Benchmarking and validating algorithms that estimate p<Emphasis Type="Italic">K</Emphasis><Subscript>a</Subscript> values of drugs based on their molecular structures

The REGDIA regression diagnostics algorithm in S-Plus is introduced in order to examine the accuracy of pK _a predictions made with four updated programs: PALLAS, MARVIN, ACD/pKa and SPARC. This report reviews the current status of computational tools for predicting the pK _a values of organic drug-like compounds. Outlier predicted pK _a values correspond to molecules that are poorly characterized by the pK _a prediction program concerned. The statistical detection of outliers can fail because of masking and swamping effects. The Williams graph was selected to give the most reliable detection of outliers. Six statistical characteristics (F _exp, R ², , MEP, AIC, and s(e) in pK _a units) of the results obtained when four selected pK _a prediction algorithms were applied to three datasets were examined. The highest values of F _exp, R ², , the lowest values of MEP and s(e), and the most negative AIC were found using the ACD/pK _a algorithm for pK _a prediction, so this algorithm achieves the best predictive power and the most accurate results. The proposed accuracy test performed by the REGDIA program can also be applied to test the accuracy of other predicted values, such as log P, log D, aqueous solubility or certain physicochemical properties of drug molecules.     

Photophysical Investigations on Determination of Ionicity and Electronic Structures for the Non-covalent Complexes of Calix[4]resorcinarene with Fullerenes C<Subscript>60</Subscript> and C<Subscript>70</Subscript> in the Solution State

Ground state non-covalent interactions between a macrocyclic receptor, C-methylcalix[4]resorcinarene (1) and fullerenes (C₆₀ and C₇₀) have been studied in benzonitrile by an absorption spectrophotometric method. Absorption bands are located in the visible region due to the charge transfer (CT) transition between 1 and various electron acceptors (including fullerenes), namely, 2,3-dichloro-5,6-dicyano-p-benzoquinone, tetracyanoquinodimethane and p-chloranil. Utilizing the CT absorption bands, various important physicochemical parameters, including oscillator strength, resonance energy, transition dipole strength of all the acceptor-1 complexes and vertical ionization potential of 1 are determined. Job’s method of continuous variation reveals 1:1 stoichiometry between fullerenes and 1. The most fascinating feature of the present study is that 1 binds selectively to C₇₀ compared to C₆₀ as obtained from binding constant (K) data of C₆₀-1 (K_C60-1K_{\mathrm{C}60\mbox{-}\mathbf{1}}) and C₇₀-1 (K_C70-1K_{\mathrm{C}70\mbox{-}\mathbf{1}}) complexes, i.e., K_C60-1=190K_{\mathrm{C}60\mbox{-}\mathbf{1}}=190 dm³⋅mol⁻¹ and K_C70-1=5,800K_{\mathrm{C}70\mbox{-}\mathbf{1}}=5{,}800 dm³⋅mol⁻¹ and selectivity (K_C70-1 /K_C60-1 ) ∼30. Quantum chemical calculations based on hybrid density functional theory estimate the enthalpies of formation of the fullerene-1 complexes in vacuo and provide very good support for selectivity in the K values of the C₇₀ and C₆₀ complexes of 1. The exchange and correlation energies have been calculated using a hybrid DFT functional method. We have opted to use the hybrid DFT functional over the Hartree-Fock method, as it can account for correlation effects also. Molecular electrostatic potential map calculations give a clear picture on the electronic structures of the fullerene-1 complexes.     

Studies on toxic oil syndrome: development of an enzyme-linked immunosorbent assay for 3-(<Emphasis Type="Italic">N</Emphasis>-phenylamino)propane-1,2-diol in human urine

The fatty acid esters of 3-(N-phenylamino)propane-1,2-diol (PAP) are biomarkers of toxic oil batches that caused toxic oil syndrome (TOS), an intoxication that caused over 400 deaths and affected 20,000 people in Spain in 1981. PAP esters are converted into PAP by human pancreatic lipase. The in vivo biotransformation of PAP in two mouse strains generated potentially toxic metabolites. Here we report an enzyme-linked immunosorbent assay (ELISA) for PAP detection incorporating antibodies generated using PAP-hapten derivatives 1 and 2. The immunizing haptens were designed to recognize the phenylamino and hydroxymethylene moieties of the PAP structure. The antisera raised against 1-HCH showed greater affinity for free PAP, as demonstrated in competitive experiments using either 1-BSA or 2-BSA as coating antigens. The developed ELISA detects PAP at a threshold of 130 μg L⁻¹ and can be used over a wide range of pH and ionic strength values. The assay can be applied to human urine samples, after a simple treatment method, with good recovery according to the correlation obtained when analyzing blind spiked urine samples. Figure Development of an ELISA for PAP in human urine     

Microstructural and chemical transformation of thin Ti/Pd and TiD<Subscript><Emphasis Type="BoldItalic">y</Emphasis></Subscript>/Pd bilayer films induced by vacuum annealing

Using a combination of scanning electron microscopy, transmission electron microscopy (TEM), X-ray diffraction and X-ray photoelectron spectroscopy (XPS), we made a comparative study of the high-temperature annealing impact on thin titanium deuteride (TiD _y ) films covered by an ultrathin Pd layer, and on Ti/Pd bilayer films. The bilayer films were prepared under ultrahigh vacuum conditions and were in situ annealed using the same annealing procedure. It was found that the surface and the bulk morphology of both films undergo different annealing-induced transformations, leading to an extensive intermixing between the Ti and Pd layers and the formation of a new PdTi₂ bimetallic phase. Energy-filtered TEM imaging and energy-dispersive X-ray spectrometry analysis, as well as XPS depth profiling all provided evidence of a different distribution of Pd and Ti in the annealed TiD _y /Pd film compared with the annealed Ti/Pd film. Our results show that thermal decomposition of TiD _y , as a consequence of annealing the TiD _y /Pd film, modifies the intermixing process, thereby promoting Ti diffusion into the Pd-rich top layer of the TiD _y film and thus providing a more likely path for the formation of the PdTi₂ phase than in an annealed Ti/Pd film. Figure Figure Microstructural and chemical characterisation of thin TiDy/Pd film after annealing     

Rapid response behavior,at room temperature,of a nanofiber-structured TiO<Subscript>2</Subscript> sensor to selected simulant chemical-warfare agents

A chemical prototype sensor was constructed based on nanofiber-structured TiO₂ and highly sensitive quartz resonators. The gas-sensing behavior of this new sensor to selected simulant warfare agents was investigated at room temperature. Results showed rapid response and good reversibility of this sensor when used with high-purity nitrogen. This provides a simple approach to preparation of materials needed as chemical sensors for selected organic volatiles or warfare agents. Figure Sensing behavior of TiO₂ nanofiber sensor to chemical vapors     

Preparation of Fe<Subscript>3</Subscript>O<Subscript>4</Subscript>-C18 nano-magnetic composite materials and their cleanup properties for organophosphorous pesticides

Magnetic Fe₃O₄-C18 composite nanoparticles of approximately 5–10 nm in size were synthesized and characterized by IR spectroscopy, atomic absorption spectroscopy, X-ray diffraction, and transmission electron microscopy. The magnetic Fe₃O₄-C18 composite nanoparticles were applied for cleanup and enrichment of organophosphorous pesticides. Comparative studies were carried out between magnetic Fe₃O₄-C18 composite nanoparticles and common C18 materials. Residues of organophosphorous pesticides were determined by gas chromatography in combination with a nitrogen/phosphorus detector. The cleanup and enrichment properties of magnetic Fe₃O₄-C18 composite nanoparticles are comparable with those of common C18 materials for enrichment of organophosphorous pesticides, but the cleanup and enrichment are faster and easier to perform. Figure Presumed mechanism for the adhesion of the OPs to the Fe₃O₄-C18 magnetic nanoparticles     

Thermodynamic dissociation constants of risedronate using spectrophotometric and potentiometric pH-titration

Risedronate inhibits bone resorption in diseases like osteoporosis, Paget’s disease, tumor bone diseases or the malfunction of phosphocalcium metabolism. The acid-base properties of risedronate in an aqueous solution have been studied in a pH range from 2 to 12 and can be described in terms of four dissociation steps: pK _a,2, pK _a,4, pK _a,5 (related to the dissociation of POH groups) and pK _a,3 related to the dissociation of protonated amino group NH₃ ⁺. The mixed dissociation constants were determined at different ionic strengths I = 0.02 to 0.20 mol dm⁻³ KCl and of 25°C and 37°C using pH-spectrophotometric and pH-potentiometric titration methods. Determination of group parameters L ₀, H _T might lead to false estimates of common parameters p K _a;therefore, the computational strategy employed is important. A comparison between the two programs ESAB and HYPERQUAD demonstrated that the ESAB program provides a better fit of potentiometric titration curve. The thermodynamic dissociation constants pK _a^T were estimated by a nonlinear regression of (pK _a, I) data and a Debye-Hückel equation at 25°C and 37°C, pK _a,2^T = 2.37(1) and 2.44(1), pK _a,3^T = 6.29(3) and 6.26(1), pK _a,4^T = 7.48(1) and 7.46(2) and pK _a,5^T = 9.31(7) and 8.70(3) at 25°C and 37°C using pH-spectroscopic data and pK _a,2^T = 2.48(3) and 2.43(1), pK _a,3^T= 6.12(2) and 6.10(2), pK _a,4^T = 7.25(2) and 7.23(1) and pK _a,5^T = 12.04(5) and 11.81(2) at 25°C and 37°C. The ascertained estimates of three dissociation constants pK _a,3, pK _a,4, pK _a,5 are in agreement with the predicted values obtained using PALLAS      

Nanostructured electrochemical DNA biosensors for detection of the effect of berberine on DNA from cancer cells

Multi walled carbon nanotubes (MWNT) in dimethylformamide (DMF) or aqueous sodium dodecyl sulfate (SDS) solution, colloidal gold nanoparticles (GNP) in phosphate buffer solution (PBS), and a GNP–MWNT mixture in aqueous SDS solution have been investigated for chemical modification of a screen-printed carbon electrode used as the signal transducer of a dsDNA-based biosensor. Differential pulse voltammetry of the DNA redox marker and the guanine moiety anodic oxidation and cyclic voltammetry with K₃[Fe(CN)₆] as indicator revealed substantial enhancement of the response of the biosensor, particularly when MWNT in SDS solution was used. The biosensor was used in testing of berberine, an isoquinoline plant alkaloid with significant antimicrobial and anticancer activity. Berberine had a very strong, concentration-dependent, effect on the structural stability of DNA from the human cancer cells (U937 cells) whereas non-cancer cells were changed only when berberine concentrations were relatively high 75 and 50 μg mL⁻¹. Figure Schematic illustration of preparation of the nanostructured films: (a) layer-to-layer coverage (DNA/nanomaterial/SPE); (b) mixed coverage (DNA-nanomaterial/SPE)     

Imidazolium-based ionic liquid derivative/Cu<Superscript>II</Superscript> complexes as efficient catalysts of the lucigenin chemiluminescence system and its application to H<Subscript>2</Subscript>O<Subscript>2</Subscript> and glucose detection

The effects of six synthetic imidazolium-based ionic liquids (ILs) on the Cu^II-catalyzed chemiluminescence of lucigenin (Luc-CL) in the pH range 6.0–11 were investigated. Preliminary experiments found that the CL emission was strongly enhanced or inhibited in the presence of the ILs. The degree of enhancement or inhibition of the CL intensity in the presence of each IL was related to the molecular structure of the IL, the medium used, and the pH. The maximum enhancement of the CL intensity was observed at pH 9.0 (amplification factor?=?443). This decrease in the pH at which maximum CL enhancement occurred and the substantial signal amplification of the Luc-CL may be related to a strong interaction between Cu^II and the imidazolium ring of superior ILs at this pH. Additionally, the formation of IL microdomains in semi-aqueous media permitted more solubility of the product yielded by the Luc-CL reaction (N-methylacridone), which could increase the CL intensity. To obtain consistent data on the catalytic efficiency of Cu^II in the presence of various ILs as well as the corresponding CL emission intensities, fluorescence quantum yields (Φ _F) of lucigenin were measured under the same conditions. Comparison of the data pointed to the mechanism that controls the properties of Luc-CL in the presence of the Cu^II/IL complexes. Based on the catalytic effect of the Cu^II/IL complex and the measurement of the enzymatically generated H₂O₂, a novel, simple, and sensitive CL method for determining glucose with a detection limit (LoD) of 6.5 μM was developed. Moreover, this method was satisfactorily applied to the determination of glucose in human serum and urine samples.

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Graphical Abstract The lucigenin chemiluminescence assay for H₂O₂ and glucose using imidazolium–based ionic liquid derivatives/Cu^II complexes as efficient catalysts at pH 9.0

     

New hexamethine–hemicyanine dyes for the development of integrated optochemical sensors

New far-visible absorbing anilino-cyanine dyes have been synthesised for future application as chromoionophores in integrated waveguide absorbance optodes based on bulk optodes. The effect of the heterocycle, of the substitution of the heterocyclic nitrogen and of the type of heptamethine central ring on the pK _a values (4.3–8.2 in ethanol–water solutions and 9.5–11.0 in plasticised PVC membranes), on the spectroscopic characteristics of the dye and on photostability is discussed. pH-selective bulk optodes have been formulated as a first approach to develop ion-selective optodes, and sensitivity, repeatability, lifetime and response time have been determined. The dyes show good analytical behaviour for use as chromoionophores for the development of ion-selective optodes. Reversible (80–87%), fast (tr_90% = 0.94–2.28 min) and pH-sensitive membranes (slopes of 0.09–0.23 ΔAbs·pHdec^–1, absorbance range 0.19–0.53) have been obtained. Moreover, they exhibit good spectroscopic features for employment with integrated optochemical sensors: absorption maxima of the acidic species in plasticised PVC membranes matched those of 650–670-nm LEDs, high molar absorption coefficients ( L mol^–1 cm^–1 and L mol⁻¹ cm⁻¹) and fluorescence. Absorption spectra of the acidic and basic structures of one of the synthesised chromoionophores at different pKa values. Electronic supplementary material Supplementary material is available in the online version of this article at and is accessible for authorized users.     

Simultaneous determination of phenylenediamine isomers and dihydroxybenzene isomers in hair dyes by capillary zone electrophoresis coupled with amperometric detection

The simultaneous determination of three isomers of phenylenediamines (o, m, and p-phenylenediamine) and two isomers of dihydroxybenzenes (catechol and resorcinol) in hair dyes was performed by capillary zone electrophoresis coupled with amperometric detection (CZE–AD). The effects of working electrode potential, pH and concentration of running buffer, separation voltage, and injection time on CZE–AD were investigated. Under the optimum conditions the five analytes could be perfectly separated in 0.30 mol L⁻¹ borate–0.40 mol L⁻¹ phosphate buffer (pH 5.8) within 15 min. A 300 μm diameter platinum electrode had good responses at +0.85 V (versus SCE) for the five analytes. Their linear ranges were from 1.0 × 10⁻⁶ to 1.0 × 10⁻⁴ mol L⁻¹ and the detection limits were as low as 10⁻⁷ mol L⁻¹ (S/N = 3). This working electrode was successfully used to analyze eight kinds of hair dye sample with recoveries in the range 91.0–108.0% and RSDs less than 5.0%. These results demonstrated that capillary zone electrophoresis coupled with electrochemical detection using a platinum working electrode as detector was convenient, highly sensitive, highly repeatable and could be used in the rapid determination of practical samples. Figure Electropherograms obtained from 10 mg mL⁻¹ hair dye sample solutions at a platinum working electrode under optimum CZE–AD conditions: (a) natural black (I), (b) golden: (1) p-phenylenediamine, (2) m-phenylenediamine, (3) o-phenylenediamine, (4) resorcinol, and (5) catechol     

(Tetramethylcyclobutadiene)cobalt complexes 7. Mono- and dinuclear arene complexes containing the [(C<Subscript>4</Subscript>Me<Subscript>4</Subscript>)Co]<Superscript>+</Superscript> fragment

The mononuclear arene complexes [Cb*Co(arene)]⁺ (3a–g; Cb* = C₄Me₄; arene is biphenyl (a), diphenylmethane (b), 1,2-diphenylethane (c), diphenyl ether (d), p-terphenyl (e), 1,2-dimesitylethane (f), or 1,3-dimesitylpropane (g)) were synthesized by the reactions of arenes either with the benzene complex [Cb*Co(C₆H₆)]⁺ (1) under visible light irradiation or with the acetonitrile derivative [Cb*Co(MeCN)₃]⁺ (2) in refluxing THF. The reactions of 2 with 1,2-diphenyle-thane, 1,3-dimesitylpropane, and p-terphenyl in a ratio of 2: 1 afforded the dinuclear complexes [Cb*Co(μ-η:η-arene)CoCb*]²⁺ (4c,e,g). The stability of the dinuclear arene complexes was estimated by DFT calculations. The structures of the complexes [3a]PF₆ and [3e]PF₆ ere established by X-ray diffraction. For Part 6, see Ref. 1. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 3, pp. 535–539, March, 2008.     

Theoretical study on structures and stability of triplet SiC<Subscript>3</Subscript>O isomers

Various levels of calculations are carried out~for exploring the potential energy surface (PES) of triplet SiC₃O, a molecule of potential interest in interstellar chemistry. A total of 38 isomers are located on the PES including chain-like, cyclic and cage-like structures, which are connected by 87 interconversion transition states at the DFT/B3LYP/6-311G(d) level. The structures of the most relevant isomers and transition states are further optimized at the QCISD/6-311G(d) level followed by CCSD(T)/6-311+G(2df) single-point energy calculations. At the QCISD level, the lowest lying isomer is a linear SiCCCO 1 (0.0 kcal/mol) with the ³ ∑ electronic state, which possesses great kinetic stability of 59.5 kcal/mol and predominant resonant structure . In addition, the bent isomers CSiCCO 2 (68.3 kcal/mol) and OSiCCC 5 (60.1 kcal/mol) with considerable kinetic stability are also predicted to be candidates for future experimental and astrophysical detection. The bond natures and possible formation pathways in interstellar space of the three stable isomers are discussed. The predicted structures and spectroscopic properties for the relevant isomers are expected to be informative for the identification of SiC₃O and even larger SiC _n O species in laboratory and interstellar medium. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Flow-injection solid surface lanthanide-sensitized luminescence sensor for determination of <Emphasis Type="Italic">p</Emphasis>-aminobenzoic acid

A single optosensing device based on lanthanide-sensitized luminescence was developed for determination of p-aminobenzoic acid (PABA). The method is based on the formation of a complex between PABA and Tb(III) immobilized on the solid phase (QAE A-25 resin) placed inside the flow cell. NaCl (1 M) was used as carrier solution and HCl (0.05 M) as eluent. The sample solutions of PABA (100 μL) containing Tb(III) and buffered at pH = 6.0 were injected into the carrier stream and the luminescence was measured at λ _ex = 290 nm and λ _em = 546 nm. The method shows a linear range from 0.2 to 6.0 μg mL⁻¹ with an RSD of 1.2% (n = 10) and a sampling frequency of 22 h⁻¹. A remarkable characteristic of the method is its high selectivity which allows it to be satisfactorily applied to the analysis of PABA in pharmaceutical samples without prior treatment. Figure Typical emission bands of Tb(III) in a solid-phase PABA–Tb(III) luminescence spectrum     

Sol-assisted spray-drying synthesis of porous Li<Subscript>3</Subscript>V<Subscript>2</Subscript>(PO<Subscript>4</Subscript>)<Subscript>3</Subscript>/C microspheres as high-activity cathode materials for lithium-ion batteries

Herein, porous Li₃V₂(PO₄)₃/C microspheres made of nanoparticles are obtained by a combination of sol spray-drying and subsequent-sintering process. Beta-cyclodextrin serves as a special chelating agent and carbon source to obtain carbon-coated Li₃V₂(PO₄)₃ grains with the size of ca. 30–50?nm. The unique porous structure and continuous carbon skeleton facilitate the fast transport of lithium ion and electron. The Li₃V₂(PO₄)₃/C microspheres offer an outstanding electrochemical performance, which present a discharge capacity of 122?mAh?g^?1 at 2?C with capacity retention of 96% at the end of 1000 cycles and a high-rate capacity of 113?mAh?g^?1 at 20?C in the voltage window of 3.0–4.3?V. Moreover, the Li₃V₂(PO₄)₃/C microspheres also give considerable cycling stability and high-rate reversible capacity at a higher end-of-charge voltage of 4.8?V.

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Porous,hollow Li<Subscript>1.2</Subscript>Mn<Subscript>0.53</Subscript>Ni<Subscript>0.13</Subscript>Co<Subscript>0.13</Subscript>O<Subscript>2</Subscript> microspheres as a positive electrode material for Li-ion batteries

A porous, hollow, microspherical composite of Li₂MnO₃ and LiMn_1/3Co_1/3Ni_1/3O₂ (composition: Li_1.2Mn_0.53Ni_0.13Co_0.13O₂) was prepared using hollow MnO₂ as the sacrificial template. The resulting composite was found to be mesoporous; its pores were about 20 nm in diameter. It also delivered a reversible discharge capacity value of 220 mAh g^?1 at a specific current of 25 mA g^?1 with excellent cycling stability and a high rate capability. A discharge capacity of 100 mAh g^?1 was obtained for this composite at a specific current of 1000 mA g^?1. The high rate capability of this hollow microspherical composite can be attributed to its porous nature.

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Graphical Abstract ?

     

Sample preparation by in-gel digestion for mass spectrometry-based proteomics

The proteomic characterization of proteins and protein complexes from cells and cell organelles is the next challenge for investigation of the cell. After isolation of the cell compartment, three steps have to be performed in the laboratory to yield information about the proteins present. The protein mixtures must be separated into single species, broken down into peptides, and, finally, identified by mass spectrometry. Most scientists engaged in proteomics separate proteins by electrophoresis. For characterization and identification of proteomes, mass spectrometry of peptides is the method of choice. To combine electrophoresis and mass spectrometry, sample preparation by “in-gel digestion” has been developed. Many procedures are available for in-gel digestion, which inspired us to review in-gel digestion approaches. Figure Classical in-gel digestion process for a protein band stained with CBB. Protein bands are cut from the polyacrylamide gel (1). CBB molecules (blue circles) bound to the protein are released by iterative incubation in a buffered organic solvent system (2). To increase digestion efficiency and sequence coverage proteins are reduced (3) and alkylated (4). Proteins are subsequently digested with proteolytic enzymes (scissors symbols), typically trypsin (5). Trypsin cleaves at the amino acid residues arginine (R) and lysine (K). The resulting peptides (A, B, and C) are extracted from the polyacrylamide matrix (6). The peptide solution can be further purified for analysis by mass spectrometry (Section “Concentration and desalting of peptides”)     

Assembly of layer-by-layer films of heme proteins and single-walled carbon nanotubes: electrochemistry and electrocatalysis

After being treated by mixed acids, single-walled carbon nanotubes (SWNTs) were shortened and had negatively charged groups on the surface. Positively charged hemoglobin or myoglobin at pH 5.0 was successfully assembled with SWNTs into layer-by-layer films on solid surfaces, designated as {SWNT/protein} _n . While only those proteins in the first few bilayers closest to the electrode surface exhibited electroactivity, the {SWNT/protein} _n films demonstrated a much higher fraction of electroactive proteins and better controllability in film construction compared with cast films of the proteins and carbon nanotubes. The proteins in the {SWNT/protein} _n films retained their near-native structure at medium pH. The stable protein film electrode showed good electrocatalytic properties toward reduction of oxygen and hydrogen peroxide, demonstrating the potential application of the {SWNT/protein} _n films as a new type of biosensor based on the direct electrochemistry of proteins without using mediators. Figure Cyclic voltammograms at 0.2 V s⁻¹ in pH 7.0 buffers with different number of bilayers (n) for layer-by-layer {single-walled carbon nanotube/hemoglobin} _n films.     

Electrospray mass spectrometry analysis of dendritic branches bearing peripheral fullerene subunits

The electrospray mass spectrometric characterization of neutral dendrons with a carboxylic acid function or a t-butyl ester moiety at the central point and up to eight peripheral C₆₀ subunits has been performed and is described in detail. Molecules bearing a carboxylic acid group at the center turned out to be preferentially ionized by deprotonation, whereas those with a t-butyl ester head group were ionized by reduction of the C₆₀ units in the infusion capillary of the electrospray source. Electronic supplementary material Supplementary material is available for this article at and is accessible for authorized users.