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86 protocols using opus 6

1

Yeast FTIR Spectroscopy Protocol

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Cultures were stopped after 32 h and harvested by centrifugation (7000 rpm, 10 min). The Pellets were washed twice with saline solution (0.7% NaCl) and re-suspended in 1 mL of the saline solution. Five microlitres of the concentrated yeast were deposited on a selenium multi-plate (96 wells) in 3 replicates and dried in a desiccator under1.5 bar. FTIR measurements were performed in transmission mode using HTS-XT Tensor 27 spectrophotometer (Bruker, Marne la vallée, France). Each experiment was replicated from 3 independent cultures, in order to optimize and control reproducibility [54 ].
The spectra were registered using 64 scans, at a resolution of 4 cm-1 baseline corrected and normalized using OPUS 6.5 (Bruker) software as previously described in [55 (link)]. An average spectrum was then calculated for each independent culture. If some spectra did not pass the ‘‘quality test” and spectrum reproducibility, 3 more independent cultures were performed to obtain 3 spectra per strain. Spectra analysis would be performed using OPUS 6.5 software (Bruker) by hierarchical cluster analysis (HCA) peaks measurements and integration. To verify the similitude between spectrums recorded from the same culture, calculation of the similitude percentage was performed in the whole spectra using search standard program: similitudes have to be more than 99% [54 ]
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2

Infrared Spectroscopy for Membrane Fluidity

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Spectral analysis was carried out using OPUS 6.5 Bruker Optics software. As a proxy to membrane fluidity, we analyzed the CH2 symmetric stretching, νs(CH2), band at ∼2850 cm−1. The band position was obtained by the “peak picking” routine in OPUS 6.5 software (BrukerOptics), using the “standard mode” evaluation (x-coordinate of the relative maximum). By plotting the νs(CH2)-peak position as a function of temperature, we obtained melting curves for the different samples and determined the temperature of the main phase transition of the membrane, Tm, from the maximum of the first derivative of the melting curves. The temperature dependences of the νs(CH2)-band position were used to evaluate the parameter β=(νs/T)/νs , which shows a very similar temperature behavior to that of the thermal expansion coefficient, α=(V/T)/V (37 (link)), and can therefore be used as a proxy to membrane thermal expansivity. Membrane-solubilized W(CO)6 was used to investigate the acyl chain organization and available free volume inside the bilayer. We measured the integrated area of the C≡O antisymmetric stretching, νas(CO), of W(CO)6 in the range between 1960 and 1990 cm−1. Spectra were normalized to the intensity of the νs(CH2) peak at 25°C to allow for a reliable comparison between different samples.
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3

Determination of Resin Composite Conversion

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Fourier transform infrared spectroscopy (FTIR, Vertex 70, Bruker Optics, Ettinger, Germany) was used to evaluate the degree of conversion in the experimental resin composites. The unpolymerized dental resins (n = 3) were placed on an attenuated total reflectance (ATR) device inside a polyvinylsiloxane matrix measuring 1 mm in thickness and 4 mm in diameter [32 (link)]. The specimens were covered with polyester matrix strips to obtain the FTIR spectra of unreacted specimens. The specimens were then photoactivated using a light-curing unit for 40 s, and other spectra were obtained. The spectra were obtained with a 4 cm−1 resolution in the spectral range between 400 and 4000 cm−1 with a mirror speed of 2.8 mm/s using Opus software (Opus 6.5, Bruker Optics, Ettlingen, Germany). The DC was calculated considering the intensity of the carbon–carbon double bond (peak at 1640 cm−1) and using the aromatic carbon–carbon double bond (peak at 1610 cm−1) as an internal standard [33 (link)].
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4

Glucose Calibration Ladder Spectroscopy

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Similarly to our previous study [27 (link)], after cultivation was terminated in the shake flasks, the glucose concentration was adjusted with a 2 M glucose stock solution to create a calibration ladder and NIR spectra were acquired, as well as samples for reference. The same instrument (see the specifications later) with the same settings and probe were used as with bioreactors, except the spectra acquisition was controlled with OPUS 6.5 (Bruker Optics GmbH, Ettlingen, Germany).
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5

Quantitative Analysis of 5-HMF and Absorbance

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The intensity of the measurements at different wavenumbers of NIR spectra can be correlated to the concentrations of the 5-HMF and 420 nm absorbance in the sample through partial least square (PLS) with the OPUS 6.5 software (Bruker Optik, Ettlingen, Germany), respectively.
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6

FTIR Spectroscopy of Gel Samples

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Gel sample infrared (IR) spectra were recorded with a Vertex 80v
Fourier Transform IR (FTIR) spectroscopy using a one-reflection ATR
computer-controlled Bruker spectrometer equipped with Opus 6.5 software
of the same manufacturer. Spectra were recorded with a 2 cm–1 resolution. For each spectrum, 1024 scans were acquired. Measurements
were performed under a decreased (6 hPa) pressure.
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7

Characterization of Chitosan-based Membranes

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Both chitosan, dBAM, and M1-1 were subjected to attenuated total reflectance infrared measurements with scanning ranger 400–4000 nm using a BRUKER FI-IR (Bruker, Karlsruhe, Germany). The data was processed by the software (Bruker OPUS 6.5) with smoothing and normalization. Afterwards, the images were obtained using Origin.
The pore morphologies of the two-layer membranes were observed with scanning electron microscope (MERLIN Compact, Zeiss, Oberkochen, Germany). ALL membranes were fractured after quenching in liquid nitrogen to obtain an interior cross-section and then were sputter-coated with a thin layer of gold for the investigation of internal topographies.
The mechanical properties of membranes were measured by tensile machine (MST, Model E43) to compare the tensile stress between a single-layer chitosan membrane and the double-layer membranes. The rectangular membranes (the rectangle of 10 cm long and 3 cm wide) containing a monolayer of chitosan were prepared, named M1-1 and M1-3. All measurements were repeated three times for each kind of membrane.
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8

FTIR Spectroscopic Analysis of Lyophilized Samples

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The spectra were recorded using a Bruker Vertex 7 FTIR spectrophotometer. The samples were analyzed in lyophilized state on a KRS-5 support, within the frequency range of 4000–600 cm−1. Data processing was done using the OPUS 6.5 software (Bruker Optik GmbH, Ettlingen, Germany).
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9

FT-IR Analysis of Freeze-Dried Samples

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A Vertex
70 instrument (Bruker) was employed in the attenuated total reflection
mode, with 64 scans and a resolution of 4 cm–1 in
the 4000–400 cm–1 region. The solid freeze-dried
product was directly analyzed. The data were processed using OPUS
6.5 software (Bruker) and replotted on origin 8.
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10

ATR-FTIR Analysis of Clove Oil and Eugenol

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ATR–FTIR spectra of clove essential oil and eugenol were recorded on a Bruker Tensor 27 FTIR spectrometer (Bruker Optics GmbH & Co. KG, Ettlingen, Germany) equipped with single-bounce diamond ATR (Platinum ATR, Bruker Optics GmbH & Co. KG, Ettlingen, Germany). The spectrometer was controlled with the software OPUS 6.5 (Bruker Optics GmbH & Co. KG, Ettlingen, Germany). The scan number of the spectra was 16, recorded at a 4 cm−1 resolution in the wavenumber range from 4000 to 400 cm−1. A small amount of each samples (approximately 10 mL) was placed on the ATR surface that was cleaned using ethanol to eliminate any contamination by the previous sample. A new background was recorded between each replicate, and the scans were run in triplicates [20 (link)].
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