SciCombinator

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Concept: Infrared spectroscopy

168

Near infrared spectroscopy (NIRS) has been successfully used for non-invasive diagnosis of diseases and abnormalities where water spectral patterns are found to play an important role. The present study investigates water absorbance patterns indicative of estrus in the female giant panda. NIR spectra of urine samples were acquired from the same animal on a daily basis over three consecutive putative estrus periods. Characteristic water absorbance patterns based on 12 specific water absorbance bands were discovered, which displayed high urine spectral variation, suggesting that hydrogen-bonded water structures increase with estrus. Regression analysis of urine spectra and spectra of estrone-3-glucuronide standard concentrations at these water bands showed high correlation with estrogen levels. Cluster analysis of urine spectra grouped together estrus samples from different years. These results open a new avenue for using water structure as a molecular mirror for fast estrus detection.

Concepts: Spectroscopy, Regression analysis, Cluster analysis, Water, Infrared spectroscopy, Infrared, Near infrared spectroscopy, Giant Panda

153

Cholesterol has been suggested to play a role in stable vesicle formation by adjusting the molecular packing of the vesicular bilayer. To explore the mechanisms involved in adjusting the bilayer structure by cholesterol, the molecular packing behavior in a mimic outer layer of cationic dialkyldimethylammonium bromide (DXDAB)/cholesterol vesicular bilayer was investigated by the Langmuir monolayer approach with infrared reflection-absorption spectroscopy (IRRAS). The results indicated that the addition of cholesterol in the DXDAB Langmuir monolayers not only restrained the desorption of the DXDAB with short hydrocarbon chains, such as ditetradecyldimethylammonium bromide or dihexadecyldimethylammonium bromide, into the aqueous phase but also induced a condensing effect on the DXDAB monolayers. At a liquid-expanded (LE) state, the ordering effect of cholesterol accompanying the condensing effect occurred in the mixed DXDAB/cholesterol monolayers due to the tendency of maximizing hydrocarbon chain contact between cholesterol and the neighboring hydrocarbon chains. However, for the mixed monolayers containing the DXDAB with long hydrocarbon chains, such as dioctadecyldimethylammonium bromide (DODAB), the disordering effect of cholesterol took place at a liquid-condensed (LC) state. This was related to the molecular structure of cholesterol and hydrocarbon chain length of DODAB. The rigid sterol ring of cholesterol hindered the portion of neighboring hydrocarbon chains from motion. However, the flexible alkyl side-chain of cholesterol along with the corresponding portion of neighboring hydrocarbon chains formed a fluidic region, counteracting the enhanced conformational order induced by the sterol ring of cholesterol. Furthermore, the long hydrocarbon chains of DODAB possessed a more pronounced motion freedom, resulting in a more disordered packing of the monolayers.

Concepts: Hydrocarbon, Physical chemistry, Steroid, Molecular geometry, Lipid bilayer, Infrared spectroscopy, Monolayer, Langmuir

149

Collisions of excitation pulses in dissipative systems lead usually to their annihilation. In this paper, we report electrochemical experiments exhibiting more complex pulse interaction with collision survival and pulse splitting, phenomena that have rarely been observed experimentally and are only poorly understood theoretically. Using spatially resolved in-situ Fourier transform infrared spectroscopy (FTIR) in the attenuated total reflection configuration, we monitored reaction pulses during the electrochemical oxidation of CO on Pt thin film electrodes in a flow cell. The system forms quasi-1d pulses that align parallel to the flow and propagate perpendicular to it. The pulses split once in a while, generating a second solitary wave in the backward moving direction. Upon collision, the waves penetrate each other in a soliton-like manner. These unusual pulse dynamics could be reproduced with a 3-component reaction-diffusion-migration model with two inhibitor species, one of them exhibiting a long-range spatial coupling. The simulations shed light on existence criteria of such dissipative solitons.

Concepts: Spectroscopy, Light, Refraction, Electrochemistry, Fourier transform, Electrochemical cell, Infrared spectroscopy, Fourier transform spectroscopy

148

Conventional arthroscopic evaluation of articular cartilage is subjective and poorly reproducible. Therefore, implementation of quantitative diagnostic techniques, such as near infrared spectroscopy (NIRS) and optical coherence tomography (OCT), is essential. Locations (n = 44) with various cartilage conditions were selected from mature equine fetlock joints (n = 5). These locations and their surroundings were measured with NIRS and OCT (n = 530). As a reference, cartilage proteoglycan (PG) and collagen contents, and collagen network organization were determined using quantitative microscopy. Additionally, lesion severity visualized in OCT images was graded with an automatic algorithm according to International Cartilage Research Society (ICRS) scoring system. Artificial neural network with variable selection was then employed to predict cartilage composition in the superficial and deep zones from NIRS data, and the performance of two models, generalized (including all samples) and condition-specific models (based on ICRS-grades), was compared. Spectral data correlated significantly (p < 0.002) with PG and collagen contents, and collagen orientation in the superficial and deep zones. The combination of NIRS and OCT provided the most reliable outcome, with condition-specific models having lower prediction errors (9.2%) compared to generalized models (10.4%). Therefore, the results highlight the potential of combining both modalities for comprehensive evaluation of cartilage during arthroscopy.

Concepts: Scientific method, Spectroscopy, Bone, Cartilage, Optical coherence tomography, Infrared spectroscopy, Infrared, Near infrared spectroscopy

137

Cystic echinococcosis (CE)/hydatid cyst is one of the most important helminthic diseases in the world. The treatment of hydatid cyst ranges from surgical intervention to chemotherapy, although the efficacy of chemotherapy is still unclear. Postoperative complication which results from the spillage of cysts during surgical operation is one of the most important concerns in surgical treatment of hydatid cyst. The aim of the current study was to solidify the hydatid cyst fluid (HCF) with an injectable and thermosensitive chitosan (CS)/carboxymethyl cellulose (CMC)/β-glycerol phosphate (BGP) hydrogel for effective control of spillage during the aspiration of hydatid cysts. Fourier-transform infrared spectroscopy (FTIR), scanning electron microscopy (SEM), water uptake, rheological analysis, and Alamar Blue cytotoxicity assay were employed to characterize the hydrogel. A five level with three times replication at the central point using a central composite design (CCD), which is a response surface methodology (RSM), was used to optimize the experimental conditions. Assessment of the produced hydrogel showed that the intermolecular interactions of amino groups of chitosan and hydrogen groups of CMC were correctively established and appreciable swelling with a good strength was obtained. Hydrogels morphology had a porous structure. Rheological analysis showed that CS/CMC/BGP blends had a phase transition (32-35 °C) of sol-gel close to the body temperature. Alamar Blue cytotoxicity assay showed that CS (1.75%)/CMC (1.4%)/BGP (2.9%) had IC50 values of 0.598, 0.235 and 0.138 (µg/µL) for 24, 48 and 72 h, which indicated that the produced polymer solution had no significant cytotoxic effect for human fibroblast cell line. In vitro injection of the polymer solution of CS/CMC/BGP with CS/CMC ratio of 1.75/1.4 was done on HCF (1 mL polymer solution to 3 mL of HCF) at 37 °C with a final concentration of 2.9% for BGP resulting in solidification of HCF in less than 45 min.

Concepts: Cell, Surgery, Effectiveness, Cytotoxicity, Scanning electron microscope, Cyst, Infrared spectroscopy, Response surface methodology

77

The present study investigates brain-to-brain coupling, defined as inter-subject correlations in the hemodynamic response, during natural verbal communication. We used functional near-infrared spectroscopy (fNIRS) to record brain activity of 3 speakers telling stories and 15 listeners comprehending audio recordings of these stories. Listeners' brain activity was significantly correlated with speakers' with a delay. This between-brain correlation disappeared when verbal communication failed. We further compared the fNIRS and functional Magnetic Resonance Imaging (fMRI) recordings of listeners comprehending the same story and found a significant relationship between the fNIRS oxygenated-hemoglobin concentration changes and the fMRI BOLD in brain areas associated with speech comprehension. This correlation between fNIRS and fMRI was only present when data from the same story were compared between the two modalities and vanished when data from different stories were compared; this cross-modality consistency further highlights the reliability of the spatiotemporal brain activation pattern as a measure of story comprehension. Our findings suggest that fNIRS can be used for investigating brain-to-brain coupling during verbal communication in natural settings.

Concepts: Spectroscopy, Brain, Magnetic resonance imaging, Correlation and dependence, Infrared spectroscopy, Functional magnetic resonance imaging, Infrared, Near infrared spectroscopy

35

Time-resolved Fourier transform infrared (FTIR) spectroscopy is a powerful tool to elucidate label-free the reaction mechanisms of proteins. After assignment of the absorption bands to individual groups of the protein, the order of events during the reaction mechanism can be monitored and rate constants can be obtained. Additionally, structural information is encoded into infrared spectra and can be decoded by combining the experimental data with biomolecular simulations. We have determined recently the infrared vibrations of GTP and guanosine diphosphate (GDP) bound to Gαi1, a ubiquitous GTPase. These vibrations are highly sensitive for the environment of the phosphate groups and thereby for the binding mode the GTPase adopts to enable fast hydrolysis of GTP. In this study we calculated these infrared vibrations from biomolecular simulations to transfer the spectral information into a computational model that provides structural information far beyond crystal structure resolution. Conformational ensembles were generated using 15 snapshots of several 100 ns molecular-mechanics/molecular-dynamics (MM-MD) simulations, followed by quantum-mechanics/molecular-mechanics (QM/MM) minimization and normal mode analysis. In comparison with other approaches, no time-consuming QM/MM-MD simulation was necessary. We carefully benchmarked the simulation systems by deletion of single hydrogen bonds between the GTPase and GTP through several Gαi1 point mutants. The missing hydrogen bonds lead to blue-shifts of the corresponding absorption bands. These band shifts for α-GTP (Gαi1-T48A), γ-GTP (Gαi1-R178S), and for both β-GTP/γ-GTP (Gαi1-K46A, Gαi1-D200E) were found in agreement in the experimental and the theoretical spectra. We applied our approach to open questions regarding Gαi1: we show that the GDP state of Gαi1 carries a Mg(2+), which is not found in x-ray structures. Further, the catalytic role of K46, a central residue of the P-loop, and the protonation state of the GTP are elucidated.

Concepts: DNA, Protein, Spectroscopy, Infrared spectroscopy, Fourier transform spectroscopy, Mode shape, Normal mode, Guanosine triphosphate

28

The mid-infrared (mid-IR) is a strategically important band for numerous applications ranging from night vision to biochemical sensing. Here we theoretically analyzed and experimentally realized a Huygens metasurface platform capable of fulfilling a diverse cross-section of optical functions in the mid-IR. The meta-optical elements were constructed using high-index chalcogenide films deposited on fluoride substrates: the choices of wide-band transparent materials allow the design to be scaled across a broad infrared spectrum. Capitalizing on a two-component Huygens' meta-atom design, the meta-optical devices feature an ultra-thin profile (λ0/8 in thickness) and measured optical efficiencies up to 75% in transmissive mode for linearly polarized light, representing major improvements over state-of-the-art. We have also demonstrated mid-IR transmissive meta-lenses with diffraction-limited focusing and imaging performance. The projected size, weight and power advantages, coupled with the manufacturing scalability leveraging standard microfabrication technologies, make the Huygens meta-optical devices promising for next-generation mid-IR system applications.

Concepts: Spectroscopy, Optics, Light, Electromagnetic radiation, Optical fiber, Polarization, Infrared spectroscopy, Infrared

28

The objective of the present work was to develop a plant-bacterial synergistic system for efficient treatment of the textile effluents. Decolorization of the dye Scarlet RR and a dye mixture was studied under in vitro conditions using Glandularia pulchella (Sweet) Tronc., Pseudomonas monteilii ANK and their consortium. Four reactors viz. soil, bacteria, plant and consortium were developed that were subjected for treatment of textile effluents and dye mixture. Under in vitro conditions G. pulchella and P. monteilii showed decolorization of the dye Scarlet RR (SRR) by 97 and 84%, within 72 and 96 h respectively, while their consortium showed 100% decolorization of the dye within 48 h. In case of dye mixture G. pulchella, P. monteilii and consortium-PG showed an ADMI removal of 78, 67 and 92% respectively within 96 h. During decolorization of SRR G. pulchella showed induction in the activities of enzymes lignin peroxidase and DCIP reductase while P. monteilii showed induction of laccase, DCIP reductase and tyrosinase, indicating their involvement in the dye metabolism. High Performance Liquid Chromatography (HPLC), Fourier Transform Infra Red Spectroscopy (FTIR) and High Performance Thin Layer Chromatography (HPTLC) confirmed the biotransformation of SRR and dye mixture into different metabolites. Soil, bacteria, plant and consortium reactors performed an ADMI removal of 42, 46, 62 and 93% in the first decolorization cycle while it showed an average ADMI removal of 21, 27, 59 and 93% in the next three (second, third and fourth) decolorization cycles respectively for the dye mixture within 24 h. Consortium reactor showed an average ADMI removal of 95% within 48 and 60 h for textile effluents A and B respectively for three decolorization cycles, while it showed an average TOC, COD and BOD removal of 74, 70 and 70%, 66, 72 and 67%, and 70, 70 and 66% for three decolorization cycles of the dye mixture (second, third and fourth decolorization cycles), effluent A and effluent B respectively. Degradation of the textile effluents and dye mixture into different metabolites by the consortium reactor was confirmed using HPLC and FTIR. Phytotoxicity studies revealed the non-toxic nature of the metabolites of degradation of dye mixture, effluents A and B by consortium reactor. The developed consortial reactor system performed efficient treatment of the dye mixture and textile effluents, and can be used for treating large amounts of textile effluents when implemented as a constructed wetland by proper engineering approach.

Concepts: Chromatography, High performance liquid chromatography, Sewage treatment, Infrared spectroscopy, Thin layer chromatography, Paper chromatography, HPTLC, Ligninase

28

Henmilite is a triclinic mineral with the crystal structure consisting of isolated B(OH)(4) tetrahedra, planar Cu(OH)(4) groups and Ca(OH)(3) polyhedra. The structure can also be viewed as having dimers of Ca polyhedra connected to each other through 2B(OH) tetrahedra to form chains parallel to the C axis. The structure of the mineral has been assessed by the combination of Raman and infrared spectra. Raman bands at 902, 922, 951, and 984cm(-1) and infrared bands at 912, 955 and 998cm(-1) are assigned to stretching vibrations of tetragonal boron. The Raman band at 758cm(-1) is assigned to the symmetric stretching mode of tetrahedral boron. The series of bands in the 400-600cm(-1) region are due to the out-of-plane bending modes of tetrahedral boron. Two very sharp Raman bands are observed at 3559 and 3609cm(-1). Two infrared bands are found at 3558 and 3607cm(-1). These bands are assigned to the OH stretching vibrations of the OH units in henmilite. A series of Raman bands are observed at 3195, 3269, 3328, 3396, 3424 and 3501cm(-1) are assigned to water stretching modes. Infrared spectroscopy also identified water and OH units in the henmilite structure. It is proposed that water is involved in the structure of henmilite. Hydrogen bond distances based upon the OH stretching vibrations using a Libowitzky equation were calculated. The number and variation of water hydrogen bond distances are important for the stability off the mineral.

Concepts: Spectroscopy, Crystal, Hydrogen, Mineral, Raman spectroscopy, Infrared spectroscopy, Boron, Borate