Establishing the standard deviation for proficiency assessment ( \hat{\sigma } ). in microbiology PT/EQA schemes

Microbiological testing can be challenging due to the unique nature of microorganisms. Studies have shown that values for reproducibility in microbiology are difficult to establish as they can vary depending upon a number of factors such as the organism under test, the matrix and the test method. The relative lack of consistent data on reproducibility means it can be difficult for providers of microbiology PT schemes to establish a suitable standard deviation for proficiency assessment ( $ \hat{\sigma } $ ). Methods for establishing $ \hat{\sigma } $ are described in BS ISO 13528: 2005, but these are not all appropriate in microbiology, given the lack of available data and the large range of possible variables. Using the robust standard deviation of participant results is not recommended as this can vary greatly from round to round and means that performance is not comparable over time. Use of a fixed standard deviation depends very much on the perception of the PT scheme organiser as to what constitutes fitness-for-purpose. In microbiology, is it really necessary to obtain precise results? Should the emphasis be on the correct isolation and identification of organisms, and on performance over time to detect laboratory bias rather than on enumeration results alone?     

Identification of possible technical problems in determination of the major inorganic constituents of brown-rice flour by evaluating proficiency test results

To support skill upgrading in analysis of inorganic constituents of environmental and food samples, the National Metrology Institute of Japan (NMIJ) and the National Food Research Institute (NFRI) have organized a proficiency test (PT) of determination of Mn, Fe, Cu, Zn, As, and Cd in brown-rice flour based on the international standard (ISO/IEC 17043:2010). One hundred and thirty-three sets of reports were assessed by use of the E _n -number and z-score approaches in accordance with ISO/IEC 17043 and the international harmonized protocol for PT. The PT results and analytical procedures, reported in detail, were reviewed, and possible technical reasons for questionable or unsatisfactory results are discussed.

CORAL: QSPRs of enthalpies of formation of organometallic compounds

Available on the Internet the CORAL software gives reasonable good prediction for standard enthalpy of formation for selected organometallic compounds (n = 132). The approach is tested using five random splits of the considered data into the sub-training set (n = 32–49), calibration set (n = 36–51), test set (n = 10–29), and the validation set (n = 22–41). Compounds of the validation set are not involved in building up the models. The average statistical quality of prediction is the following: correlation coefficient ( $\overline{R^{2}} )$ R 2 ¯ ) $0.991\pm 0.005$ 0.991 ± 0.005 and standard error of estimation ( $\overline{s} )$ s ¯ ) $22.9 \pm 5.6$ 22.9 ± 5.6  kJ/mol.     

On-line optimizing control of the intermittent simulated moving bed process

The I-SMB process is one of the modifications to the standard SMB process that has been demonstrated both theoretically and experimentally to exhibit rather competitive performance (Katsuo and Mazzotti in J Chromatogr A 1217:1354, 2010a, 3067, 2010b; Katsuo et al. in J Chromatogr A 1218:9345, 2011). This work aims at showing that also the I-SMB process can be controlled and optimized by using the optimizing on-line controller developed at ETH Zurich for the standard SMB process (Erdem et al. in Ind Eng Chem Res 43:405, 2004a, 3895, 2004b; Grossmann et al. in Adsorption 14:423, 2008, AIChE J 54:1942008). This is achieved by using a virtual I-SMB unit based on a detailed model of the process; past experience with the on-line controller shows that the controller’s behavior on a virtual platform is essentially the same as in laboratory experiments.     

Reflections on the conformation, topology and thermodynamics of a polyelectrolyte chain in the presence of counterions with plausible applications

The simulation results from a basic polyelectrolyte chain consisting of an anionic string of 150 univalent negatively charged particles connected under various harmonic-like potential interactions with each other in the presence of a similar number of positive and free counter ions found in Jesudason et al. (EPJE $30$ 30 :341–350, 2009) forms the focal point for further discussion on chain models based on a survey of more recent developments in general polyelectrolyte theory. The topics discussed include persistence length definition, forcefields and methods of controlling simulation parameters, and thermodynamics. The data for the basic system was derived for the temperature range $0.1$ 0.1 – $10.0$ 10.0 in reduced units (corresponding to $\xi =10\text{-- }0.1$ ξ = 10 -- 0.1 ); the augmented data involves a $360$ 360 monomer chain. The data include the total and Coulombic energies, radial distribution functions, radii of gyration, end-to-end distances and snapshots of the system which are all discussed anew. Polyelectrolyte systems have been overwhelmingly associated with biophysical interpretations, but here it is suggested that these detailed studies and the consequent theoretical formulations could be extended further afield; non-biological ionic liquid systems with catalytic and energy storage applications are some of many other possibilities. However, the approach used by MD simulations to validate ionic liquid systems as carriers of molecules with catalytic moieties often refer to CPMD and DFT quantum methods, which is not the current norm as judged by the literature in especially coarse grained polyelectrolyte MD. The quantum approach could also be used for more detailed analysis of biophysical systems where one trend seems to be that the incorporation of details in simulations accounts for phenomena not explicable in coarser grained MD, for instance if conventional atomic ionic charges are assigned to all atom modeling. This is illustrated by a linear chain modeling a DNA polymer using different charge and size assignments for the same linear charge density. The trends are such that it might be expected that some form of routine standardization of force fields in the spirit of the Jorgensen OPLS-AA method that incorporates quantum calculations specific to a system will be implemented as a routine as refinements are seen to lead to more comprehensive rationalization.     

Volumetric Properties of l-Alanine and l-Serine in Aqueous N,N-Dimethylformamide Solutions at 298.15 K

The densities of l-alanine and l-serine in aqueous solutions of N,N-dimethylformamide (DMF) have been measured at 298.15 K with an Anton Paar Model 55 densimeter. Apparent molar volumes $ (V_{\phi } ) $ ( V ? ) , standard partial molar volumes $ (V_{\phi }^{0} ) $ ( V ? 0 ) , standard partial molar volumes of transfer $ (\Updelta_{\text{tr}} V_{\phi }^{0} ) $ ( Δ tr V ? 0 ) and hydration numbers have been determined for the amino acids. The $ \Updelta_{\text{tr}} V_{\phi }^{0} $ Δ tr V ? 0 values of l-serine are positive which suggest that hydrophilic–hydrophilic interactions between l-serine and DMF are predominant. The –CH₃ group of l-alanine has much more influence on the volumetric properties and the $ \Updelta_{\text{tr}} V_{\phi }^{0} $ Δ tr V ? 0 have smaller negative values. The results have been interpreted in terms of the cosphere overlap model.     

Heat capacity and density of solutions of calcium and cadmium nitrates in N-methylpyrrolidone at 298.15 K

The heat capacity and density of solutions of calcium and cadmium nitrates in N-methylpyrrolidone (MP) at 298.15 K are studied by calorimetry and densimetry. The obtained data are discussed in relation to certain features of solvation and complex formation in solutions of these salts. The standard partial molar heat capacities and volumes ( $\overline {C_{p^2 }^0 }$ and $\overline {V_2^0 }$ ) of the electrolytes in MP are calculated. The standard heat capacities $\overline {C_{p^i }^0 }$ and volumes $\overline {V_i^0 }$ of Ca²⁺ and Cd²⁺ ions in MP at 298.15 K were determined, along with the contribution from specific interactions to the values of $\overline {C_{p^i }^0 }$ and $\overline {V_i^0 }$ of Cd²⁺ ions in MP solution.     

Symmetry-itemized enumeration of RS-stereoisomers of allenes. I. The fixed-point matrix method of the USCI approach combined with the stereoisogram approach

After the RS-stereoisomeric group \(\mathbf{D}_{2d\widetilde{\sigma }\widehat{I}}\) of order 16 has been defined by starting point group \(\mathbf{D}_{2d}\) of order 8, the isomorphism between \(\mathbf{D}_{2d\widetilde{\sigma }\widehat{I}}\) and the point group \(\mathbf{D}_{4h}\) of order 16 is thoroughly discussed. The non-redundant set of subgroups (SSG) of \(\mathbf{D}_{2d\widetilde{\sigma }\widehat{I}}\) is obtained by referring to the non-redundant set of subgroups of \(\mathbf{D}_{4h}\) . The coset representation for characterizing the orbit of the four positions of an allene skeleton is clarified to be \(\mathbf{D}_{2d\widetilde{\sigma }\widehat{I}}(/\mathbf{C}_{s\widetilde{\sigma }\widehat{I}})\) , which is closely related to the \(\mathbf{D}_{4h}(/\mathbf{C}_{2v}^{\prime \prime \prime })\) . According to the unit-subduced-cycle-index (USCI) approach (Fujita, Symmetry and combinatorial enumeration of chemistry. Springer, Berlin 1991), the subduction of \(\mathbf{D}_{2d\widetilde{\sigma }\widehat{I}}(/\mathbf{C}_{s\widetilde{\sigma }\widehat{I}})\) is examined so as to generate unit subduced cycle indices with chirality fittingness (USCI-CFs). Then, the fixed-point matrix method of the USCI approach is applied to the USCI-CFs. Thereby, the numbers of quadruplets are calculated in an itemized fashion with respect to the subgroups of \(\mathbf{D}_{2d\widetilde{\sigma }\widehat{I}}\) . After the subgroups of \(\mathbf{D}_{2d\widetilde{\sigma }\widehat{I}}\) are categorized into types I–V, type-itemized enumeration of quadruplets is conducted to illustrate the versatility of the stereoisogram approach.     

The thermodynamic properties and solvation of lithium halides in N-methylpyrrolidone at 298.15 K

The heat capacity and density of solutions of lithium chloride, bromide, and iodide in N-methylpyrrolidone (I) were determined by calorimetry and densimetry techniques. The standard partial molar heat capacities and volumes ( $\overline {C^\circ _{p2} } $ and $\overline {V^\circ _2 } $ ) of lithium halides in I were calculated. The $\overline {C^\circ _{pi} } $ and $\overline {V^\circ _i } $ values for halogen and lithium ions in I were determined. The coordination numbers of the Li⁺, Cl^?, Br^?, and I^? ions in solutions in I at 298.15 K were calculated.     

Heats of formation of the amino acids re-examined by means of W1-F12 and W2-F12 theories

We have obtained accurate heats of formation for the twenty natural amino acids by means of explicitly correlated high-level thermochemical procedures. Our best theoretical heats of formation, obtained by means of the ab initio W1-F12 and W2-F12 thermochemical protocols, differ significantly (RMSD = 2.3 kcal/mol, maximum deviation 4.6 kcal/mol) from recently reported values using the lower-cost G3(MP2) method. With the more recent G4(MP2) procedure, RMSD drops slightly to 1.8 kcal/mol, while full G4 theory offers a more significant improvement to 0.72 kcal/mol (max. dev. 1.4 kcal/mol for glutamine). The economical G4(MP2)-6X protocol performs equivalently at RMSD = 0.71 kcal/mol (max. dev. 1.6 kcal/mol for arginine and glutamine). Our calculations are in excellent agreement with experiment for glycine, alanine and are in excellent agreement with the recent revised value for methionine, but suggest revisions by several kcal/mol for valine, proline, phenylalanine, and cysteine, in the latter case confirming a recent proposed revision. Our best heats of formation at 298 K ( $\Delta H_{f,298}^{\circ }$ ) are as follows: at the W2-F12 level: glycine ?94.1, alanine $-$ 101.5, serine $-$ 139.2, cysteine $-$ 94.5, and methionine $-$ 102.4  kcal/mol, and at the W1-F12 level: arginine $-$ 98.8, asparagine $-$ 146.5, aspartic acid $-$ 189.6, glutamine $-$ 151.0, glutamic acid $-$ 195.5, histidine $-$ 69.8, isoleucine $-$ 118.3, leucine $-$ 118.8, lysine $-$ 110.0, phenylalanine $-$ 76.9, proline $-$ 92.8, threonine $-$ 149.0, and valine $-$ 113.6 kcal/mol. For the two largest amino acids, an average over G4, G4(MP2)-6X, and CBS-QB3 yields best estimates of $-$ 58.4 kcal/mol for tryptophan, and of $-$ 117.5 kcal/mol for tyrosine. For glycine, we were able to obtain a “quasi-W4” result corresponding to $\hbox {TAE}_e$  = 968.1, $\hbox {TAE}_0$  = 918.6, $\Delta H_{f,298}^{\circ }=-90.0$ , and $\Delta H_{f,298}^{\circ }=-94.0$  kcal/mol.     

Determination of Tryptophan in Lysozyme and Lysozyme Hydrolysate by Chiral LC Using d-Tryptophan as Internal Standard

In the present study, a new LC method is described for the quantitation of tryptophan (Trp) in lysozyme and enzymatic lysozyme hydrolysate. To compensate for partial breakdown of Trp during hydrolysis with 4 M methanesulfonic acid, an enantiomer dilution method was developed. The method makes use of free d-Trp or a d-Trp-containing dipeptide as internal standard for the quantitation of l-tryptophan in these matrices. After acid hydrolysis in 4 M methanesulfonic acid, LC analysis is performed on a Crownpak CR chiral column in combination with fluorescence detection. Optimum time and temperature for the acid hydrolysis were investigated in order to obtain complete hydrolysis of the source materials. A comparison of the l-Trp recoveries was made for d-Trp and Gly-d-Trp as internal standards. By choosing a hydrolysis time of 150 min at 150 °C, 93% recovery of l-Trp from lysozyme was achieved. Under these conditions, no racemization occurred. When choosing d-Trp as internal standard, a direct LC method for l-Trp in lysozyme and enzymatic lysozyme hydrolysate was established without the need for pre-column derivatization and without the need to use Trp protecting agents during acid hydrolysis.     

Note on the bimodal distribution of PT results

The practitioner’s report "Treatment of bimodality in proficiency test of pH in bioethanol matrix" by Sarmanho et al. deals with a proficiency test (PT) for the measurement of pH in bioethanol. One group of 19 participating laboratories used an electrode that contained saturated LiCl and the other one KCl. The results of the LiCl group are biased, and those of the KCl group are unbiased as compared with the assigned reference value \(y_\mathrm{{RM}}\), and hence, the distribution of the laboratory means is bimodal. In order to deal with this situation, Sarmanho et al. present and carry out two different methods of fitting the bimodal distribution of the laboratory means: a fit by a mixture of two normal distributions and a Gaussian kernel estimation. Since this rather advanced statistical analysis does not help to solve the practical problem, some recomendations of ISO 17043 are discussed that might be useful for the coordinator of the PT and as well for the participating laboratories.     

Clar and Fries numbers for benzenoids

A Kekulé structure of a benzenoid or a fullerene $\Gamma $ Γ is a set of edges $K$ K such that each vertex of $\Gamma $ Γ is incident with exactly one edge in $K$ K . The set of faces in $\Gamma $ Γ that have exactly three edges in $K$ K are called the benzene faces of $K$ K . The Fries number of $\Gamma $ Γ is the maximum number of benzene faces over all possible Kekulé structures for $\Gamma $ Γ . The Clar number is the maximum number of independent benzene faces over all possible Kekulé structures for $\Gamma $ Γ . It is often assumed, but never proved, that some set of independent benzene faces giving the Clar number is a subset of a set of benzene faces giving the Fries number. In Hartung (The Clar structure of fullerenes, Ph.D. Dissertation. Syracuse University, 2012) it is shown that this assumption is false for a large class of fullerenes. In this paper, we prove that this assumption is valid for a large a class of benzenoids.     

Carbon nanotori and nanotubes encapsulating carbon atomic-chains

In this paper we investigate toroidal carbon nanotubes (carbon nanotori) encapsulating a single symmetrically located carbon atomic-chain. The interaction energy of the carbon chain is found from the Lennard-Jones potential using the continuous approach which assumes that atoms are uniformly distributed over the surface of the torus and the line of the circular chain with constant atomic surface and line densities, respectively. We assume that the chain is centrally located and that the carbon nanotorus is synthesized from a perfect carbon nanotube. We predict that the carbon chain can be encapsulated inside the carbon nanotorus when the cross-sectional radius \(r\) of the nanotorus is larger than 3.17 Å. At the minimum energy, a value of the toroidal radius \(R\) lies between 3.6 and 3.7 Å corresponding to each value of \(r\) . We also investigate the energy of carbon chains inside carbon nanotubes, which are (4,4), (5,5) and (10,0) tubes. We find that they are energetically favourable in (5,5) and (10,0) tubes, but not in a (4,4) tube, because it is geometrically too small, and these results are in agreement with existing studies. The same results for these three carbon nanotubes can also be obtained from the corresponding nanotori when \(R\) goes to infinity.     

A method for the determination of d-kynurenine in biological tissues

d-Kynurenine (d-KYN), a metabolite of d-tryptophan, can serve as the bioprecursor of kynurenic acid (KYNA) and 3-hydroxykynurenine, two neuroactive compounds that are believed to play a role in the pathophysiology of several neurological and psychiatric diseases. In order to investigate the possible presence of d-KYN in biological tissues, we developed a novel assay based on the conversion of d-KYN to KYNA by purified d-amino acid oxidase (d-AAO). Samples were incubated with d-AAO under optimal conditions for measuring d-AAO activity (100 mM borate buffer, pH 9.0), and newly produced KYNA was detected by high-performance liquid chromatography (HPLC) with fluorimetric detection. The detection limit for d-KYN was 300 fmol, and linearity of the assay was ascertained up to 300 pmol. No assay interference was noted when other d-amino acids, including d-serine and d-aspartate, were present in the incubation mixture at 50-fold higher concentrations than d-KYN. Using this new method, d-KYN was readily detected in the brain, liver, and plasma of mice treated systemically with d-KYN (300 mg/kg). In these experiments, enantioselectivity was confirmed by determining total kynurenine levels in the same samples using a conventional HPLC assay. Availability of a sensitive, specific, and simple method for d-KYN measurement will be instrumental for evaluating whether d-KYN should be considered for a role in physiology and pathology.     

Thermodynamic study of metal corrosion and inhibitor adsorption processes in copper/N-1-naphthylethylenediamine dihydrochloride monomethanolate/nitric acid system: part 2

N-1-Naphthylethylenediamine dihydrochloride monomethanolate (N-NEDHME) was tested as a corrosion inhibitor for copper in 2 M HNO₃ solution using the standard gravimetric technique at 303–343 K. N-NEDHME acts as an inhibitor for copper in an acidic medium. Inhibition efficiency increases with increase in concentration of N-NEDHME but decreases with a rise in temperature. Thermodynamic parameters such as adsorption heat ( $ \Updelta H_{\text{ads}}^\circ $ ), adsorption entropy ( $ \Updelta S_{\text{ads}}^\circ $ ) and adsorption free energy ( $ \Updelta G_{\text{ads}}^\circ $ ) were obtained from experimental data of the temperature studies of the inhibition process at five temperatures ranging from 303 to 343 K. Kinetic parameters activation such as $ E_{a} $ , $ \Updelta H_{\text{a}}^\circ $ , $ \Updelta S_{\text{a}}^\circ $ and pre-exponential factors have been calculated and are discussed. Adsorption of N-NEDHME on the copper surface in 2 M HNO₃ follows the Langmuir isotherm model.     

A new approach to maturity of molecules by rationality of finite groups

These two concepts, maturity in chemistry and rationality in group theory were discovered by a chemist, Fujita. In the present study, we introduce a new approach to maturity and immaturity of simple groups, using the deep theorem (Feit and Seitz in Ill J Math 33:101–131, 1988). Additionally, we prove that 1,3,5-trimethyl-2,4,6-trinitrobenzene are always unmatured and tetra platinum(II) with point group $D_{2n}$ , dihedral group of order $2n$ , is unmatured if $n\ne 1,2,3,4,6$ . Also, we compute integer-valued characters of the simple sporadic group $Ly$ .     

Symmetry-itemized enumeration of quadruplets of RS-stereoisomers: I—the fixed-point matrix method of the USCI approach combined with the stereoisogram approach

The RS-stereoisomeric group $\mathbf{T}_{d\widetilde{\sigma }\widehat{I}}$ is examined to characterize quadruplets of RS-stereoisomers based on a tetrahedral skeleton and found to be isomorphic to the point group $\mathbf{O}_{h}$ of order 48. The non-redundant set of subgroups (SSG) of $\mathbf{T}_{d\widetilde{\sigma }\widehat{I}}$ is obtained by referring to the non-redundant SSG of $\mathbf{O}_{h}$ . The coset representation for characterizing the orbit of the four positions of the tetrahedral skeleton is clarified to be $\mathbf{T}_{d\widetilde{\sigma }\widehat{I}}(/\mathbf{C}_{3v\widetilde{\sigma }\widehat{I}})$ , which is closely related to the $\mathbf{O}_{h}(/\mathbf{D}_{3d})$ . According to the unit-subduced-cycle-index (USCI) approach (Fujita in Symmetry and combinatorial enumeration in chemistry. Springer, Berlin, 1991), the subdution of $\mathbf{T}_{d\widetilde{\sigma }\widehat{I}}(/\mathbf{C}_{3v\widetilde{\sigma }\widehat{I}})$ is examined so as to generate unit subduced cycle indices with chirality fittingness (USCI-CFs). The fixed-point matrix method of the USCI approach is applied to the USCI-CFs. Thereby, the numbers of quadruplets are calculated in an itemized fashion with respect to the subgroups of $\mathbf{T}_{d\widetilde{\sigma }\widehat{I}}$ . After the subgroups of $\mathbf{T}_{d\widetilde{\sigma }\widehat{I}}$ are categorized into types I–V, type-itemized enumeration of quadruplets is conducted to illustrate the versatility of the stereoisogram approach.     

On k-resonance of grid graphs on the plane,torus and cylinder

Grid graphs on the plane, torus and cylinder are finite 2-connected bipartite graphs embedded on the plane, torus and cylinder, respectively, whose every interior face is bounded by a quadrangle. Let \(k\) be a positive integer, a grid graph is \(k\) -resonant if the deletion of any \(i \le k\) vertex-disjoint quadrangles from \(G\) results in a graph either having a perfect matching or being empty. If \(G\) is \(k\) -resonant for any integer \(k \ge 1\) , then it is called maximally resonant. In this study, we provide a complete characterization for the \(k\) -resonance of grid graphs \(P_m\times P_n\) on plane, \(C_m\times C_n\) on torus and \(P_m\times C_n\) on cylinder.