Maximally efficient two-stage screening

In DNA library screening, blood testing, and monoclonal antibody generation, significant savings in the number of assays can be realized by employing group sampling. Practical considerations often limit the number of stages of group testing that can be performed. We address situations in which only two stages of testing are used. We define efficiency to be the expected number of positives isolated per assay performed and assume gold-standard tests with unit sensitivity and specificity. Although practical tests never are golden, polymerase chain reaction (PCR) methods provide procedures for screening recombinant libraries that are strongly selective yet retain high sensitivity even when samples are pooled. Also, results for gold-standard tests serve as bounds on the performance of practical testing procedures. First we derive formulas for the efficiency of certain extensions of the popular rows-and-columns technique. Then we derive an upper bound on the efficiency of any two-stage strategy that lies well below the classical upper bound for situations with no constraint on the number of stages. This establishes that a restriction to only two stages necessitates performing many more assays than efficient multistage procedures need. Next, we specialize the bound to cases in which each item belonging only to pools that tested positive in stage 1 must be tested individually in stage 2. The specialized bound for such positive procedures is tight because we show that an appropriate multidimensional extension of the rows-and-columns technique achieves it. We also show that two-stage positive procedures in which the stage-1 groups are selected at random perform suboptimally, thereby establishing that efficient tests must be structured carefully.     

Informative Dorfman screening

Since the early 1940s, group testing (pooled testing) has been used to reduce costs in a variety of applications, including infectious disease screening, drug discovery, and genetics. In such applications, the goal is often to classify individuals as positive or negative using initial group testing results and the subsequent process of decoding of positive pools. Many decoding algorithms have been proposed, but most fail to acknowledge, and to further exploit, the heterogeneous nature of the individuals being screened. In this article, we use individuals' risk probabilities to formulate new informative decoding algorithms that implement Dorfman retesting in a heterogeneous population. We introduce the concept of "thresholding" to classify individuals as "high" or "low risk," so that separate, risk-specific algorithms may be used, while simultaneously identifying pool sizes that minimize the expected number of tests. When compared to competing algorithms which treat the population as homogeneous, we show that significant gains in testing efficiency can be realized with virtually no loss in screening accuracy. An important additional benefit is that our new procedures are easy to implement. We apply our methods to chlamydia and gonorrhea data collected recently in Nebraska as part of the Infertility Prevention Project.     

Two-dimensional informative array testing

Summary Array-based group-testing algorithms for case identification are widely used in infectious disease testing, drug discovery, and genetics. In this article, we generalize previous statistical work in array testing to account for heterogeneity among individuals being tested. We first derive closed-form expressions for the expected number of tests (efficiency) and misclassification probabilities (sensitivity, specificity, predictive values) for two-dimensional array testing in a heterogeneous population. We then propose two "informative" array construction techniques which exploit population heterogeneity in ways that can substantially improve testing efficiency when compared to classical approaches that regard the population as homogeneous. Furthermore, a useful byproduct of our methodology is that misclassification probabilities can be estimated on a per-individual basis. We illustrate our new procedures using chlamydia and gonorrhea testing data collected in Nebraska as part of the Infertility Prevention Project.     

Ultrastructural changes of the intracellular surfactant pool in a rat model of lung transplantation-related events

Background

Ischemia/reperfusion (I/R) injury, involved in primary graft dysfunction following lung transplantation, leads to inactivation of intra-alveolar surfactant which facilitates injury of the blood-air barrier. The alveolar epithelial type II cells (AE2 cells) synthesize, store and secrete surfactant; thus, an intracellular surfactant pool stored in lamellar bodies (Lb) can be distinguished from the intra-alveolar surfactant pool. The aim of this study was to investigate ultrastructural alterations of the intracellular surfactant pool in a model, mimicking transplantation-related procedures including flush perfusion, cold ischemia and reperfusion combined with mechanical ventilation.

Methods

Using design-based stereology at the light and electron microscopic level, number, surface area and mean volume of AE2 cells as well as number, size and total volume of Lb were determined in a group subjected to transplantation-related procedures including both I/R injury and mechanical ventilation (I/R group) and a control group.

Results

After I/R injury, the mean number of Lb per AE2 cell was significantly reduced compared to the control group, accompanied by a significant increase in the luminal surface area per AE2 cell in the I/R group. This increase in the luminal surface area correlated with the decrease in surface area of Lb per AE2. The number-weighted mean volume of Lb in the I/R group showed a tendency to increase.

Conclusion

We suggest that in this animal model the reduction of the number of Lb per AE2 cell is most likely due to stimulated exocytosis of Lb into the alveolar space. The loss of Lb is partly compensated by an increased size of Lb thus maintaining total volume of Lb per AE2 cell and lung. This mechanism counteracts at least in part the inactivation of the intra-alveolar surfactant.     

Correlation between richness per unit area and the species pool cannot be used to demonstrate the species pool effect

Abstract. Significant correlation between the size of the species pool and richness per unit area is usually taken as a demonstration of the effect of the species pool on the species richness per unit area. This is not logically necessary. It has to be emphasized that such a correlation cannot be interpreted as a demonstration of the effect of species pool on the species richness per unit area. More generally, correlation cannot be used to demonstrate a one‐directional effect of one variable upon another, since several types of (functional) relationships could produce correlations between such variables; the same caution has to be taken when analysing the species pool vs. richness per unit area correlation. In this paper, a simple Monte Carlo simulation model is used to demonstrate that (1) statistical processes acting only at the local scale (such as competitive exclusion) can generate exactly the same correlation that has been used to infer the effect of the species pool on richness per unit area; (2) this correlation would be deemed significant even if the mathematical dependency between species pool and richness per unit area is taken into account; and (3) the strength of this relation depends on beta diversity within the contiguous area used to determine the species pool.     

Reversibility of Photosynthetic Inhibition in Cotton after Long-Term Exposure to Elevated CO(2) Concentrations

Cotton (Gossypium hirsutum L. cv Stoneville 213) was grown at 350 and 1000 microliters per liter CO₂. The plants grown at elevated CO₂ concentrations contained large starch pools and showed initial symptoms of visible physical damage. Photosynthetic rates were lower than expected based on instantaneous exposure to high CO₂.

A group of plants grown at 1000 microliters per liter CO₂ was switched to 350 microliters per liter CO₂. Starch pools and photosynthetic rates were monitored in the switched plants and in the two unswitched control groups. Photosynthetic rates per unit leaf area recovered to the level of the 350 microliters per liter CO₂ grown control group within four to five days. To assess only nonstomatal limitations to photosynthesis, a measure of photosynthetic efficiencies was calculated (moles CO₂ fixed per square meter per second per mole intercellular CO₂). Photosynthetic efficiency also recovered to the levels of the 350 microliters per liter CO₂ grown controls within three to four days.

Recovery was correlated to a rapid depletion of the starch pool, indicating that the inhibition of photosynthesis is primarily a result of feedback inhibition. However, complete recovery may involve the repair of damage to the chloroplasts caused by excessive starch accumulation. The rapid and complete reversal of photosynthetic inhibition suggests that the appearance of large, strong sinks at certain developmental stages could result in reduction of the large starch accumulations and that photosynthetic rates could recover to near the theoretical capacity during periods of high photosynthate demand.

     

Motor unit discharge rate is correlated within individuals: A case for multilevel model statistical analysis

Statistical analysis of motor unit discharge rate commonly uses the ordinary least squares based ANOVA and regression analyses or a repeated-measures ANOVA is used to account for within motor unit variance when the same motor unit is assessed multiple times. Both of these methods assume statistical independence of multiple motor units assessed within an individual. This investigation details two studies which quantify the statistical dependence of motor units within an individual. During a ramp contraction, motor unit initial discharge rate is mildly correlated within an individual (ICC: 0.11), though accounting for this effect significantly impacts regression analysis (p = 0.01). When a contraction is held at constant force and multiple observations are made on a motor unit, the motor unit discharges are more highly correlated (ICC: 0.41), even after accounting for the effects of multiple motor unit observations. A subject-level ICC of 0.01 can increase Type 1 error rate to 3.9–19.7%, depending on the number of motor units and study subjects. The increase in Type 1 error due to subject-level effects can be mitigated through the use of multilevel modeling techniques. This study details the use and benefit of multilevel models when statistically analyzing motor unit discharge data.     

Comparison of group testing algorithms for case identification in the presence of test error

We derive and compare the operating characteristics of hierarchical and square array-based testing algorithms for case identification in the presence of testing error. The operating characteristics investigated include efficiency (i.e., expected number of tests per specimen) and error rates (i.e., sensitivity, specificity, positive and negative predictive values, per-family error rate, and per-comparison error rate). The methodology is illustrated by comparing different pooling algorithms for the detection of individuals recently infected with HIV in North Carolina and Malawi.     

Oxidative capacity and capillary density of diaphragm motor units

Motor units in the cat diaphragm (DIA) were isolated in situ by microdissection and stimulation of C5 ventral root filaments. Motor units were classified based on their isometric contractile force responses and fatigue indexes (FI). The muscle fibers belonging to individual units (i.e., the muscle unit) were identified using the glycogen-depletion method. Fibers were classified as type I or II based on histochemical staining for myofibrillar adenosine triphosphatase (ATPase) after alkaline preincubation. The rate of succinate dehydrogenase (SDH) activity of each fiber was determined using a microphotometric procedure. The location of capillaries was determined from muscle cross sections stained for ATPase after acid (pH = 4.2) preincubation. The capillarity of muscle unit fibers was determined by counting the number of capillaries surrounding fibers and by calculating the number of capillaries per fiber area. A significant correlation was found between the fatigue resistance of DIA units and the mean SDH activity of muscle unit fibers. A significant correlation was also observed between DIA unit fatigue resistance and both indexes of muscle unit fiber capillarity. The mean SDH activity and mean capillary density of muscle unit fibers were also correlated. We conclude that DIA motor unit fatigue resistance depends, at least in part, on the oxidative capacity and capillary density of muscle unit fibers.     

Selection of the experimental unit in teratology studies.

In teratology experiments the litter (pregnant female) rather than the fetus is advocated as being the proper experimental unit upon which to base the statistical analysis. It is pointed out that per litter tests, by being based on the average fetal response within a litter, do take the individual fetus into account. Actual experimental data are used to show that when litter effects are present a per fetus analysis is invalid and may seriously exaggerate the significance level. It is also shown that there appears to be little loss in sensitivity in performing per litter tests even in the unlikely event that there are no litter effects. Thus it certainly seems prudent to analyze teratology data with test procedures that treat the litter as the experimental unit.     

Effect of sampling grain on patterns of species richness and turnover in Amazonian forests

Grain (size of sampling units) affects the spatial resolution at which ecological patterns can be observed and analysed, and potentially has an important effect on the results of broad‐scale studies on diversity gradients. Here we examine the effect of grain on patterns of species richness and turnover in lowland rainforests of western Amazonia (Peru and Colombia). We inventoried pteridophytes (ferns and lycophytes), melastomes (Melastomataceae) and palms (Arecaceae) in four line transects of 22–29 km length. Different grains were obtained by aggregating original 100‐m‐long sampling units into larger segments up to 19.2 km long. With any given grain and plant group, local species richness varied considerably both within and among transects, and a transect segment that was species‐rich with one grain could be relatively species‐poor with another. Which transect had the highest vs lowest mean species richness per sampling unit (α richness) differed among plant groups. It also varied to some degree with grain, as transects differed in how rapidly local species richness increased with increasing grain. Patterns of species turnover were more consistently correlated among plant groups than patterns of species richness were, and NMDS ordinations were rather similar with all grains and plant groups. Floristic heterogeneity within the Amazonian terra firme rainforest seems to contain a general compositional pattern that is sufficiently robust to be detectable with various sampling schemes, but patterns of species richness appear more case‐specific. Therefore, using one plant group as an indicator for patterns in other plant groups can be expected to work better for species turnover than for species richness.     

Decline of photosynthetic capacity with leaf age and position in two tropical pioneer tree species

The effect of leaf age on photosynthetic capacity, a critical parameter in the theory of optimal leaf longevity, was studied for two tropical pioneer tree species, Cecropia longipes and Urera caracasana, in a seasonally dry forest in Panama. These species continuously produce short-lived leaves (74 and 93 d, respectively) during the rainy season (May-December) on orthotropic branches. However, they differ in leaf production rate, maximum number of leaves per branch, light environment experienced by the leaves, leaf mass per unit area, and nitrogen content. Light-saturated photosynthetic rates for marked leaves of known ages (±1 wk) were measured with two contrasting schemes (repeated measurements vs. chronosequence within branch), which overall produced similar results. In both species, photosynthetic rates and nitrogen use efficiency were negatively correlated with leaf age and positively correlated with light availability. Photosynthetic rates declined faster with leaf age in Cecropia than in Urera as predicted by the theory. The rate of decline was faster for leaves on branches with faster leaf turnover rates. Nitrogen per unit leaf area decreased with leaf age only for Urera. Leaf mass per unit area increased with leaf age, either partly (in Cecropia) or entirely (in Urera) due to ash accumulation.     

Molecular resolution imaging of macromolecular crystals by atomic force microscopy.

Atomic force microscopy (AFM) images at the molecular level have been obtained for a number of different protein and virus crystals. They can be utilized in some special cases to obtain information useful to crystal structure analyses by x-ray diffraction. In particular, questions of space group enantiomer, the packing of molecules within a unit cell, the number of molecules per asymmetric unit, and the dispositions of multiple molecules within the asymmetric unit may be resolved. In addition, because of the increasing sensitivity and resolution of the AFM technique, some molecular features of very large asymmetric units may be within reach. We describe here high-resolution studies, using AFM, to visualize individual molecules and viruses in their crystal lattices. These investigations included fungal lipase, lysozyme, thaumatin, canavalin, and satellite tobacco mosaic virus (STMV).     

Three-Dimensional Array-Based Group Testing Algorithms

Summary .  We derive the operating characteristics of three-dimensional array-based testing algorithms for case identification in the presence of testing error. The operating characteristics investigated include efficiency (i.e., expected number of tests per specimen) and error rates (e.g., sensitivity, specificity, positive, and negative predictive values). The methods are illustrated by comparing the proposed algorithms with previously studied hierarchical and two-dimensional array algorithms for detecting recent HIV infections in North Carolina. Our results indicate that three-dimensional array-based algorithms can be more efficient and accurate than previously proposed algorithms in settings with test error and low prevalence.     

Use of binomial group testing in tests of hypotheses for classification or quantitative covariables

In group testing, the test unit consists of a group of individuals. If the group test is positive, then one or more individuals in the group are assumed to be positive. A group observation in binomial group testing can be, say, the test result (positive or negative) for a pool of blood samples that come from several different individuals. It has been shown that, when the proportion (p) of infected individuals is low, group testing is often preferable to individual testing for identifying infected individuals and for estimating proportions of those infected. We extend the potential applications of group testing to hypothesis-testing problems wherein one wants to test for a relationship between p and a classification or quantitative covariable. Asymptotic relative efficiencies (AREs) of tests based on group testing versus the usual individual testing are obtained. The Pitman ARE strongly favors group testing in many cases. Small-sample results from simulation studies are given and are consistent with the large-sample (asymptotic) findings. We illustrate the potential advantages of group testing in hypothesis testing using HIV-1 seroprevalence data.     

Calves as social hubs: dynamics of the social network within sperm whale units

It is hypothesized that the primary function of permanent social relationships among female sperm whales (Physeter macrocephalus) is to provide allomothers for calves at the surface while mothers make foraging dives. In order to investigate how reciprocity of allocare within units of sperm whales facilitates group living, we constructed weighted social networks based on yearly matrices of associations (2005–2010) and correlated them across years, through changes in age and social role, to study changes in social relationships within seven sperm whale units. Pairs of association matrices from sequential years showed a greater positive correlation than expected by chance, but as the time lag increased, the correlation coefficients decreased. Over all units considered, calves had high values for all measured network statistics, while mothers had intermediate values for most of the measures, but high values for connectedness and affinity. Mothers showed sharp drops in strength and connectedness in the first year of their new calves'' lives. These broad patterns appear to be consistent across units. Calves appeared to be significant nodes in the network of the social unit, and thus provide quantitative support for the theory in which communal care acts as the evolutionary force behind group formation in this species.     

Relationships between carotenoid composition and growth habit in British plant species

The pigment composition of leaves from a number of different plant species collected from field sites in the region of Sheffield, UK, have been compared using high-performance liquid chromatography. Expression of pigment content per unit leaf area was dominated by variation in the total leaf chlorophyll. Neither chlorophyll per unit area nor the chlorophyll a/b ratio were found to be correlated with the habitat from which the plants originated. When the amounts of different carotenoids were expressed relative to the total carotenoid pool, it was found that whilst neither total carotene (α- +β-carotene) nor neoxanthin correlated with ability to grow in shade, the leaf content of both lutein and the total xanthophyll cycle carotenoids (zeaxanthin, anther-axanthin and violaxanthin) did, with lutein content being high in shade species and xanthophyll cycle intermediates low. There was a strong negative correlation between the relative amounts of each of these groups of carotenoids. The ratio of lutein to xanthophyll cycle carotenoids was strongly correlated to an index of shade tolerance.     

Effects of a medical team coordinator on length of hospital stay.

OBJECTIVE: To determine the effect of a medical team coordinator (MTC) on the length of stay in a teaching hospital. DESIGN: Randomized controlled trial. SETTING: Two of four general medical clinical teaching units (CTUs). PATIENTS: Patients admitted to the CTUs between July and October 1990 except those who were admitted directly to an intensive care unit or whose death was expected within 48 hours. The 267 patients were randomly assigned to receive either standard medical care or standard medical care plus MTC services. INTERVENTION: The MTC was a baccalaureate nurse whose role was to facilitate administrative tasks such as discharge planning, to coordinate tests and procedures, and to collect and collate patient information. MAIN OUTCOME MEASURES: Length of hospital stay. A subgroup of 40 patients was asked to complete a brief survey on medical care information and satisfaction. RESULTS: The MTC intervention reduced the mean length of stay by 1.97 days (p less than or equal to 0.04, 95% confidence interval [CI] 1.02 to 2.92 days). Subanalysis by diagnostic group revealed that most of this effect was in an ill-defined group of disorders. In the survey more patients in the MTC group than in the other group reported being satisfied with their medical care (89% v. 62%; p less than or equal to 0.05, 95% CI 2% to 52%). CONCLUSIONS: The services of an MTC help to reduce the length of hospital stay for some groups of patients. Further research is necessary to examine which components of the MTC intervention are most effective and in what conditions.