Languages for Statistics and Data Analysis

Abstract

Languages for data analysis and statistics must be able to cover the entire spectrum from improvisation and fast prototyping to the implementation of streamlined, specialized systems for routine analyses. Such languages must not only be interactive but also programmable, and the distinctions between language, operating system, and user interface get blurred. The issues are discussed in the context of natural and computer languages, and of the different types of user interfaces (menu, command language, batch). It is argued that while such languages must have a completely general computing language kernel, they will contain surprisingly few items specific to data analysis—the latter items more properly belong to the “literature” (i.e., the programs) written in the language.     

Comparison of direct infusion and on-line liquid chromatography/electrospray ionization mass spectrometry for the analysis of nucleic acids

The applicability of ion-pair reversed-phase high-performance liquid chromatography/electrospray ionization mass spectrometry (IP-RP-HPLC/ESI-MS) and direct infusion/ESI-MS to the characterization of nucleic acid mixtures was evaluated by the analysis of the reaction products obtained from solid-phase synthesis of a 39-mer oligonucleotide. IP-RP-HPLC/ESI-MS was performed using 200 microm i.d. capillary columns packed with octadecylated, micropellicular poly(styrene-divinylbenzene) particles and applying gradients of acetonitrile in 50 mM triethylammonium bicarbonate (TEAB). Three different solvent systems were utilized for direct infusion/ESI-MS with removal of metal cations by on-line cation exchange: (1) 10 mM triethylamine (TEA) in 50% aqueous acetonitrile, (2) 2.2 mM TEA, 400 mM hexafluoro-2-propanol (HFIP) in 20% aqueous methanol and (3) 50 mM TEAB in 10% aqueous acetonitrile. Owing to its separation capability, the highest selectivity and specificity were achieved with IP-RP-HPLC/ESI-MS, which, apart form the 39-mer target sequence, allowed the identification of two isobutyryl-protected target sequences and a 10-mer and 20-mer failure sequence. Direct infusion/ESI-MS with TEA-acetonitrile or TEA-HFIP-methanol as solvent revealed signals for the 39-mer in the m/z range 700-1600. The presence of derivatives containing one, two, three and four isobutyryl groups indicated that the hydrolysis of the protecting groups after solid-phase synthesis was not complete. Failure sequences could not be identified by direct infusion/ESI-MS under conditions favoring multiple charging of the analytes owing to the high chemical background and coincidental overlapping of m/z signals. However, efficient charge state reduction upon addition of carbonic acid to the electrosprayed solvent shifted the signals of the 39-mer and derivatives to m/z values >2400 and allowed the detection of seven different failure sequences, ranging from the 8-mer to the 23-mer, in the mixture.     

Towards a modular,versatile and portable sensor system for measurements in gaseous environments based on microcantilevers

Microfabricated silicon cantilever sensor arrays represent a powerful platform for sensing applications in physics, chemistry, material science, biology and medicine. The sensor response is mechanical bending due to absorption of molecules. In gaseous environment, polymer-coated microcantilevers are used as electronic nose for characterization of vapors, resulting in cantilever bending due to polymer swelling upon exposure. Medical applications involve fast characterization of exhaled patient's breath samples for detection of diseases, based on the presence of certain chemicals in breath. We present a portable, compact, modular microcantilever setup, which uses a micropump for aspiration and a bluetooth interface for remote data acquisition.     

Lactide Polymerisation with Air‐Stable and Highly Active Zinc Complexes with Guanidine–Pyridine Hybrid Ligands

New class of air‐stable catalysts for lactide polymerisation: Guanidine–pyridine hybrid ligands (picture, left) were used to prepare a series of zinc complexes (e.g., depicted cation [ZnL₂(CF₃SO₃)]⁺, where L is the quinoline‐containing ligand with R¹=R²=R³=R⁴=Me), in which the ligand binds through two different N‐donor atoms. The zinc complexes show high activity in ring‐opening polymerisation of d,l ‐lactide (right), giving polylactide with molecular masses up to 176 000 g mol^?1 and in high yield.

     

Optically detected magnetic resonance study of the lowest excited triplet state of aromatic thioketones: Xanthione

The aromatic thioketone xanthione has been investigated by means of the optically detected magnetic resonance (ODMR) technique in a n-hexane matrix at ≈ 1.1 K. It was established that the short-lived red emission, which is characteristic for many thione molecules, is phosphorescence. At high temperatures (77 K) this phosphorescence originates mainly (>80%) from the T₁^z (n, π*) sublevel (k_z^(r) >k_x^(r), k_y^(r). At low temperature (1.1 K) the intersystem crossing following S₂ (π, π*) ← S₀ excitation is a highly spin-sublevel selective process which populates predominantly the T₁^x and T₁^y, levels. Hence, the slow spin—lattice relaxation phosphorescence at low temperature originates from these sublevels. A value of 0.0611 cm^?1 was obtained for the zero-field parameter |E|/hc. A lower limit of 0.66 cm^?1 has been found for the zero-field parameter |D|/hc. This value is considerably larger than those observed for ketones, and it is shown that spin—orbit coupling contributes strongly to the zero-field splitting.     

Probing structural determinants distal to the site of hydrolysis that control substrate specificity of the 20S proteasome

The 20S proteasome is a large multicomponent protease complex. Relatively little is known about the mechanisms that control substrate specificity of its multiple active sites. We present here the crystal structure at 2.95 A resolution of a beta2-selective inhibitor (MB1) bound to the yeast 20S proteasome core particle (CP). This structure is compared to the structure of the CP bound to a general inhibitor (MB2) that covalently modified all three (beta1, beta2, beta5) catalytic subunits. These two inhibitors differ only in their P3 and P4 residues, thereby highlighting binding interactions distal to the active site threonine that control absolute substrate specificity of the complex. Comparisons of the CP-bound structures of MB1, MB2, and the natural products epoxomycin and TMC-95A also provide information regarding general binding modes for several classes of proteasome inhibitors.     

Characterisation of five technical mixtures of brominated flame retardants

The main components of five technical mixtures of brominated flame retardants were identified by mass spectroscopy, H-NMR, IR spectroscopy, elementary analysis, and HRGC-MS, respectively. The mixtures have been identified as: phosphoric acid bromopropylates: Bromcal P 67-6 HP; C18-alkylated bromophenols: Bromcal P 40-3; dibromopropyl-2,4,6-tribromophenyl ether: Bromcal 73-5 PE; brominated diphenyl ethers (PBrDE): Bromcal 70-5 DE; decabromodiphenyl ether: Bromcal 82-0. Gas chromatographic retention data of the various constituents were measured on standard GC columns. The data prove the interference of some of the brominated compounds with PCBs and other halogenated pesticides in HRGC using the electron capture detector.     

Influence of Cyclodextrins on the Kinetics of Oxidation of Amino Acids and BSA by Hydrazyl Radicals

The kinetics of oxidation of amino acids (Arg, His, Lys, Phe, Thr and Tyr), a dipeptide (Gly-His), and BSA (bovine serum albumin) by two persistent water soluble free radicals of the hydrazyl type has been studied.The rate decreases in the order Arg>Lys>Tyr>Thr>HisBSAPheGly-His with bothfree radicals. Addition to the reaction mixture of - and -cyclodextrin decreases the oxidation rate, probably due to amino acidencapsulation in the cyclodextrin cavity. -Cyclodextrin protects more efficiently against oxidation than -cyclodextrin.     

Sulfonylcarbamimidic azides from sulfonyl chlorides and 5-aminotetrazole

Treatment of o-nitrobenzenesulfonyl chloride ( 3 ) with 5-aminotetrazole (5-AT) gave [(2-nitrophenyl)-sulfonyl]carbamimidic azide ( 6 ), a ring-opened isomer of the expected N-(1H-tetrazol-5-yl)-2-nitrobenzenesulfonamide ( 4 ). Sulfonylcarbamimidic azide 6 was converted to 2-amino-N-(aminoiminomethyl)benzene-sulfonamide ( 7 ) with ethanolic stannous chloride, and to 3-amino-1,2,4-thiadiazine 1,1-dioxide ( 8 ) with sodium dithionite. Methanesulfonyl chloride ( 9 ) and 5-AT gave 2-(methylsulfonyl)carbamimidic azide ( 10 ), which isomerized to 5-[(methylsulfonyl)amino]-1H-tetrazole ( 11 ) in warm ethanol. Attempted cycloaddition of 2-(phenylsulfonyl)carbamimidic azide ( 13 ) and ethyl vinyl ether led only to alkylated tetrazole products. In addition, other tetrazole-alkylating reactions are described. Isomers produced from these alkylations were differentiated with ¹³C nmr spectroscopy.     

Local elevation: A method for improving the searching properties of molecular dynamics simulation

Summary The concept of memory has been introduced into a molecular dynamics algorithm. This was done so as to persuade a molecular system to visit new areas of conformational space rather than be confined to a small number of low-energy regions. The method is demonstrated on a simple model system and the 11-residue cyclic peptide cyclosporin A. For comparison, calculations were also performed using simulated temperature annealing and a potential energy annealing scheme. Although the method can only be applied to systems with a small number of degrees of freedom, it offers the chance to generate a multitude of different low-energy structures, where other methods only give a single one or few. This is clearly important in problems such as drug design, where one is interested in the conformational spread of a system.