A note on model diagnostics in longitudinal data analysis

Longitudinal study has become one of the most commonly adopted designs in medical research. The generalized estimating equations (GEE) method and/or mixed effects models are employed very often in causal inferences. The related model diagnostic procedures are not yet fully formalized, and perhaps never will be. The potential causes of major problems are the high variety of the dependence within subjects and/or the number of repeated measurements. A single testing procedure, e.g., run test, is not possible to resolve all model diagnostics problems in longitudinal data analysis. Multiple quantitative indexes for model diagnostics are needed to take into account this variety. We propose eight testing procedures for randomness accompanied with some conventional and/or non-conventional plots to remedy model diagnostics in longitudinal data analysis. The proposed issue in this paper is well illustrated with four clinical studies in Taiwan.     

Synthetic erythropoietic proteins: tuning biological performance by site-specific polymer attachment

Chemical synthesis in combination with precision polymer modification allows the systematic exploration of the effect of protein properties, such as charge and hydrodynamic radius, on potency using defined, homogeneous conjugates. A series of polymer-modified synthetic erythropoiesis proteins were constructed that had a polypeptide chain similar to the amino acid sequence of human erythropoietin but differed significantly in the number and type of attached polymers. The analogs differed in charge from +5 to -26 at neutral pH and varied in molecular weight from 30 to 54 kDa. All were active in an in vitro cell proliferation assay. However, in vivo potency was found to be strongly dependent on overall charge and size. The trends observed in this study may serve as starting points for the construction of more potent synthetic EPO analogs in the future.     

Role of adsorption in zeolite-catalyzed hydrocarbon cracking reaction

The activity for hydrocarbon cracking of zeolite catalysts depends on the type of zeolite and steam treatment. By comparing the activities of different zeolites under the condition where the catalyst did not undergo deactivation and the product distributions were identical, and presumably for the monomolecular mechanism, it was found that there were no differences in the chemical properties of the active sites in the zeolites. The apparent differences in catalytic activities among zeolites could be attributed to different concentrations of adsorbed alkane reactants, which is a consequence of the different strength of interaction of the alkyl groups with the zeolite walls. The latter may also be a significant contribute to the observed different strengths of interaction of alkyl amines with the Brønsted acid sites in zeolites.     

Biradicals/zwitterions from thermolysis of enyne-isocyanates. Application to the synthesis of 2(1H)-pyridones, benzofuro[3,2-c]pyridin-1(2H)-ones, 2,5-dihydro-1H-pyrido[4,3-b]indol-1-ones, and related compounds

Thermolysis of benzannulated enyne-isocyanates 13 and enyne-isocyanates 36 and 37 promoted the cycloaromatization reactions to generate in situ O,4-didehydro-2-hydroxyquinolines and O,4-didehydro-2-hydroxypyridines, respectively, as reactive intermediates. These cycloaromatized intermediates could be captured either as biradicals and/or as zwitterions depending on the nature of the substituent at the alkynyl terminus. The intermediate derived from cycloaromatization of 13a bearing a phenyl substituent could be regarded as biradical 14, which then abstracts hydrogen atoms from gamma-terpinene leading to 2(1H)-quinolinone 15. Alternatively, the same intermediate could also be regarded as zwitterion 14', which then undergoes an initial hydride abstraction from gamma-terpinene followed by protonation to produce 15. The presence of a 2-phenylethyl substituent in 13b and 37a or a 2-methylphenyl substituent in 37b also allowed the resulting intermediates to be captured intramolecularly either as biradicals or as zwitterions, producing 2(1H)-quinolinone 19, 2(1H)-pyridone 39, and benzopyranopyridine 43, respectively. On the other hand, with a 2-methoxyphenyl, a 2-(dimethylamino)phenyl, or a 3-methoxypropyl substituent, the chemical behavior of the cycloaromatized adduct could be best accounted for in terms of a zwitterionic intermediate leading to benzofuro[3,2-c]quinolin-6(5H)-one (20), 5,11-dihydro-11-methyl-6H-indolo[3,2-c]quinolin-6-one (25), benzofuro[3,2-c]pyridin-1(2H)-one 44, 2,5-dihydro-2,5-dimethyl-1H-pyrido[4,3-b]indol-1-one 46, and related compounds. Interestingly, thermolysis of 37f bearing a 2-(methoxymethyl)phenyl substituent at the alkynyl terminus produced the unexpected benzopyranopyridine 56 as the major product in a process involving the cleavage of the bond between the methoxyl oxygen and the adjacent methylene carbon. The efficiency and selectivity of the cycloaromatization reaction could also be enhanced by the introduction of 1.1 to 10 equiv of dimethylphenylsilyl chloride to the reaction mixture to capture the resulting zwitterion.     

Mechanism of sorption of phenols from aqueous solutions onto surfactant-modified montmorillonite

Equilibrium and kinetic studies on the sorption of phenol, m-nitrophenol (m-NP), and o-cresol from water onto montmorillonite modified with cetyltrimethylammounium bromide (CTAB) were conducted. Experiments were carried out as a function of solution pH, sorbate concentration, and temperature (25-55 degrees C). It was shown that the sorption capacity decreased in the order phenol>o-cresol>m-NP. The Langmuir, dual-mode sorption, and Redlich-Peterson models were tested to fit the sorption isotherms of single-solute systems, whereas the Langmuir competitive model was used to describe bisolute sorption equilibria. Thermodynamic parameters (DeltaH degrees and DeltaS degrees ) and the mean free energy (E) for the sorption of phenols were determined from the temperature dependence of the distribution constant and the Dubinin-Radushkevick equation, respectively. A simplified kinetic model was proposed to confirm the sorption mechanism.     

Cascade cyclizations via N,4-didehydro-2-(phenylamino)pyridine biradicals/zwitterions generated from enyne-carbodiimides

Thermolysis of the enyne-carbodiimides 7 having the central carbon-carbon double bond incorporated as part of the cyclopentene ring favors the formation of the corresponding N,4-didehydro-2-(phenylamino)pyridine intermediates, either as the sigma,pi-biradicals 8 or as the zwitterions 8', for subsequent synthetic elaborations. By placing appropriate substituents at the acetylenic terminus, a variety of the intramolecular decay routes are available for the initially formed sigma,pi-biradicals/zwitterions, leading to the 5,6-dihydrobenzo[c][1,8]naphthyridine 21, the 1,2,3,4-tetrahydro[1,8]naphthyridine 24 and related compounds 25 and 26, the 5,6-dihydrobenz[f]isoquinoline 28, and the benzofuro[3,2-c]pyridine 30. Surprisingly, the use of the dimethylamino group of the 2-(dimethylamino)phenyl substituent to capture the carbocationic center in the zwitterion 8e' furnished the 5H-pyrido[4,3-b]indole 32 in only 14% yield. The majority of the products were the 1H-pyrrolo[2,3-b]quinolines 34 and 35, isolated in 48 and 7% yields, respectively. However, it was possible to redirect the reaction toward 32 by conducting thermolysis of the enyne-carbodiimide 7e in the presence of 5 equiv of dimethylphenylsilyl chloride. Under this reaction condition, the 2-pyridone imine 37 was isolated in 86% yield, which on exposure to silica gel was converted to 32 in essentially quantitative yield. Thermolysis of the enyne-carbodiimide 42 having a methoxymethyl substituent at the acetylenic terminus led to the formation of 46' as a pyridine analogue of ortho-quinone methide imine. An intramolecular hetero-Diels-Alder reaction of 46' then furnished the tetrahydro[1,8]naphthyridino[2,1-c][1,4]benzoxazine 47.     

The foam analogy: from phases to elasticity

By mapping the interactions of colloidal particles onto the problem of minimizing areas, the physics of foams can be used to understand the phase diagrams of both charged and fuzzy colloids. We extend this analogy to study the elastic properties of such colloidal crystals and consider the face-centered cubic, body-centered cubic and A15 lattices. We discuss two types of soft interparticle potentials corresponding to charged and fuzzy colloids, respectively, and we analyze the dependence of the elastic constants on density as well as on the parameters of the potential. We show that the bulk moduli of the three lattices are generally quite similar, and that the shear moduli of the two non-close-packed lattices are considerably smaller than in the face-centered cubic lattice. We find that in charged colloids, the elastic constants are the largest at a finite screening length, and we discuss a shear instability of the A15 lattice.     

Recovery of thick shear bands in atactic polystyrene

The DSC thermograms of the shear band material cut out by a diamond saw to include some undeformed material revealed two T_g's clearly separated by about 10°C. The first T_g was at the same temperature as the T_g of the undeformed material. The second T_g, which was at a higher temperature than the first T_g, appeared shortly after the shear strain recovery during the heating of the shear band material in the DSC. When the shear strain in the shear band was partially reversed by mechanical means before taking the DSC thermogram, the ΔT between the two T_g's decreased and when the shear strain was mechanically reversed to almost zero, the second T_g disappeared. The stored energy of shear band material was found to be similar to that of the bulk compressed material for large strains. Dimensional recovery during heating of specimens with thick and fine bands was similar, both taking place above T_g.     

Discovery of a new phosphotyrosine mimetic for PTP1B using breakaway tethering

Protein tyrosine phosphatases play important roles in many signaling cascades involved in human disease. The identification of druglike inhibitors for these targets is a major challenge, and the discovery of suitable phosphotyrosine (pY) mimetics remains one of the key difficulties. Here we describe an extension of tethering technology, "breakaway tethering", which is ideally suited for discovering such new chemical entities. The approach involves first irreversibly modifying a protein with an extender that contains both a masked thiol and a known pY mimetic. The extender is then cleaved to release the pY mimetic, unmasking the thiol. The resulting protein is screened against a library of disulfide-containing small molecule fragments; any molecules with inherent affinity for the pY binding site will preferentially form disulfides with the extender, allowing for their identification by mass spectrometry. The ability to start from a known substrate mimimizes perturbation of protein structure and increases the opportunity to probe the active site using tethering. We applied this approach to the anti-diabetic protein PTP1B to discover a pY mimetic which belongs to a new molecular class and which binds in a novel fashion.