Blind separation of fluorescence spectra using sparse non‐negative matrix factorization on right hand factor

Sparse non‐negative matrix factorization on right side factor (SNMF/R) has better performance in feature extraction than non‐negative matrix factorization. In this work, SNMF/R was first used to separate the overlapped three‐dimensional fluorescence spectra of polycyclic aromatic hydrocarbons mixtures in pure water, lake water, and river water, respectively. It is found that the similarity coefficients between the acquired three‐dimensional spectra and the corresponding reference spectra with random initials are all above 0.80; the recognition rate of SNMF/R is higher than that of PARAFAC and non‐negative matrix factorization algorithms, especially in the case of lake water and river water samples. In addition, SNMF/R does not need any initialization scheme designing during spectra separation. These results demonstrate that SNMF/R is an appropriate algorithm to separate the overlapped fluorescence spectra of polycyclic aromatic hydrocarbons in aquatic environment accurately and effectively. Copyright © 2015 John Wiley & Sons, Ltd.     

Nonlinear mixture‐wise expansion approach to underdetermined blind separation of nonnegative dependent sources

Underdetermined blind separation of nonnegative dependent sources consists in decomposing a set of observed mixed signals into greater number of original nonnegative and dependent component (source) signals. That is an important problem for which very few algorithms exist. It is also practically relevant for contemporary metabolic profiling of biological samples, such as biomarker identification studies, where sources (a.k.a. pure components or analytes) are aimed to be extracted from mass spectra of complex multicomponent mixtures. This paper presents a method for underdetermined blind separation of nonnegative dependent sources. The method performs nonlinear mixture‐wise mapping of observed data in high‐dimensional reproducible kernel Hilbert space (RKHS) of functions and sparseness‐constrained nonnegative matrix factorization (NMF) therein. Thus, the original problem is converted into new one with increased number of mixtures, increased number of dependent sources, and higher‐order (error) terms generated by nonlinear mapping. Provided that amplitudes of original components are sparsely distributed, which is the case for mass spectra of analytes, sparseness‐constrained NMF in RKHS yields, with significant probability, improved accuracy relative to the case when the same NMF algorithm is performed on the original problem. The method is exemplified on numerical and experimental examples related respectively to extraction of 10 dependent components from five mixtures and to extraction of 10 dependent analytes from mass spectra of two to five mixtures. Thereby, analytes mimic complexity of components expected to be found in biological samples. Copyright © 2013 John Wiley & Sons, Ltd.     

Accurate grading of brain gliomas by soft independent modeling of class analogy based on non‐negative matrix factorization of proton magnetic resonance spectra

Hydrogen magnetic resonance spectroscopy (¹H‐MRS) is a non‐invasive technique which provides a ‘frequency‐signal intensity’ spectrum of biochemical compounds of tissues in the body. Although this method is currently used in human brain studies, accurate classification of in‐vivo ¹H‐MRS is a challenging task in the diagnosis of brain tumors. Problems such as overlapping metabolite peaks, incomplete information on background component and low signal‐to‐noise ratio disturb classification results of this spectroscopic method. This study presents an alternative approach to the soft independent modeling of class analogy (SIMCA) technique, using non‐negative matrix factorization (NMF) for dimensionality reduction. In the adopted strategy, the performance of SIMCA was improved by application of a robust algorithm for classification in the presence of noisy measurements. Total of 219 spectra from two databases were taken by water‐suppressed short echo‐time ¹H‐MRS, acquired from different subjects with different stages of glial brain tumors (Grade II (26 cases), grade III (24 cases), grade IV (41 cases), as well as 25 healthy cases). The SIMCA was performed using two approaches: (i) principal component analysis (PCA) and (ii) non‐negative matrix factorization (NMF), as a modified approach. Square prediction error was considered to assess the class membership of the external validation set. Finally, several figures of merit such as the correct classification rate (CCR), sensitivity and specificity were calculated. Results of SIMCA based on NMF showed significant improvement in percentage of correctly classified samples, 91.4% versus 83.5% for PCA‐based model in an independent test set. Copyright © 2015 John Wiley & Sons, Ltd.     

Micro‐/Nanostructured Multicomponent Molecular Materials: Design,Assembly, and Functionality

Molecule‐based micro‐/nanomaterials have attracted considerable attention because their properties can vary greatly from the corresponding macro‐sized bulk systems. Recently, the construction of multicomponent molecular solids based on crystal engineering principles has emerged as a promising alternative way to develop micro‐/nanomaterials. Unlike single‐component materials, the resulting multicomponent systems offer the advantages of tunable composition, and adjustable molecular arrangement, and intermolecular interactions within their solid states. The study of these materials also supplies insight into how the crystal structure, molecular components, and micro‐/nanoscale effects can influence the performance of molecular materials. In this review, we describe recent advances and current directions in the assembly and applications of crystalline multicomponent micro‐/nanostructures. Firstly, the design strategies for multicomponent systems based on molecular recognition and crystal engineering principles are introduced. Attention is then focused on the methods of fabrication of low‐dimensional multicomponent micro‐/nanostructures. Their new applications are also outlined. Finally, we briefly discuss perspectives for the further development of these molecular crystalline micro‐/nanomaterials.     

Three‐Dimensional Control of DNA Hybridization by Orthogonal Two‐Color Two‐Photon Uncaging

We successfully introduced two‐photon‐sensitive photolabile groups ([7‐(diethylamino)coumarin‐4‐yl]methyl and p‐dialkylaminonitrobiphenyl) into DNA strands and demonstrated their suitability for three‐dimensional photorelease. To visualize the uncaging, we used a fluorescence readout based on double‐strand displacement in a hydrogel and in neurons. Orthogonal two‐photon uncaging of the two cages is possible, thus enabling complex scenarios of three‐dimensional control of hybridization with light.     

Resolving overlapping GC–MS signals with a multistep screening chemometric approach for the fast determination of pesticides

For the rapid analysis of multicomponent mixtures using GC–MS, a chemometric multistep screening approach was proposed to extract the signals of the components from the overlapping signals measured with a very fast temperature program. At first, independent component analysis was used to find all the possible mass spectra from the overlapping signal in the moving windows along the retention time, and iterative target transformation factor analysis was employed to validate the existence of the extracted spectra from each window. Then, identical signals in the validated spectra were excluded using match ratio as a criterion. Finally, the chromatographic profiles for each spectrum were calculated using non‐negative immune algorithm, and the spectra with a reasonable profile were taken as the identified components. A mixture of 53 pesticides was analyzed with a very fast temperature program of 7 min. A total of 48 pesticides and 16 interferences were identified from the overlapping GC–MS signal.     

pH‐Responsive Host−Guest Complexation between a Water‐soluble Pillar[7]Arene and a 2,7‐Diazapyrenium Salt and Its Application in Controllable Self‐assembly

A novel host−guest recognition motif based on a water‐soluble pillar[7]arene ( WP7 ) and a 2,7‐diazapyrenium salt ( DMDAP ) was prepared. According to the integrated results of ¹H NMR, 2D NOESY, UV–vis spectroscopy and fluorescence titration experiments, we demonstrated that the molecular recognition of WP7 to DMDAP in water not only has high association constant but also has pH‐responsiveness. Subsequently, we took advantage of this molecular recognition motif to fabricate a supra‐amphiphile based on WP7 and an amphiphilic 2,7‐diazapyrenium derivative DAPAC . Its controllable self‐assembly in water was also investigated by means of TEM and DLS techniques.     

One‐Pot Synthesis of 4‐(2,3‐Dihydro‐2‐hydroxy‐1,3‐dioxo‐1H‐inden‐2‐yl)‐Substituted 1‐Aryl‐1H‐pyrazole‐3‐carboxylates via a Tandem Three‐Component Reaction

The hitherto unreported, highly functionalized 1H‐pyrazole‐3‐carboxylates 3 have been synthesized in good yields via a one‐pot three‐component domino reaction of phenylhydrazines, dialkyl acetylenedicarboxylates, and ninhydrin under mild conditions for the first time. No co‐catalyst or activator is required for this multicomponent reaction, and the reaction is, from an experimental point of view, simple to perform (Scheme 1). The structures of compounds 3 were corroborated spectroscopically (IR, ¹H‐ and ¹³C‐NMR, and EI‐MS) and by elemental analyses. A plausible mechanism for this type of cyclization/addition reaction is proposed (Scheme 2).     

Quality evaluation of Hypericum ascyron extract by two‐dimensional high‐performance liquid chromatography coupled with the colorimetric 3‐(4,5‐dimethylthiazol‐2‐yl)‐2,5‐diphenyltetrazolium bromide method

In this paper, a heart‐cutting two‐dimensional high‐performance liquid chromatography coupled with the 3‐(4,5‐dimethylthiazol‐2‐yl)‐2,5‐diphenyltetrazolium bromide (MTT) method was established for controlling the quality of different batches of Hypericum ascyron extract for the first time. In comparison with the common one‐dimensional fingerprint, the second‐dimensional fingerprint compiled additional spectral data and was hence more informative. The quality of H. ascyron extract was further evaluated by similarity measures and the same results were achieved, the correlation coefficients of the similarity of ten batches of H. ascyron extract were ＞0.99. Furthermore, we also evaluated the quality of the ten batches of H. ascyron extract by antibacterial activity. The result demonstrated that the quality of the ten batches of H. ascyron extract was not significantly different by MTT. Finally, we demonstrated that the second‐dimensional fingerprint coupled with the MTT method was a more powerful tool to characterize the quality of samples of batch to batch. Therefore the proposed method could be used to comprehensively conduct the quality control of traditional Chinese medicines.     

Light‐driven and aggregation‐induced emission from side‐chain azoindazole polymers

The well‐defined azoindazole‐containing homopolymer, poly(6‐{6‐[(4‐dimethylamino) phenylazo]‐indazole}‐hexyl methacrylate) (PDHMA), and amphiphilic diblock copolymer, poly({6‐[6‐(4‐dimethylamino)phenylazo]‐indazole}‐hexyl methacrylate)‐b‐poly(2‐(dimethylamino)ethylmethacrylate) (PDHMA_m‐b‐PDMAEMA_n), were successfully prepared via reversible addition‐fragmentation chain transfer polymerization technique. The homopolymer and amphiphilic diblock copolymer in CH₂Cl₂ exhibited intense fluorescence emission accompanied by trans–cis photoisomerization of azoindazole group under UV irradiation. The experiment results indicated that the intense fluorescence emission may be attributed to an inhibition of photoinduced electron transfer of the cis form of azoindazole. On the other hand, the intense fluorescence emission of amphiphilic diblock copolymers in water‐tetrahydrofuran mixture was observed, which increased with the volume ratio of water in the mixed solvent. The self‐aggregation behaviors of three amphiphilic diblock copolymers were examined by transmission electron microscopy, laser light scattering, and UV–vis spectra. The restriction of intramolecular rotation of the azoindazole groups in aggregates was considered as the main cause of aggregation‐induced fluorescence emission. © 2011 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2011.     

A Green Approach for the One‐Pot,Three‐Component Synthesis of 2‐Arylpyrroloacridin‐1(2H)‐Ones using Lactic Acid as a Bio‐based Catalyst under Solvent‐Free Conditions

A facile and benign synthetic strategy is proposed for the synthesis of 2‐arylpyrroloacridin‐1(2H )‐ones via a lactic acid‐catalyzed three‐component reaction of dimedone, various anilines, and isatins under solvent‐free conditions. Avoidance of hazardous organic solvents, the use of a one‐pot multicomponent procedure for the synthesis of 2‐arylpyrroloacridin‐1(2H )‐ones, operational simplicity, no need for column chromatography, lactic acid utilization as a bio‐based organic compound, reusability, homogeneity, and commercial availability of the catalyst, and superior synthetic performance are some important aspects of this methodology to access a series of pyrroloacridine motifs with potentially biological scaffolds.     

Multicomponent Supramolecular Systems: Self‐Organization in Coordination‐Driven Self‐Assembly

The self‐organization of multicomponent supramolecular systems involving a variety of two‐dimensional (2 D) polygons and three‐dimensional (3 D) cages is presented. Nine self‐organizing systems, SS₁ – SS₉ , have been studied. Each involves the simultaneous mixing of organoplatinum acceptors and pyridyl donors of varying geometry and their selective self‐assembly into three to four specific 2 D (rectangular, triangular, and rhomboid) and/or 3 D (triangular prism and distorted and nondistorted trigonal bipyramidal) supramolecules. The formation of these discrete structures is characterized using NMR spectroscopy and electrospray ionization mass spectrometry (ESI‐MS). In all cases, the self‐organization process is directed by: 1) the geometric information encoded within the molecular subunits and 2) a thermodynamically driven dynamic self‐correction process. The result is the selective self‐assembly of multiple discrete products from a randomly formed complex. The influence of key experimental variables ‐ temperature and solvent ‐ on the self‐correction process and the fidelity of the resulting self‐organization systems is also described.     

X‐tended target projection (XTP)—comparison with orthogonal partial least squares (OPLS) and PLS post‐processing by similarity transformation (PLS + ST)

Target projection (TP) also called target rotation (TR) was introduced to facilitate interpretation of latent‐variable regression models. Orthogonal partial least squares (OPLS) regression and PLS post‐processing by similarity transform (PLS + ST) represent two alternative algorithms for the same purpose. In addition, OPLS and PLS + ST provide components to explain systematic variation in X orthogonal to the response. We show, that for the same number of components, OPLS and PLS + ST provide score and loading vectors for the predictive latent variable that are the same as for TP except for a scaling factor. Furthermore, we show how the TP approach can be extended to become a hybrid of latent‐variable (LV) regression and exploratory LV analysis and thus embrace systematic variation in X unrelated to the response. Principal component analysis (PCA) of the residual variation after removal of the target component is here used to extract the orthogonal components, but X‐tended TP (XTP) permits other criteria for decomposition of the residual variation. If PCA is used for decomposing the orthogonal variation in XTP, the variance of the major orthogonal components obtained for OPLS and XTP is observed to be almost the same, showing the close relationship between the methods. The XTP approach is tested and compared with OPLS for a three‐component mixture analyzed by infrared spectroscopy and a multicomponent mixture measured by near infrared spectroscopy in a reactor. Copyright © 2008 John Wiley & Sons, Ltd.     

Are formalin‐fixed and paraffin‐embedded tissues fit for proteomic analysis?

Formalin‐fixed and paraffin‐embedded (FFPE)–tissue archives are potential treasure troves in the search for clinically interesting specimens. However, while the FFPE‐treatment provides excellent conservation of the three‐dimensional structure of the tissue and prevents degradation over decades, it also introduces numerous nonspecific and irreversible protein modifications. In this study, we have evaluated several published workflows for FFPE‐tissue by fit‐for‐purpose proteomics technologies. We demonstrate that many protein modifications and cross‐links remain after treatment and conclude that the proteomics of FFPE‐tissue is of value, but clear‐cut limitations must be kept in mind. The analysis of abundant proteins in FFPE is straightforward, but confident identification of low‐level proteins and/or biologically relevant modifications is seriously hampered by the FFPE‐treatment. Peptide assignment should only be performed on high‐quality spectra, even if this is at the cost of lower numbers of protein IDs. As Yergey and Coorssen stated in 2015: “Data quality is considered the primary criterion, and we thus emphasize that the standards of Analytical Chemistry must apply throughout any proteomic analysis.”     

Partial‐Homogeneity‐Based Two‐Dimensional High‐Resolution Nuclear Magnetic Resonance Spectroscopy under Inhomogeneous Magnetic Fields

High‐resolution multidimensional nuclear magnetic resonance (NMR) spectroscopy serves as an irreplaceable and versatile tool in various chemical investigations. In this study, a method based on the concept of partial homogeneity is developed to offer two‐dimensional (2D) high‐resolution NMR spectra under inhomogeneous fields. Oscillating gradients are exerted to encode the high‐resolution information, and a field‐inhomogeneity correction algorithm based on pattern recognition is designed to recover high‐resolution spectra. Under fields where inhomogeneity primarily distributes along a single orientation, the proposed method will improve performances of 2D NMR spectroscopy without increasing the experimental duration or significant loss in sensitivity, and thus may open important perspectives for studies of inhomogeneous chemical systems.     

N‐Alkylacylamides in Thin Films Display Infrared Spectra of 310‐, α‐, and π‐Helices with Visible Static and Dynamic Growth Phases

A peptide model is a physical system containing a CONH group, the simplest being HCONHCH₃, N‐methylformamide (NMF). We have discovered that NMF and N‐methylacetamide (NMA), which form hydrogen‐bonded oligomers in thin films on a planar AgX fiber, display infrared (IR) spectra with peaks like those of polypeptide helices. Structures can be assigned by their amide I maxima near 1672 (3₁₀), 1655 (3₁₀), 1653 (α), 1655 (π), and 1635 cm^?1 (π), which are the first IR data for the π‐helix. Sharp peaks are an outcome of immobilization of polar species on the polar surface of silver halides. We report the first use of expanded thin‐film IR spectroscopy, in which plots of every spectrum over the amide I–II range show pauses or slow stages in the increase or decrease of absorption. These are identified as static phases followed by dynamic phases, with the incremental gain or loss of a helix turn. A general theory can be stated for such processes. Density functional calculations show that the NMA α‐helix pentamer (crystal structure geometry) is transformed into a π‐helix‐like form. For the first time, an entire sequence (3₁₀‐helix, α‐helix, π‐helix, quasiplanar species) of spectra has been recorded for NMA.     

稀土与N-对甲苯磺酰甘氨酸配合物的合成、晶体结构与性质

Complexes { [Ln（H20）2（TsGlyH）a]m·nH2O}∞ （Ln=La （1）, m=2, n=6; Nd （2）, m=2, n=7; Eu （3）, m=2, n= 0; Gd （4）, m=2, n=2; Er （5）, m=3, n=5 and Yb （6）, m=3, n=0, TsGlyH=N-p-tosylglycine monoanion）, have been prepared and characterized by IR spectra, elemental analysis, and TG-DTG 4 and 5 were structurally determined by X-ray diffraction analysis, showing that both of them are comprised of a one dimensional chain structure established via the coordination of μ-carboxylate groups from N-p-tosylglycinate to the corresponding lanthanide（Ⅲ） ions. The one dimensional chains were found inclined to form two-dimensional network via hydrogen bonding and then three dimensional network structure via non-classical hydrogen bonding. The fluorescence spectra of them revealed that the fluorescence of the ligand was quenched by Ln（Ⅲ） ions. In the tested biological activity experiments, they behaved inhibiting effects against the growth of bacteria, indicating that it is a potential medicament worthy of further investigation.     

One‐ and two‐dimensional NMR characterization of N‐vinyl‐2‐pyrrolidone/methyl acrylate copolymers

N‐vinyl‐2‐pyrrolidone/methyl acrylate (V/M) copolymers were prepared by free‐radical bulk polymerization using benzoyl peroxide as an initiator. The copolymer composition of these copolymers was calculated from ¹H NMR spectra. The radical reactivity ratios for N‐vinyl‐2‐pyrrolidone (V) and methyl acrylate (M) were r_V = 0.09, r_M = 0.44. These reactivity ratios for the copolymerization of V and M were determined using the Kelen–Tudos and nonlinear least‐squares error‐in‐variable methods. The ¹³C{¹H} and ¹H NMR spectra of these copolymers overlapped and were complex. The complete spectral assignment of the ¹³C and ¹H NMR spectra were done with distortionless enhancement by polarization transfer and two dimensional ¹³C‐¹H heteronuclear single quantum correlation spectroscopic experiments. The two‐dimensional ¹H‐¹H homonuclear total correlation spectroscopic NMR spectrum showed the various bond interactions, thus inferring the possible structure of the copolymers. © 2002 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 40: 2225–2236, 2002     

One‐ and two‐dimensional NMR characterization of N‐vinyl‐2‐pyrrolidone/methyl acrylate copolymers

N‐vinyl‐2‐pyrrolidone/methyl acrylate (V/M) copolymers were prepared by free‐radical bulk polymerization using benzoyl peroxide as an initiator. The copolymer composition of these copolymers was calculated from ¹H NMR spectra. The radical reactivity ratios for N‐vinyl‐2‐pyrrolidone (V) and methyl acrylate (M) were r_V = 0.09, r_M = 0.44. These reactivity ratios for the copolymerization of V and M were determined using the Kelen–Tudos and nonlinear least‐squares error‐in‐variable methods. The ¹³C{¹H} and ¹H NMR spectra of these copolymers overlapped and were complex. The complete spectral assignment of the ¹³C and ¹H NMR spectra were done with distortionless enhancement by polarization transfer and two dimensional ¹³C‐¹H heteronuclear single quantum correlation spectroscopic experiments. The two‐dimensional ¹H‐¹H homonuclear total correlation spectroscopic NMR spectrum showed the various bond interactions, thus inferring the possible structure of the copolymers. © 2002 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 40: 2225–2236, 2002     

A three‐dimensional CdII coordination framework: poly[di‐μ2‐aqua‐{μ2‐1,4‐bis[(1H‐1,2,4‐triazol‐1‐yl)methyl]benzene‐κ2N4:N4′}di‐μ3‐terephthalato‐κ3O:O′:O′′‐dicadmium(II)]

The title Cd^II coordination polymer, [Cd(C₁₀H₈O₄)(C₁₂H₁₂N₆)_0.5(H₂O)]_n, has been obtained by the hydrothermal method and studied by single‐crystal X‐ray diffraction, elemental analysis, thermogravimetric analysis, IR spectroscopy and fluorescence spectroscopy. The compound forms a novel three‐dimensional framework with 3,8‐connected three‐dimensional binodal {4.5²}₂{4².5¹⁰.6¹².7.8³} topology. An investigation of its photoluminescence properties shows that the compound exhibits a strong fluorescence emission in the solid state at room temperature.