Incorporating Inter‐item Correlations in Item Response Data Analysis

This paper concerns with the analysis of item response data, which are usually measured on a rating scale and are therefore ordinal. These study items tended to be highly inter‐correlated. Rasch models, which convert ordinal categorical scales into linear measurements, are widely used in ordinal data analysis. In this paper, we improve the current methodology in order to incorporate inter‐item correlations. We have advocated the latent variable approach for this purpose, in combination with generalized estimating equations to estimate the Rasch model parameters. The data on a study of families of lung cancer patients demonstrate the utility of our methods.     

A New Format of Single Chain Tri-specific Antibody with Diminished Molecular Size Efficiently Induces Ovarian Tumor Cell Killing

A combination of bi-specific antibodies (BsAb), anti-tumor×anti-CD3 and anti-tumor×anti-CD28, is effective in vitro and in vivo, whereas production of two kinds of bi-specific antibodies is labor intensive and administration is complicated. Accordingly, we previously developed a new model of single chain tri-specific antibody (scTsAb), sTRI, which linked both the CD3 and CD28 signals for T-cell activation in one molecule, and demonstrated its capacity for triggering T-cells to kill ovary tumor cells. To improve the pharmacokinetics further and decrease the immunogenicity of scTsAb, we have now generated a new format of scTsAb, TR3H, whose molecular size is smaller than sTRI. Here we describe the construction, purification and characterization of TR3H. TR3H scTsAb bound to effector cells and tumor target cells specifically and induced redirected lyses of ovary tumor cells through freshly isolated, unstimulated human peripheral blood lymphocytes (PBLs). This new format of scTsAb possesses properties that support its potential as a new tumor immunotherapeutic agent. Revisions requested August 2005; Revisions received 14 September 2005     

Changes of primary sequence and secondary structure proximal to the 5′ end of the stop codon substantially increases the expression of the variable region of an antibody in <Emphasis Type="Italic">E. coli</Emphasis>

The sequence context at the 5 end of the stop codon may influence the efficiency of termination and translation. To increase the expression of a designed variable region of an antibody (named as VH5) against tumor necrosis factor (TNF), two nucleotides (TC) at 25 and 26 nucleotides (nt) upstream of termination codon were substituted with AG, respectively. The free energy of 70 nt (arbitrarily defined from the 32 nt upstream of termination codon to 38 nt downstream) was changed from –13.5 kcal mol^-1 to –17.3 kcal mol^-1. The expression level was increased from 1 ± 0.3% to 10 ± 1.2% of total cellular protein. Although the precise mechanism of this phenomenon remains to be elucidated, this report provides an alternative means to increase the expression of a foreign gene in E. coli. Revisions requested 18 October 2004; Revisions received 26 November 2004     

The photosynthesis of individual algal cells during the cell cycle of Scenedesmus quadricauda studied by chlorophyll fluorescence kinetic microscopy

A microscope for imaging of chlorophyll fluorescence kinetics was equipped with a chamber that allows the growth of an immobilised population of algae and their study under well-defined conditions. Single cells of the chlorococcal alga Scenedesmus quadricauda were grown and recorded for periods of whole cell cycles (up to 48 h) displaying a normal course of cell development. Heterogeneity in fluorescence yield among individual coenobia in the population and among different cells in one coenobium were analysed. Differences were observed both in the shape of Kautsky transients and in the modulation of fluorescence parameter values during the progress of the cell cycle. The extent of heterogeneity in fluorescence parameters was cell cycle dependent – in some phases of the cycle, the population was almost homogeneous, while distinct heterogeneity was observed, in particular between the protoplast division and the release of the daughter coenobia. The heterogeneity was not random but reflected developmental processes.     

A longitudinal measurement error model with a semicontinuous covariate

Covariate measurement error in regression is typically assumed to act in an additive or multiplicative manner on the true covariate value. However, such an assumption does not hold for the measurement error of sleep-disordered breathing (SDB) in the Wisconsin Sleep Cohort Study (WSCS). The true covariate is the severity of SDB, and the observed surrogate is the number of breathing pauses per unit time of sleep, which has a nonnegative semicontinuous distribution with a point mass at zero. We propose a latent variable measurement error model for the error structure in this situation and implement it in a linear mixed model. The estimation procedure is similar to regression calibration but involves a distributional assumption for the latent variable. Modeling and model-fitting strategies are explored and illustrated through an example from the WSCS.     

Antigen binding and stability properties of non-covalently linked anti-CD22 single-chain Fv dimers

By varying linker length and domain orientation three multivalent derivatives of a monovalent anti-CD22 single-chain fragment variable (scFv) antibody were generated. Shortening the linker of the V(H)-V(L) oriented scFv to 5 or 0 residues resulted in the formation of diabodies or a mixture of tetramers and trimers, respectively. Unexpectedly, a V(L)-0-V(H) scFv assembled to homogenous dimers, remained substantially more stable than the V(H)-5-V(L) diabody when incubated in human serum at 37 degrees C, and retained its dimeric state when concentrated up to 4 mg/ml. These properties suggest the V(L)-0-V(H) scFv could become an attractive vehicle for the selective delivery of multiple effector molecules to CD22(+) tumor cells.     

Studies on water-vapor flux characteristic and the relationship with environmental factors over a planted coniferous forest in Qianyanzhou Station

Water-vapor flux over a planted coniferous forest ecosystem near Qianyanzhou, Jiangxi Province, China, was continuously measured with the eddy covariance technique for 2004. How environmental variables, including net radiation, air temperature, and soil moisture, affected water-vapor flux variation was studied in detail. Results showed that winter had the lowest monthly water-vapor flux value, whereas summer had the highest. The diurnal variation of water-vapor flux showed different patterns for clear and cloudy days. The annual total evapotranspiration was 736.1 mm. Regression analysis showed that daily water-vapor flux was significantly correlated with net radiation, air temperature, soil temperature, and soil heat flux on both clear and cloudy days, all in quadratic relationships. Stepwise regression analysis demonstrated that a different set of environmental factors controlled water-vapor flux on days with different weather conditions. From this study, it was clear that these environmental variables, especially net radiation and soil temperature, regulated water-vapor flux over the planted coniferous ecosystem.     

Single chain variable fragment antibodies selected by phage display against the sporozoite surface antigen S16 of Cryptosporidium parvum

Two human single chain variable fragment (scFv) libraries were used to select clones that bound to the surface glycoprotein S16 of Cryptosporidium parvum. Panning of the Tomlinson libraries I and J resulted in the isolation of nine distinct clones. Of the four clones which had full-length scFv, three contained stop codons. The remaining five clones were truncated, with four missing the heavy chain, and one missing most of the light chain. The full-length clones exhibited better binding to native C. parvum proteins and recombinant S16 than the truncated clones, with the exception of one truncated clone. None of the selected clones cross-reacted with Giardia lamblia, Escherichia coli, Streptococcus pyogenes, Listeria monocytogenes, Bacillus cereus or another immunogenic target of C. parvum, P23. Clones expressed as the soluble scFv-gIIIp construct were able to detect C. parvum native proteins and sporozoites. Panning from naïve libraries was an useful method for isolation and identification of recombinant antibodies that have the potential for use in pathogen detection and immunotherapy.     

Geostatistical analysis of regional differences in stem taper form of Pinus densiflora in central Korea

This study verified regional differences in the stem form of Pinus densiflora Sieb. et Zucc. (red pine) and identified the relationship between stem form and climatic factors in the central region of the Korean peninsula. Regional differences in stem form index at tree base (butt) and top stem section were found. Compared to the stem form in the eastern uplands, the stem form in the western lowlands could be characterized by a more conical butt section and more cylindrical middle and upper section. Through geostatistical analysis of kriging and spatial regression, several climatic factors proved to exert a meaningful influence on stem taper form. On the stem form at the butt section, the precipitation during the late growing season exerts statistically significant effects. High precipitation during the growing season in the western lowland and coastal region causes the stem form at the butt section to be more tapered. On the stem form at the middle and upper section, temperature and precipitation during the growing season, and wind during the late growing season have statistically meaningful influences. High temperature, precipitation, and wind during the growing season in the western lowland and coastal region jointly influence the stem form at the middle and upper sections which result in more cylindrical profiles. This study can be considered an initial investigation into the factors controlling stem form variability in the central region of the Korean peninsula. The results can be used to develop more accurate regional stem taper models needed for reasonable management of red pine stands in different regions.

Human impact during the Bronze Age on the vegetation at Lago Lucone (northern Italy)

Lake-sediment records were used to reconstruct human impact on the landscape around Lago Lucone (45°33′N, 10°29′E, 249 m a.s.l.), a former lake in the western amphitheatre system of the Lago di Garda. Presence of prehistoric human populations is attested by pile-dwelling settlements from the Early-Middle Bronze Age, with one settlement at a distance of only 100 m from the coring site. Pollen, plant-macrofossil and microscopic charcoal analyses were applied to a 250 cm sediment core with four dates providing the time control. A mixed oak forest that was important during the Early-Middle Holocene was cleared and replaced by open vegetation during the Bronze Age (∼2000–1100 b.c.) when open lands were estimated to have covered more than 60% of the total relevant pollen-source area. During a phase of high human impact, independent climatic proxies suggest warm and dry climatic conditions. Later, ca. 1100 b.c., palaeobotanical evidence indicates a sharp decrease in human pressure in the Lago Lucone area. The comparison with other sedimentary palaeocultural records shows that the period 1300–1100 b.c. was characterised by general declines of agricultural activities both south and north of the Alps. These declines have been previously attributed to a change towards wetter and colder climatic conditions in and around the Alps. However, the decline in human impact around Lago Lucone cannot be exclusively attributed to climatic variation. Therefore other forcing factors independent of climatic changes, such as cultural crises or changes in spatial organisation of the habitats, cannot be ruled out under the present state of knowledge.