Design of a binary biomarker study from the results of a pilot study

Biomarkers are increasingly used in clinical and epidemiologic studies. Prior to these studies, small pilot studies are often conducted to assess the reproducibility of the biomarker. This article discusses how the results of a pilot study can be used to design subsequent studies when the biomarker is a binary assessment. We consider situations in which the pilot study has two factors (e.g., laboratory and individual) that are either crossed or nested. We discuss how binary random-effects models can be used for estimating the sources of variation and how parameter estimates from these models can be used to appropriately design future studies. We also show that fitting a linear variance components model that ignores the binary nature of the data is a simple alternative method that results in nearly unbiased and moderately efficient estimators of important design parameters. We illustrate the methodology with data from a study assessing the reproducibility of p53 immunohistochemistry in bladder tumors.     

Species: a praxiographic study

Taxonomists, who describe new species, are acutely aware of how political, economic, and ecological forces bring new forms of life into being. Conducting ethnographic research among taxonomic specialists – experts who bring order to categories of animals, plants, fungi, and microbes – I found that they pay careful attention to the ebb and flow of agency in multispecies worlds. Emergent findings from genomics and information technologies are transforming existing categories and bringing new ones into being. This article argues that the concept of species remains a valuable sense‐making tool despite recent attacks from cultural critics.     

Outdoor thermal comfort study in a sub-tropical climate: a longitudinal study based in Hong Kong

This paper presents the findings of an outdoor thermal comfort study conducted in Hong Kong using longitudinal experiments—an alternative approach to conventional transverse surveys. In a longitudinal experiment, the thermal sensations of a relatively small number of subjects over different environmental conditions are followed and evaluated. This allows an exploration of the effects of changing climatic conditions on thermal sensation, and thus can provide information that is not possible to acquire through the conventional transverse survey. The paper addresses the effects of changing wind and solar radiation conditions on thermal sensation. It examines the use of predicted mean vote (PMV) in the outdoor context and illustrates the use of an alternative thermal index—physiological equivalent temperature (PET). The paper supports the conventional assumption that thermal neutrality corresponds to thermal comfort. Finally, predictive formulas for estimating outdoor thermal sensation are presented as functions of air temperature, wind speed, solar radiation intensity and absolute humidity. According to the formulas, for a person in light clothing sitting under shade on a typical summer day in Hong Kong where the air temperature is about 28°C and relative humidity about 80%, a wind speed of about 1.6 m/s is needed to achieve neutral thermal sensation.     

Herpesviruses: a study of parts

Dormancy, an adaptation to survival in a hostile environment, is a trait common to herpesviruses. Two other features are a large (0.1-0.25 Mb) and mutile (inherently easily mutable) genome. The complete nucleotide sequences of four herpesviruses have recently been determined. This database is unparalleled in allowing the comparative evolutionary study of a complex group of viruses in eukaryotes. In this article, we examine aspects of herpesvirus diversity in the light of recent studies which have revealed characteristics that unify the family at the genetic level.     

Ecological study of a bioaugmentation failure

A nitrifying sequencing batch reactor was inoculated twice with the aerobic denitrifying bacterium Microvirgula aerodenitrificans and fed with acetate. No improvement was obtained on nitrogen removal. The second more massive inoculation was even followed by a nitrification breakdown, while at the same time, nitrification remained stable in a second reactor operated under the same conditions without bioaugmentation. Fluorescent in situ hybridization with rRNA-targeted probes revealed that the added bacteria almost disappeared from the reactor within 2 days, and that digestive vacuoles of protozoa gave strong hybridization signals with the M. aerodenitrificans -specific probe. An overgrowth of protozoa, coincident with the disappearance of free-living bacteria, was monitored by radioactive dot-blot hybridization only in the bioaugmented reactor. Population dynamics were analysed with a newly developed in situ quantification procedure of the probe-targeted bacteria. The nitrifying groups of bacteria decreased in a similar way in the bioaugmented and non-bioaugmented reactors. Other bacterial groups evolved differently. The involvement of different ecological parameters are discussed separately for each reactor. These results underline the importance of predator–prey interaction and illustrate the undesirable effects of massive bioaugmentation.     

Gaulin homogenization: a mechanistic study

Free radical-based oxidation has been detected in the normal operating regime of the Gaulin homogenizer, demonstrating that cavitation occurs in this important industrial bioprocessing equipment. Free radical generation is suppressed by imposition of back pressure, proving that such cavitation occurs in the impingement section. The calculated value of the cavitation number is consistent with submerged jet cavitation, wherein a high-speed jet exiting from the valve gap accelerates fluid in the impingement region, creating the vacuum conditions for cavitation. Using polysaccharides as a model shear-sensitive compound, their breakage pattern in the homogenizer was characterized by molecular size and polydispersity and compared to those of fluid shear flows in capillary tubes and cavitating flow from a sonic horn. The results indicate that breakage occurs primarily by fluid shear, although a contribution by cavitation is also apparent when back pressure is applied. Because biological molecules can readily react with free radicals and the alterations caused thereby are subtle in nature, a thorough evaluation of the impact of free radicals in upstream homogenization is warranted.     

The Etruscans: a population-genetic study

The origins of the Etruscans, a non-Indo-European population of preclassical Italy, are unclear. There is broad agreement that their culture developed locally, but the Etruscans' evolutionary and migrational relationships are largely unknown. In this study, we determined mitochondrial DNA sequences in multiple clones derived from bone samples of 80 Etruscans who lived between the 7th and the 3rd centuries b.c. In the first phase of the study, we eliminated all specimens for which any of nine tests for validation of ancient DNA data raised the suspicion that either degradation or contamination by modern DNA might have occurred. On the basis of data from the remaining 30 individuals, the Etruscans appeared as genetically variable as modern populations. No significant heterogeneity emerged among archaeological sites or time periods, suggesting that different Etruscan communities shared not only a culture but also a mitochondrial gene pool. Genetic distances and sequence comparisons show closer evolutionary relationships with the eastern Mediterranean shores for the Etruscans than for modern Italian populations. All mitochondrial lineages observed among the Etruscans appear typically European or West Asian, but only a few haplotypes were found to have an exact match in a modern mitochondrial database, raising new questions about the Etruscans' fate after their assimilation into the Roman state.     

Amelogenesis imperfecta: a genetic study

The mode of inheritance and the clinical manifestations of amelogenesis imperfecta (AI) were studied in 51 families from the county of V?sterbotten, northern Sweden. Autosomal dominant (AD) was the most probable mode of inheritance in 33 families, but X-linked dominant (XD) inheritance was a possible alternative in one family. Autosomal recessive (AR) inheritance was found likely in 6 and X-linked recessive inheritance in 2 families. Ten probands were sporadic cases. In the families with AD inheritance, a sex difference was observed between affected and non-affected cases, with an excess of females in the affected group (p less than 0.05). In addition to the 78 index cases, 107 new cases were diagnosed. The clinical manifestations of AI observed could be divided into 2 forms, the hypoplastic form in 72% and the hypomineralization form in 28% of the individuals. AD inheritance was seen in 89% of the cases with the hypoplastic form, and in 44% of the cases with the hypomineralization form. In most families with AD or AR inheritance, each family displayed a characteristic manifestation of either hypoplastic or hypomineralization defects. In 3 families, both hypoplastic and hypomineralization forms of AI were seen. In families with X-linked inheritance, the clinical manifestation differed between females and males with males more seriously affected.     

Calorimetric study on a dipalmitoylphosphatidylcholine-propylgallate mixture

The effect of propylgallate (PrG, an antioxidant) on the thermotropic behavior of dipalmitoylphosphatidylcholine (DPPC) was studied by means of differential scanning calorimetry. A DPPC/PrG mixture displayed distinctive thermotropic behavior that was significantly different from that of a DPPC/cholesterol or DPPC/vitamin E mixture. Although the enthalpy of the phase transition (delta H) for DPPC decreased at a low concentration of the PrG and the transition peak became broadened, delta H increased again and the peak became sharper on the addition of more PrG. The same was observed for DPPC/methylgallate and DPPC/ethylgallate mixtures, but not for a DPPC/butylgallate mixture. On the other hand, the transition temperature (Tm) of the DPPC/gallate derivative mixtures decreased with an increase in the chain length of the acyl moiety of the gallate derivatives. The pre-transition and subtransition of the DPPC/PrG mixture were eliminated on the addition of a PrG, and Tm of the DPPC/PrG mixture approached about 26 degrees C. These results suggested that the chain length of the acyl moiety must be C1 to C3 for the unique effect of the gallate derivatives described above, and that DPPC forms a complex with PrG as a pure component.