Estimating missing data: an iterative regression approach

The problem of missing data is common in all fields of science. Various methods of estimating missing values in a dataset exist, such as deletion of cases, insertion of sample mean, and linear regression. Each approach presents problems inherent in the method itself or in the nature of the pattern of missing data. We report a method that (1) is more general in application and (2) provides better estimates than traditional approaches, such as one-step regression. The model is general in that it may be applied to singular matrices, such as small datasets or those that contain dummy or index variables. The strength of the model is that it builds a regression equation iteratively, using a bootstrap method. The precision of the regressed estimates of a variable increases as regressed estimates of the predictor variables improve. We illustrate this method with a set of measurements of European Upper Paleolithic and Mesolithic human postcranial remains, as well as a set of primate anthropometric data. First, simulation tests using the primate data set involved randomly turning 20% of the values to "missing". In each case, the first iteration produced significantly better estimates than other estimating techniques. Second, we applied our method to the incomplete set of human postcranial measurements. MISDAT estimates always perform better than replacement of missing data by means and better than classical multiple regression. As with classical multiple regression, MISDAT performs when squared multiple correlation values approach the reliability of the measurement to be estimated, e.g., above about 0. 8.     

The multiple decisions made by growth cones of RGCs as they navigate from the retina to the tectum in Xenopus embryos

Retinal ganglion cells (RGCs) of Xenopus laevis send axons along a stereospecific pathway from the retina to their target the optic tectum. Viewed from the point of the growth cone, this journey is reflected by discrete processes of axon initiation, axon outgrowth, navigation, target recognition, and innervation. These processes are characterised by distinct signalling mechanisms that trigger dynamic changes in growth cone morphology and behavior. Here we review work primarily from our laboratory, examining these events from a cellular and molecular perspective, focusing on the roles of FGFs, netrins, receptors, and intracellular effectors.     

Unfolded phosphopolypeptides enable soft and hard tissues to coexist in the same organism with relative ease

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Highlights? Some unfolded phosphoproteins form stable complexes with amorphous calcium phosphate. ? Stable complexes require ≥3 phosphorylated residues within a short sub-sequence. ? Soft and hard tissues can co-exist in the same organism because of these complexes.     

ESR spectroscopy in the study of antigen processing--uptake of spin-labelled antigens by macrophages

Macrophages were briefly pulsed with a spin-labelled synthetic polypeptide, poly(L-tyrosine:L-glutamic acid) poly DL-alanine:poly L-lysine (n-TGAL) in the presence and absence of anti-TGAL-antibody, and the electron spin resonance (ESR) spectra of the cell suspension compared with the spectrum of free n-TGAL in solution. Spectral analysis indicated two cell-associated n-TGAL pools, one composed of freely rotating label held in an aqueous environment, susceptible to protease digestion and ascorbate reduction, and a second highly concentrated pool, sequestered intracellularly, and held within a highly ordered, polar microenvironment. The ESR analyses were completed within minutes of antigen pulsing, employed very small numbers of live cells, and did not damage the cells being tested. The utility of the technique in screening fatty acid-antigen conjugates for macrophage uptake was demonstrated.     

Ecology of soil arthrobacters in clarion-webster toposequences of iowa

Toposequence variations in soil properties were characterized and related to variations in populations of total isolatable bacteria and arthrobacters. Increases in soil NO₃-N, available phosphorous, NO₃-N-producing power, Arthrobacter counts, and the percentage of the total counts represented by arthrobacters were correlated with decreases in soil acidity. The total bacterial counts were not correlated with soil acidity but were associated with percentage of soil organic matter and percentage of clay. The percentage of the total counts represented by arthrobacters was lowest at the summit position and increased downslope to the highest value in the toeslope position. Factor analysis of the data revealed that 67 to 81% of the total variance exhibited by all variables per site-sampling period could be accounted for by soil acidity, soil structure, soil fertility, soil moisture, and bacterial factors. A selective medium was developed for soil arthrobacters and tested on a wide variety of central Iowa soils to determine its potential as a medium for enumeration as well as isolation. The medium developed in this study was found to be superior to the other available direct-isolation media for soil arthrobacters.     

Analysis of the oxidation of short chain alkynes by flavocytochrome P450 BM3

Bacillus megaterium flavocytochrome P450 BM3 (BM3) is a high activity fatty acid hydroxylase, formed by the fusion of soluble cytochrome P450 and cytochrome P450 reductase modules. Short chain (C6, C8) alkynes were shown to be substrates for BM3, with productive outcomes (i.e. alkyne hydroxylation) dependent on position of the carbon-carbon triple bond in the molecule. Wild-type P450 BM3 catalyses ω-3 hydroxylation of both 1-hexyne and 1-octyne, but is suicidally inactivated in NADPH-dependent turnover with non-terminal alkynes. A F87G mutant of P450 BM3 also undergoes turnover-dependent heme destruction with the terminal alkynes, pointing to a key role for Phe87 in controlling regioselectivity of alkyne oxidation. The terminal alkynes access the BM3 heme active site led by the acetylene functional group, since hydroxylated products are not observed near the opposite end of the molecules. For both 1-hexyne and 1-octyne, the predominant enantiomeric product formed (up to ～90%) is the (S)-(-)-1-alkyn-3-ol form. Wild-type P450 BM3 is shown to be an effective oxidase catalyst of terminal alkynes, with strict regioselectivity of oxidation and potential biotechnological applications. The absence of measurable octanoic or hexanoic acid products from oxidation of the relevant 1-alkynes is also consistent with previous studies suggesting that removal of the phenyl group in the F87G mutant does not lead to significant levels of ω-oxidation of alkyl chain substrates.     

Production of Solvents by Clostridium acetobutylicum Cultures Maintained at Neutral pH

The formation of acetone and n-butanol by Clostridium acetobutylicum NCIB 8052 (ATCC 824) was monitored in batch culture at 35°C in a glucose (2% [wt/vol]) minimal medium maintained throughout at either pH 5.0 or 7.0. At pH 5, good solvent production was obtained in the unsupplemented medium, although addition of acetate plus butyrate (10 mM each) caused solvent production to be initiated at a lower biomass concentration. At pH 7, although a purely acidogenic fermentation was maintained in the unsupplemented medium, low concentrations of acetone and n-butanol were produced when the glucose content of the medium was increased (to 4% [wt/vol]). Substantial solvent concentrations were, however, obtained at pH 7 in the 2% glucose medium supplemented with high concentrations of acetate plus butyrate (100 mM each, supplied as their potassium salts). Thus, C. acetobutylicum NCIB 8052, like C. beijerinckii VPI 13436, is able to produce solvents at neutral pH, although good yields are obtained only when adequately high concentrations of acetate and butyrate are supplied. Supplementation of the glucose minimal medium with propionate (20 mM) at pH 5 led to the production of some n-propanol as well as acetone and n-butanol; the final culture medium was virtually acid free. At pH 7, supplementation with propionate (150 mM) again led to the formation of n-propanol but also provoked production of some acetone and n-butanol, although in considerably smaller amounts than were obtained when the same basal medium had been fortified with acetate and butyrate at pH 7.     

Conversion of low-affinity platelet factor 4 to beta-thromboglobulin by plasmin and trypsin

Low-affinity platelet factor 4 and beta-thromboglobulin are platelet-secreted proteins that bind with low affinity to heparin. They show extensive immunological cross-reactivity and appear to differ in amino acid sequence only by an amino-terminal peptide unique to low-affinity platelet factor 4. The possibility that beta-thromboglobulin is derived from low-affinity platelet factor 4 by proteolysis was investigated by exposing this protein to the action of plasmin, thrombin and trypsin. While thrombin had no effect, plasmin and trypsin converted low-affinity platelet factor 4 to a species with the same electrophoretic mobility and isoelectric point as beta-thromboglobulin. We conclude that beta-thromboglobulin is a breakdown product of low-affinity platelet factor 4.     

The positive effect of role models in evolution instruction

Background

Previous research has identified numerous factors to explain why students have difficulty learning about evolution. Some of these factors include a student’s background (including their religion and major of study), the type of evolution instruction, and the inclusion of the nature of science (NOS) instruction. Sparse but more recent work has investigated the impact of a religious-scientist role model to help dampen perceptions of conflict between evolutionary science and worldview. We had two research goals: (1) to identify which of these factors influence students’ learning of evolution in post-secondary education; and (2) to describe the relationships among incoming biology students’ creationist reasoning, knowledge of evolution, and perceived conflict between evolution and their worldview.

Results

The single factor linked with the reduction in both creationist reasoning and in students’ perceived conflict between evolution and their worldview through a semester was the presence of a role model. Likewise, knowledge and perceived relevance of evolution increased in sections with a role model instructor and with evidence-based evolution instruction. Otherwise, tested factors (the type of evolution instruction, inclusion of NOS, biology-major/nonmajor, GPA, or religiosity) were not shown to be associated with these three constructs. We found that in the first week of the semester students with higher knowledge of evolution had lower creationist reasoning and lower perceived conflict.

Conclusions

The single factor that collectively reduced erroneous beliefs, increased scientific knowledge, and minimized perceived conflict was the presence of a religious-scientist role model. Previous work has suggested a role model could positively impact students’ learning of evolution, yet this is the first quasi-experimental evidence supporting the importance of the course instructor as the role model in students’ learning of evolution. These findings are especially relevant to institutions with a greater proportion of religious students who could benefit from modeling to help foster their learning of evolution.