamics in conditions of positive refractive index structures and uniform voids is indicating two different paths of electronic relaxation and energy deposition: a fast defect mediated relaxation for positive index structures and slow thermomechanical relaxation for nanosize void structures. Finally, by correlating the results of time resolved studies, simulations and post-irradiated photoluminescence results, we formulate potential formation scenarios for the positive refractive index and low index or uniform void structures
Localization of Au Nanoclusters on Layered Double Hydroxides Nanosheets: Confinement‐Induced Emission Enhancement and Temperature‐Responsive Luminescence

Gold nanoclusters (Au NCs) stand for a new type of fluorescent nanomaterials with outstanding optical properties due to their discrete electronic energy and direct electron transition. However, relative low quantum yield (QY) of Au NCs in aqueous or solid state has limited their photofunctional applications. To improve the fluorescent performances of Au NCs and find an effective approach for the fabrication of Au NCs‐based films, in this work, Au NCs are localized onto 2D layered double hydroxides (LDHs) nanosheets via a layer‐by‐layer assembly process; the as‐fabricated (Au NCs/LDH)n ultrathin films (UTFs) show an ordered and dense immobilization of Au NCs. The localization and confinement effects imposed by LDH nanosheets induce significantly increased emissive Au(I) units as confirmed by X‐ray photoelectron spectroscopy and periodic density functional theoretical simulation, which further results in promoted QY (from 2.69% to 14.11%) and prolonged fluorescence lifetime (from 1.84 µs to 14.67 µs). Moreover, the ordered (Au NCs/LDH)n UTFs exhibit well‐defined temperature‐dependent photoluminescence (PL) and electrochemiluminescence (ECL) responses. Therefore, this work supplies a facile strategy to achieve the immobilization of Au NCs and obtain Au NCs‐based thin films with high luminescent properties, which have potential applications in PL and ECL temperature sensors.
Invasive tunicate (Ascidiacea) metabolic and filtration rates in comparison to native tunicate and bivalve species

Several invasive species of tunicates (Ascidiacea) have become cosmopolitan and widely distributed in coastal areas worldwide over the past few decades. These nonindigenous tunicates have consequently caused fouling problems in aquaculture and marine harbors. The goal of our project was to enrich the understanding of how invasive tunicates interact with other organisms in the ecosystem. Two species of invasive tunicates (Didemnum vexillum and Botrylloides violaceus) and one species of native tunicate (Aplidium glabrum) were evaluated for their metabolic rates. The filtration rates for native blue mussels (Mytilus edulis) and invasive tunicates (Diplosoma listerianum) were determined. D. vexillum regenerated NH4 at a faster rate than A. glabrum and B. violaceus. Both tunicates and blue mussels were feeding on phytoplankton as their major food source, although the size of particles utilized by different organisms was not examined in this study. Invasive tunicates were strongly competing with mussels to filter feed, but were not inhibiting mussel’s filtration rate.
Consortium diversity of a sulfate‐reducing biofilm developed at acidic pH influent conditions in a down‐flow fluidized bed reactor

Sulfate reduction is an appropriate approach for the treatment of effluents with sulfate and dissolved metals. In sulfate‐reducing reactors, acetate may largely contribute to the residual organic matter, because not all sulfate reducers are able to couple the oxidation of acetate to the reduction of sulfate, limiting the treatment efficiency. In this study, we investigated the diversity of a bacterial community in the biofilm of a laboratory scale down‐flow fluidized bed reactor, which was developed under sulfidogenic conditions at an influent pH between 4 and 6. The sequence analysis of the microbial community showed that the 16S rRNA gene sequence of almost 50% of the clones had a high similarity with Anaerolineaceae. At second place, 33% of the 16S rRNA phylotypes were affiliated with the sulfate‐reducing bacteria Desulfobacca acetoxidans and Desulfatirhabdium butyrativorans, suggesting that acetotrophic sulfate reduction was occurring in the system. The remaining bacterial phylotypes were related to fermenting bacteria found at the advanced stage of reactor operation. The results indicate that the acetotrophic sulfate‐reducing bacteria were able to remain within the biofilm, which is a significant result because few natural consortia harbor complete oxidizing sulfate‐reducers, improving the acetate removal via sulfate reduction in the reactor.
Nanocomposite electrode materials in alcohol oxidation reactions

1 Institute of Non-Ferrous Metals, Division in Poznan, Central Laboratory of Batteries and Cells, ul. Forteczna 12, 61-362 Poznan, Poland 2 Poznan Science and Technology Park of Adam Mickiewicz University Foundation, ul. Rubiez 46, 61-612 Poznan, Poland 3 Centre of Advanced Technologies, Adam Mickiewicz University, ul. Grunwaldzka 6, 60-780 Poznan, Poland *Corresponding author. E-mail: agnieszka.martyla@claio.poznan. pl
Electronic Structure of Lithium Tetraborate

Abstract : Due to interest as neutron detection material, an investigation of Li2B4O7(110) and Li2B4O7(100) was undertaken, utilizing photoemission and inverse photoemission spectroscopic techniques. The measured band gap depended on crystallographic direction with the band gaps ranging from 8.9 plus or minus 0.5 eV to 10.1 plus or minus 0.5 eV. The measurement yielded a density of states that qualitatively agreed with the theoretical results from model bulk band structure calculations for Li2B4O7; albeit with a larger band gap than predicted, but consistent with the known deficiencies of LDA and DFT calculations. The occupied states of both surfaces were extremely flat; to the degree that resolving periodic dispersion of the occupied states was inconclusive, within the resolution of the system. However, both surfaces demonstrated clear periodic dispersion within the empty states very close to theoretical Brillouin zone values. These attributes also translated to a lighter charge carrier effective mass in the unoccupied states. Li2B4O7(110) yielded the more consistent values in orthogonal directions for energy states. The presence of a bulk band gap surface state and image potential state in Li2B4O7(110) was indicative of a defect-free surface. The absence of both in the more polar, more dielectric Li2B4O7(100) was attributed to the presence of defects determined to be O vacancies. The results from Li2B4O7(110) were indicative of a more stable surface than Li2B4O7(100). In addition, Li 1s bulk and surface core level components were determined at the binding energies of -56.5+0.4 and -53.7+0.5 eV. Resonance features were observed along the [001] direction and were attributed to a Coster-Kronig process. The pyroelectric and piezoelectric character of Li2B4O7 was explored more deeply and a non-zero, off-axis pyroelectric coefficient for the Li2B4O7(110) direction was discovered.
Isolated Clusters of PF Catalogue

The properties of isolated galaxy clusters are discussed. The clusters were found among 1746 PF clusters inclusive 50 and more galaxies in structure field. For 19 clusters with distances to the nearest neighbour larger than 68.5 h Mpc we assigned the morphological types of these clusters according to Abell and Bauts & Morgan. The existence of preferential planes and angular momenta of isolated clusters was assumed. We connect evolution of isolated clusters with common large-scale characteristics.