Distinguishing Electron Diffusion and Extraction in Methylammonium Lead Iodide.

Charge diffusion and extraction are crucial steps in the operation of solar cells. Here we show that time-resolved photoluminescence can be used to study electron diffusion in hybrid perovskite films and subsequent transfer to the adjacent electron extraction layer. As diffusion and transfer to the extraction layer are consecutive processes, they can be hard to distinguish, but by exciting from each side of the sample we can separate them and identify which process limits charge extraction. We find that the introduction of a fullerene monolayer between the methylammonium lead iodide (MAPbI3) and the electron-transporting SnO2 layers greatly increases the electron transfer velocity between them to the extent that electron diffusion limits the rate of electron extraction. Our results suggest that increasing the electron diffusion coefficient in MAPbI3 would further enhance the electron extraction rate, which could result in more efficient n-i-p type solar cells.

Estimation of screening sensitivity and sojourn time from an organized screening program.

Regular screening with mammography is widely recommended to reduce breast cancer mortality. However, whether breast screening does more harm than good has long been debated. Since a full evaluation of the effect on mortality could take 10-15 years in order to provide a reliable estimate of the eventual benefits and harms, it is unrealistic to expect each new modification of a screening technique to be evaluated in this way. Therefore, one needs to rapidly estimate suitable measures of the screening effect. In this paper, two measures of interest, the length of the pre-clinical state and the screening false negative rate, are discussed. A procedure is proposed to model the pre-clinical disease state duration, the false negative rate of the screening exam, and the underlying incidence rate in the screened population. We applied the model to data from the Ontario Breast Screening Program in Canada. Our results suggest that the mean preclinical duration is longer than 2 years. We also find only small marginal gains by screening every two instead of three years. The most important objective of a screening program should be to encourage first-time screening attendance.

Inference on cancer screening exam accuracy using population-level administrative data.

This paper develops a model for cancer screening and cancer incidence data, accommodating the partially unobserved disease status, clustered data structures, general covariate effects, and dependence between exams. The true unobserved cancer and detection status of screening participants are treated as latent variables, and a Markov Chain Monte Carlo algorithm is used to estimate the Bayesian posterior distributions of the diagnostic error rates and disease prevalence. We show how the Bayesian approach can be used to draw inferences about screening exam properties and disease prevalence while allowing for the possibility of conditional dependence between two exams. The techniques are applied to the estimation of the diagnostic accuracy of mammography and clinical breast examination using data from the Ontario Breast Screening Program in Canada.

Affinity filtration coupled with capillary-based affinity purification for the isolation of protein complexes.

The isolation of complex macromolecular assemblies at the concentrations required for structural analysis represents a major experimental challenge. Here we present a method that combines the genetic power of site-specific recombination in order to selectively "tag" one or more components of a protein complex with affinity-based rapid filtration and a final step of capillary-based enrichment. This modified form of tandem affinity purification produces highly purified protein complexes at high concentrations in a highly efficient manner. The application of the method is demonstrated for the yeast Arp2/3 heptameric protein complex involved in mediating reorganization of the actin cytoskeleton.

Mapping cancer risk in southwestern Ontario with changing census boundaries.

Mapping disease risk often involves working with data that have been spatially aggregated to census regions or postal regions, either for administrative reasons or confidentiality. When studying rare diseases, data must be collected over a long time period in order to accumulate a meaningful number of cases. These long time periods can result in spatial boundaries of the census regions changing over time, as is the case with the motivating example of exploring the spatial structure of mesothelioma lung cancer risk in Lambton County and Middlesex County of southwestern Ontario, Canada. This article presents a local-EM kernel smoothing algorithm that allows for the combining of data from different spatial maps, being capable of modeling risk for spatially aggregated data with time-varying boundaries. Inference and uncertainty estimates are carried out with parametric bootstrap procedures, and cross-validation is used for bandwidth selection. Results for the lung cancer study are shown and discussed.

Quantifying within- and between-animal variation and uncertainty associated with counts of Escherichia coli O157 occurring in naturally infected cattle faeces.

Cattle faeces are considered the most important reservoir for human infection with Escherichia coli O157. We have previously described shedding of E. coli O157 in the faeces of naturally infected cattle cohorts. However, the data require further investigation to quantify the uncertainty and variability in the estimates previously presented. This paper proposes a method for analysing both the presence and the quantity of E. coli O157 in cattle faecal samples, using two isolation procedures, one of which enumerates E. coli O157. The combination of these two measurements, which are fundamentally different in nature and yet measuring a common outcome, has necessitated the development of a novel statistical model for ascertaining the contribution of the various components of variation (both natural and observation induced) and for judging the influence of explanatory variables. Most of the variation within the sampling hierarchy was attributable to multiple samples from the same animal. The contribution of laboratory-level variation was found to be low. After adjusting for fixed and random effects, short periods of increased intensity of shedding were identified in individual animals. We conclude that within-animal variation is greater than between animals over time, and studies aiming to elucidate the dynamics of shedding should focus resources, sampling more within than between animals. These findings have implications for the identification of persistent high shedders and for assessing their role in the epidemiology of E. coli O157 in cattle populations. The development of this non-standard statistical model may have many applications to other microbial count data.

Inference for clustered inhomogeneous spatial point processes.

SUMMARY: We propose a method to test for significant differences in the levels of clustering between two spatial point processes (cases and controls) while taking into account differences in their first-order intensities. The key advance on earlier methods is that the controls are not assumed to be a Poisson process. Inference and diagnostics are based around the inhomogeneous K-function with confidence envelopes obtained from either resampling events in a nonparametric bootstrap approach, or simulating new events as in a parametric bootstrap. Methods developed are demonstrated using the locations of adult and juvenile trees in a tropical forest. A simulation study briefly examines the accuracy and power of the inferential procedures.

Second-order analysis of inhomogeneous spatial point processes using case-control data.

Methods for the statistical analysis of stationary spatial point process data are now well established, methods for nonstationary processes less so. One of many sources of nonstationary point process data is a case-control study in environmental epidemiology. In that context, the data consist of a realization of each of two spatial point processes representing the locations, within a specified geographical region, of individual cases of a disease and of controls drawn at random from the population at risk. In this article, we extend work by Baddeley, Møller, and Waagepetersen (2000, Statistica Neerlandica54, 329-350) concerning estimation of the second-order properties of a nonstationary spatial point process. First, we show how case-control data can be used to overcome the problems encountered when using the same data to estimate both a spatially varying intensity and second-order properties. Second, we propose a semiparametric method for adjusting the estimate of intensity so as to take account of explanatory variables attached to the cases and controls. Our primary focus is estimation, but we also propose a new test for spatial clustering that we show to be competitive with existing tests. We describe an application to an ecological study in which juvenile and surviving adult trees assume the roles of controls and cases.

Sources of variation in the ampicillin-resistant Escherichia coli concentration in the feces of organic broiler chickens.

Currently, there are limited published data for the population dynamics of antimicrobial-resistant commensal bacteria. This study was designed to evaluate both the proportions of the Escherichia coli populations that are resistant to ampicillin at the level of the individual chicken on commercial broiler farms and the feasibility of obtaining repeated measures of fecal E. coli concentrations. Short-term temporal variation in the concentration of fecal E. coli was investigated, and a preliminary assessment was made of potential factors involved in the shedding of high numbers of ampicillin-resistant E. coli by growing birds in the absence of the use of antimicrobial drugs. Multilevel linear regression modeling revealed that the largest component of random variation in log-transformed fecal E. coli concentrations was seen between sampling occasions for individual birds. The incorporation of fixed effects into the model demonstrated that the older, heavier birds in the study were significantly more likely (P = 0.0003) to shed higher numbers of ampicillin-resistant E. coli. This association between increasing weight and high shedding was not seen for the total fecal E. coli population (P = 0.71). This implies that, in the absence of the administration of antimicrobial drugs, the proportion of fecal E. coli that was resistant to ampicillin increased as the birds grew. This study has shown that it is possible to collect quantitative microbiological data on broiler farms and that such data could make valuable contributions to risk assessments concerning the transfer of resistant bacteria between animal and human populations.

Spatial and management factors associated with exposure of smallholder dairy cattle in Tanzania to tick-borne pathogens.

A cross-sectional study of serum antibody responses of cattle to tick-borne pathogens (Theileria parva, Theileria mutans,Anaplasma marginale, Babesia bigemina and Babesia bovis) was conducted on smallholder dairy farms in Tanga and Iringa Regions of Tanzania. Seroprevalence was highest for T. parva (48% in Iringa and 23% in Tanga) and B. bigemina (43% in Iringa and 27% in Tanga) and lowest for B. bovis (12% in Iringa and 6% in Tanga). We use spatial and non-spatial models, fitted using classical and Bayesian methods, to explore risk factors associated with seroprevalence. These include both fixed effects (age, grazing history and breeding status) and random effects (farm and local spatial effects). In both regions, seroprevalence for all tick-borne pathogens increased significantly with age. Animals pasture grazed in the 3 months prior to the start of the sampling period were significantly more likely to be seropositive for Theileria spp. and Babesia spp. Pasture grazed animals were more likely to be seropositive than zero-grazed animals for A. marginale, but the relationship was weaker than that observed for the other four pathogens. This study did not detect any significant differences in seroprevalence associated with other management-related variables, including the method or frequency of acaricide application. After adjusting for age, there was weak evidence of localised (<5 km) spatial correlation in exposure to some of the tick borne diseases. However, this was small compared with the 'farm-effect', suggesting that risk factors specific to the farm were more important than those common to the local neighbourhood. Many animals were seropositive for more than one pathogen and the correlation between exposure to the different pathogens remained after adjusting for the identified risk factors. Identifying the determinants of exposure to multiple tick-borne pathogens and characterizing local variation in risk will assist in the development of more effective control strategies for smallholder dairy farms.

Frequency and spatial distribution of environmental Campylobacter spp.

Humans are exposed to Campylobacter spp. in a range of sources via both food and environmental pathways. For this study, we explored the frequency and distribution of thermophilic Campylobacter spp. in a 10- by 10-km square rural area of Cheshire, United Kingdom. The area contains approximately 70, mainly dairy, farms and is used extensively for outdoor recreational activities. Campylobacter spp. were isolated from a range of environmental samples by use of a systematic sampling grid. Livestock (mainly cattle) and wildlife feces and environmental water and soil samples were cultured, and isolates were presumptively identified by standard techniques. These isolates were further characterized by PCR. Campylobacter jejuni was the most prevalent species in all animal samples, ranging from 11% in samples from nonavian wildlife to 36% in cattle feces, and was isolated from 15% of water samples. Campylobacter coli was commonly found in water (17%) and sheep (21%) samples, but rarely in other samples. Campylobacter lari was recovered from all sample types, with the exception of sheep feces, and was found in moderate numbers in birds (7%) and water (5%). Campylobacter hyointestinalis was only recovered from cattle (7%) and birds (1%). The spatial distribution and determinants of C. jejuni in cattle feces were examined by the use of model-based spatial statistics. The distribution was consistent with very localized within-farm or within-field transmission and showed little evidence of any larger-scale spatial dependence. We concluded that there is a potentially high risk of human exposure to Campylobacter spp., particularly C. jejuni, in the environment of our study area. The prevalence and likely risk posed by C. jejuni-positive cattle feces in the environment diminished as the fecal material aged. After we took into account the age of the fecal material, the absence or presence of rain, and the presence of bird feces, there was evidence of significant variation in the prevalence of C. jejuni-positive cattle feces between grazing fields but no evidence of spatial clustering beyond this resolution. The spatial pattern of C. jejuni is therefore consistent with that for an organism that is ubiquitous in areas contaminated with cattle feces, with a short-scale variation in infection intensity that cannot be explained solely by variations in the age of the fecal material. The observed pattern is not consistent with large-scale transmission attributable to watercourses, wildlife territories, or other geographical features that transcend field and farm boundaries.

Morphology and ultrastructure of sense organs on the ovipositor of Trybliographa rapae, a parasitoid of the cabbage root fly.

The ovipositor of the parasitoid wasp Trybliographa rapae was examined by scanning and transmission electron microscopy. Characteristic peg-like sensilla with a cuticular ring at the base are found at the tip of the ventral valves, where they occur in a characteristic arrangement of triplets. The unusual basal structure probably protects the sensilla against damage during movement through the substrate and piercing of the host cuticle. These sensilla are each innervated by six dendrites, some of which have lamellated tips, generally considered to be characteristic of thermosensitivity. It is suggested that the remaining dendrites are gustatory, and as such probably respond to factors present in host haemolymph. A second type of peg-like sensillum is found on both the dorsal and the ventral valves. These are set in deep pits so that only the tip of the peg protrudes above the surface of the cuticle. These occur along the length of the ovipositor shaft and ultrastructural studies reveal the pegs to be innervated by a single mechanosensitive dendrite, probably monitoring the movement of the ovipositor through the substrate.

Association of purified skeletal-muscle AMP deaminase with a histidine-proline-rich-glycoprotein-like molecule.

Denaturation of rabbit skeletal-muscle AMP deaminase in acidic medium followed by chromatography on DEAE-cellulose in 8 M urea atpH 8.0 allows separation of two main peptide components of similar apparent molecular mass (75-80 kDa) that we tentatively assume correspond to two different enzyme subunits. Whereas the amino acid composition of one of the two peptides is in good agreement with that derived from the nucleotide sequence of the known rat and human AMPD1 cDNAs, the second component shows much higher contents of proline, glycine and histidine. N-Terminal sequence analysis of the fragments liberated by limited proteolysis with trypsin of the novel peptide reveals a striking similarity to the fragments produced by plasmin cleavage of the rabbit plasma protein called histidine-proline-rich glycoprotein (HPRG). However, some divergence is observed between the sequence of one of the fragments liberated from AMP deaminase by a more extensive trypsinization and rabbit plasma HPRG in the region containing residues 472-477. A fragment with a blocked N-terminus, which was found among those liberated by proteolysis with pepsin of either whole AMP deaminase or the novel component of the enzyme, shows an amino acid composition quite different from that of the N-terminus of the known subunit of AMP deaminase. By coupling this observation with the detection in freshly prepared AMP deaminase of a low yield of the sequence (LTPTDX) corresponding to that of HPRG N-terminus, it can be deduced that in comparison with HPRG, the putative HPRG-like component of AMP deaminase contains an additional fragment with a blocked N-terminus, which is liberated by a proteolytic process during purification of the enzyme. The implications of the association to rabbit skeletal-muscle AMP deaminase of a HPRG-like protein species are discussed.

Evidence of a species-differentiated regulatory domain within the N-terminal region of skeletal muscle AMP deaminase.

Rabbit skeletal muscle AMP deaminase was submitted to limited proteolysis by trypsin that converts the native 80 kDa enzyme subunit to a stable product of approx. 70 kDa, which, in contrast to the native enzyme, is not sensitive to regulation by ATP at pH 6.5. Tryptic peptide mapping indicates that proteolysis is confined to the N-terminal region of the molecule, identifying in this region of AMP deaminase a non-catalytic, 95 residue regulatory domain that stabilises the binding of ATP to a distant site in the molecule. Protein sequence analysis reveals a marked degree of divergence between rat and rabbit skeletal muscle AMP deaminases in the regions containing residues 7-12 and 51-52, giving molecular basis to the hypothesis of the existence of isoenzymes of AMP deaminase in the mature skeletal muscle of the mammals.

Site and significance of chemically modifiable cysteine residues in glutamate dehydrogenase of Clostridium symbiosum and the use of protection studies to measure coenzyme binding.

Protein chemical studies of NAD(+)-dependent glutamate dehydrogenase (GDH; EC 1.4.1.2) from Clostridium symbiosum indicate only two cysteine residues/subunit, in good agreement with the gene sequence. Experiments with various thiol-modifying reagents reveal that in native clostridial GDH only one of these two cysteines is accessible for reaction. This residue does not react with iodoacetate, iodoacetamide, N-ethylmaleimide or N-phenylmaleimide, but reaction with either p-chloromercuribenzene sulphonate or 5,5'-dithiobis(2-nitrobenzoic acid) causes complete inactivation, preventable by NAD+ or NADH but not by glutamate or 2-oxoglutarate. Protection studies with combinations of substrates show that glutamate enhances protection by NADH, whereas 2-oxoglutarate diminishes it. These studies were also used to determine a dissociation constant (0.69 mM) for the enzyme-NAD+ complex. Similar data for NADH indicated mildly cooperative binding with a Hill coefficient of 1.32. The significance of these results is discussed in the light of the high-resolution crystallographic structure for clostridial GDH and in relation to information for GDH from other sources.

The Cohen test does not predict outcome in achalasia after pneumatic dilation.

The Cohen test has been recommended to evaluate the efficacy of pneumatic dilation of the lower esophageal sphincter in patients with achalasia. It consists of ingestion of 8 ounces of heavy barium. Upright radiographs are performed 5 minutes later to determine the height of the barium column in the esophagus in relation to the diaphragm. A column less than 1 cm above the diaphragm is a negative test indicating successful dilation and the high probability of dysphagia resolution. A positive Cohen test, a column exceeding 1 cm, is said to correlate with persistent symptoms and need for redilation. We evaluated this in a prospective manner for a 6-year period. Twenty-eight patients underwent standard technique pneumatic dilation at our institution. Achalasia was confirmed in all patients by way of upper endoscopy and manometry. A Cohen test was performed in all patients. Post-dilation symptoms and weight were analyzed at follow-up 6 weeks after dilation. Contrary to the original report, relief of dysphagia after dilation was not related to the results of the Cohen test (p = 0.77). A positive Cohen test was inversely correlated with both symptom duration (0.037) and lower esophageal sphincter pressure before dilation (p = 0.005). Weight gain after dilation was unrelated to Cohen test results (p = 0.67). We conclude that the Cohen test is not an accurate predictor of symptom relief after dilation and do not recommend its use to determine the end point of therapy in patients with achalasia.

The Acute Physiology and Chronic Health Evaluation II classification system is a valid marker for physiologic stress in the critically ill patient.

OBJECTIVE: To compare the Acute Physiology and Chronic Health Evaluation (APACHE II) score with resting energy expenditure obtained from indirect calorimetry to determine whether the APACHE II scoring system is an accurate, objective measure of the degree of critical illness and physiologic stress between groups of patients. DESIGN: Prospective study. SETTING: University hospital, tertiary referral center. PATIENTS: Seventy critically ill patients, consecutively sampled from burn, surgical, and medical intensive care units. INTERVENTIONS: Indirect calorimetric studies were performed on each patient using a metabolic cart. The acute physiologic score component of the APACHE II scoring system was determined at the time of metabolic testing, a mean of 15.9 days after hospital admission. MEASUREMENTS AND MAIN RESULTS: True resting energy expenditure was calculated by adjusting the measured energy expenditure for diet-induced thermogenesis and fever. A predicted resting energy expenditure was calculated for each patient using the Harris-Benedict equation alone, and by using the Harris-Benedict value corrected for previously published metabolic activity factors. To eliminate differences in body composition and size, true resting energy expenditure was divided by weight, body surface area, and Harris-Benedict resting energy expenditure. Results showed no significant correlation between APACHE II scores and either the Harris-Benedict resting energy expenditure or the Harris-Benedict value corrected by metabolic activity factors. However, there was a significant (p < or = .001; r2 = .18 to .20) relationship between increasing APACHE II scores and both increasing measured and true resting energy expenditure. The true resting energy expenditure divided by body surface area, kilogram body weight, and Harris-Benedict predicted value, were all shown to be significantly (p < .01) related to APACHE II score, but showed no better degree of correlation (r2 = .12 to .23) than comparison of APACHE II score with measured or true resting energy expenditure. CONCLUSIONS: The APACHE II classification may be a valid marker of physiologic stress as demonstrated by its statistically significant (although weak) relationship with indirect calorimetric measures of energy expenditure associated with varying degrees of critical illness.

The partial amino acid sequence of the NAD(+)-dependent glutamate dehydrogenase of Clostridium symbiosum: implications for the evolution and structural basis of coenzyme specificity.

The amino acid sequence is reported for CNBr and tryptic peptide fragments of the NAD(+)-dependent glutamate dehydrogenase of Clostridium symbiosum. Together with the N-terminal sequence, these make up about 75% of the total sequence. The sequence shows extensive similarity with that of the NADP(+)-dependent glutamate dehydrogenase of Escherichia coli (52% identical residues out of the 332 compared) allowing confident placing of the peptide fragments within the overall sequence. This demonstrated sequence similarity with the E. coli enzyme, despite different coenzyme specificity, is much greater than the similarity (31% identities) between the GDH's of C. symbiosum and Peptostreptococcus asaccharolyticus, both NAD(+)-linked. The evolutionary implications are discussed. In the 'fingerprint' region of the nucleotide binding fold the sequence Gly X Gly X X Ala is found, rather than Gly X Gly X X Gly. The sequence found here has previously been associated with NADP+ specificity and its finding in a strictly NAD(+)-dependent enzyme requires closer examination of the function of this structural motif.