Pangenome graph construction from genome alignments with Minigraph-Cactus

Pangenome references address biases of reference genomes by storing a representative set of diverse haplotypes and their alignment, usually as a graph. Alternate alleles determined by variant callers can be used to construct pangenome graphs, but advances in long-read sequencing are leading to widely available, high-quality phased assemblies. Constructing a pangenome graph directly from assemblies, as opposed to variant calls, leverages the graph's ability to represent variation at different scales. Here we present the Minigraph-Cactus pangenome pipeline, which creates pangenomes directly from whole-genome alignments, and demonstrate its ability to scale to 90 human haplotypes from the Human Pangenome Reference Consortium. The method builds graphs containing all forms of genetic variation while allowing use of current mapping and genotyping tools. We measure the effect of the quality and completeness of reference genomes used for analysis within the pangenomes and show that using the CHM13 reference from the Telomere-to-Telomere Consortium improves the accuracy of our methods. We also demonstrate construction of a Drosophila melanogaster pangenome.

A draft human pangenome reference

Here the Human Pangenome Reference Consortium presents a first draft of the human pangenome reference. The pangenome contains 47 phased, diploid assemblies from a cohort of genetically diverse individuals1. These assemblies cover more than 99% of the expected sequence in each genome and are more than 99% accurate at the structural and base pair levels. Based on alignments of the assemblies, we generate a draft pangenome that captures known variants and haplotypes and reveals new alleles at structurally complex loci. We also add 119 million base pairs of euchromatic polymorphic sequences and 1,115 gene duplications relative to the existing reference GRCh38. Roughly 90 million of the additional base pairs are derived from structural variation. Using our draft pangenome to analyse short-read data reduced small variant discovery errors by 34% and increased the number of structural variants detected per haplotype by 104% compared with GRCh38-based workflows, which enabled the typing of the vast majority of structural variant alleles per sample.

Body shape perception in men and women without obesity during caloric restriction: a secondary analysis from the CALERIE study

OBJECTIVE

To examine body shape perception in 218 adults without obesity or history of eating disorders during caloric restriction (CR).

METHODS

Comprehensive Assessment of Long-term Effects of Reducing Intake of Energy (CALERIE) is a 2-year, randomized clinical trial using a 2:1 assignment (CR, 25% reduction in calories; Control, typical diet). For this secondary analysis, we examined perceived body shape using the Body Shape Questionnaire (BSQ). Analyses of BSQ scores are reported by group, over time, by sex, and by BMI. Data for body fat percentage, symptoms of depression, food cravings, maximal oxygen consumption, and stress were analyzed for their association with BSQ scores.

RESULTS

Compared to control, CR reduced BSQ scores. Women tended to have greater concern with body shape than men across all measurement times. There was no difference in change in BSQ scores at 12 or 24 months between those with a BMI < 25 kg/m² or ≥ 25 kg/m². Change in body fat percentage was most correlated with change in BSQ score from 0 to 12 (r = 0.39) and 0-24 months (r = 0.38). For change in BSQ score, Akaike/ Bayesian information criterion (AIC/BIC) found that the model of best fit included the following three change predictors: change in body fat percentage, depression symptoms, and food cravings. For 0-12 months, AIC/BIC = 1482.0/1505.6 and for 0-24 months AIC/BIC = 1364.8/1386.5.

CONCLUSIONS

CR is associated with reduced concern for body shape in men and women without obesity and with no history of eating disorders. Body shape perception among this sample was complex and influenced by multiple factors.

LEVEL OF EVIDENCE

Level I, randomized controlled trial.

Liquid crystals of neat boron nitride nanotubes and their assembly into ordered macroscopic materials

Boron nitride nanotubes (BNNTs) have attracted attention for their predicted extraordinary properties; yet, challenges in synthesis and processing have stifled progress on macroscopic materials. Recent advances have led to the production of highly pure BNNTs. Here we report that neat BNNTs dissolve in chlorosulfonic acid (CSA) and form birefringent liquid crystal domains at concentrations above 170 ppmw. These tactoidal domains merge into millimeter-sized regions upon light sonication in capillaries. Cryogenic electron microscopy directly shows nematic alignment of BNNTs in solution. BNNT liquid crystals can be processed into aligned films and extruded into neat BNNT fibers. This study of nematic liquid crystals of BNNTs demonstrates their ability to form macroscopic materials to be used in high-performance applications.

Boron nitride nanotubes (BNNTS) have only been shown to dissolve in chlorosulfonic acid (CSA) at low concentrations. Here the authors successfully demonstrate the formation of liquid crystals of BNNTs in CSA that can be used to produce macroscopically aligned neat fibers of BNNTs.

Prevalence of Shiga Toxin-Producing Escherichia coli and Salmonella in Native Pecan Orchards as Influenced by Waiting Periods between Grazing and Harvest

ABSTRACT

Animals (grazing, working, or intrusion) in produce production areas may present a potential contamination source of foodborne pathogens on produce. Cattle grazing on native pecan production orchards, a common practice in the southern United States, provides an opportunity to study the impact of grazing practice and waiting periods on contamination rates of foodborne pathogens of tree nuts. Therefore, the objective of this study was to determine the prevalence of Salmonella and Shiga toxin-producing Escherichia coli (STEC) in native pecan production orchards as influenced by waiting periods between grazing cattle and pecan harvest. Soil (10 g), cattle feces (10 g), and in-shell pecans (25 g) were sampled from five cattle-grazed orchards in areas with cattle removed 2 or 4 months before harvest and not removed. Five nongrazing orchards were sampled at harvest for comparison. Detection and isolation of the pathogens were performed by enrichment, selective isolation, and multiplex PCR. Statistical analyses were performed using contingency tables with Pearson's chi-square test. The prevalence of STEC (36%) and Salmonella (29%) in cattle-grazed orchards was significantly higher than in nongrazed orchards (13 and 7%, respectively). STEC prevalence in cattle-grazed orchards was higher (38%) in areas with cattle at harvest than in fenced areas where cattle were removed 2 (29%) and 4 (27%) months before harvest. Salmonella prevalence was similar in areas without fencing (31%) and areas with cattle removed at 2 (22%) and 4 (30%) months before harvest. However, there were no significant differences (P > 0.05) in contamination rates between waiting periods for either pathogen, suggesting a limited impact of waiting periods on reducing the risk of contamination.

HIGHLIGHTS

Skeletal Muscle Mitochondrial Function after a 100-km Ultramarathon: A Case Study in Monozygotic Twins

PURPOSE

Very little research has investigated the effects of ultraendurance exercise on the bioenergetic status of muscle. The primary objective of this case study was to characterize the changes that occur in skeletal muscle mitochondria in response to a 100-km ultramarathon in monozygotic twins. A second objective was to determine whether mitochondrial function is altered by consuming a periodized low-carbohydrate, high-fat diet during training compared with a high-carbohydrate diet.

METHODS

One pair of male monozygotic twins ran 100 km on treadmills after 4 wk of training on either a high-carbohydrate or periodized low-carbohydrate, high-fat diet. Muscle biopsies were collected 4 wk before the run, as well as 4 and 52 h postrun. Blood draws were also performed immediately before as well as 4 and 52 h after the run.

RESULTS

Four hours postrun, respiratory capacity, citrate synthase activity, and mitochondrial complex protein content were decreased. Two days later, both twins showed signs of rapid recovery in several of these measures. Furthermore, blood levels of creatine phosphokinase, C-reactive protein, and aspartate transaminase were elevated 4 h after the run but partially recovered 2 d later.

CONCLUSION

Although there were some differences between the twins, the primary finding is that there is significant mitochondrial impairment induced by running 100 km, which rapidly recovers within 2 d. These results provide ample rationale for future investigations of the effects of ultraendurance activity on mitochondrial function.

Measurement of the Positive Muon Anomalous Magnetic Moment to 0.46 ppm

We present the first results of the Fermilab National Accelerator Laboratory (FNAL) Muon g-2 Experiment for the positive muon magnetic anomaly a_{μ}≡(g_{μ}-2)/2. The anomaly is determined from the precision measurements of two angular frequencies. Intensity variation of high-energy positrons from muon decays directly encodes the difference frequency ω_{a} between the spin-precession and cyclotron frequencies for polarized muons in a magnetic storage ring. The storage ring magnetic field is measured using nuclear magnetic resonance probes calibrated in terms of the equivalent proton spin precession frequency ω[over ˜]_{p}^{'} in a spherical water sample at 34.7 °C. The ratio ω_{a}/ω[over ˜]_{p}^{'}, together with known fundamental constants, determines a_{μ}(FNAL)=116 592 040(54)×10^{-11} (0.46 ppm). The result is 3.3 standard deviations greater than the standard model prediction and is in excellent agreement with the previous Brookhaven National Laboratory (BNL) E821 measurement. After combination with previous measurements of both μ^{+} and μ^{-}, the new experimental average of a_{μ}(Exp)=116 592 061(41)×10^{-11} (0.35 ppm) increases the tension between experiment and theory to 4.2 standard deviations.

Application of Human Factors Methods to Understand Missed Follow-up of Abnormal Test Results

OBJECTIVE

This study demonstrates application of human factors methods for understanding causes for lack of timely follow-up of abnormal test results ("missed results") in outpatient settings.

METHODS

We identified 30 cases of missed test results by querying electronic health record data, developed a critical decision method (CDM)-based interview guide to understand decision-making processes, and interviewed physicians who ordered these tests. We analyzed transcribed responses using a contextual inquiry (CI)-based methodology to identify contextual factors contributing to missed results. We then developed a CI-based flow model and conducted a fault tree analysis (FTA) to identify hierarchical relationships between factors that delayed action.

RESULTS

The flow model highlighted barriers in information flow and decision making, and the hierarchical model identified relationships between contributing factors for delayed action. Key findings including underdeveloped methods to track follow-up, as well as mismatches, in communication channels, timeframes, and expectations between patients and physicians.

CONCLUSION

This case report illustrates how human factors-based approaches can enable analysis of contributing factors that lead to missed results, thus informing development of preventive strategies to address them.

Incorporating hydrology into climate suitability models changes projections of malaria transmission in Africa

Continental-scale models of malaria climate suitability typically couple well-established temperature-response models with basic estimates of vector habitat availability using rainfall as a proxy. Here we show that across continental Africa, the estimated geographic range of climatic suitability for malaria transmission is more sensitive to the precipitation threshold than the thermal response curve applied. To address this problem we use downscaled daily climate predictions from seven GCMs to run a continental-scale hydrological model for a process-based representation of mosquito breeding habitat availability. A more complex pattern of malaria suitability emerges as water is routed through drainage networks and river corridors serve as year-round transmission foci. The estimated hydro-climatically suitable area for stable malaria transmission is smaller than previous models suggest and shows only a very small increase in state-of-the-art future climate scenarios. However, bigger geographical shifts are observed than with most rainfall threshold models and the pattern of that shift is very different when using a hydrological model to estimate surface water availability for vector breeding.

Prior studies mapping climatologically suitable areas for malaria transmission have used relatively simple thresholds for precipitation. Here the authors show that when models incorporate hydrological processes a more complex pattern of malaria suitability emerges in Africa and future shifts in suitability are more pronounced.

The effects of land use and topographic changes on sediment connectivity in mountain catchments

Understanding the evolution of sediment connectivity associated with different land use and topographic changes is a prerequisite for a better understanding of sediment budgets and sediment transport processes. We used the Index of Sediment Connectivity (IC) developed by Cavalli et al. (2013) based on the original approach by Borselli et al. (2008) to study the effects of decadal-scale land use and topographic changes on sediment connectivity in mountain catchments. The input variables of the IC (i.e. land cover and topography) were derived from historical aerial photos using Structure from Motion-Multi View Stereo algorithms (SfM-MVS). The method was applied in different sub-catchments of the Upper River Cinca Catchment (Central Pyrenees), representative of three scenarios: (a) Land cover changes; (b) Topographic changes in agricultural fields (terracing); and (c) Topographic changes associated with infrastructure (road construction). In terms of land cover changes, results show that although connectivity is increased in some areas due to the establishment of new field crops, for most of the study area connectivity decreased due to afforestation caused by rural abandonment. Topographic changes due to the establishment of agricultural terraces affected connectivity to a larger degree than land cover changes. Terracing generally reduced connectivity due to the formation of flat areas in step-slopes, but in certain points, an increase in connectivity caused by the topographic convergence produced by terraces was observed. Finally, topographic changes associated with road construction greatly modified surface flow directions and the drainage network, resulting in changes in connectivity that may affect erosional processes nearby. The methodology used in this paper allows to study the effects of real decadal-scale land use and topographic changes on sediment connectivity and also evaluating and disentangling those changes. Furthermore, this approach can be a useful tool to identify potential risks associated with morphological and land use changes, involving road infrastructures.

Incorporating Guideline Adherence and Practice Implementation Issues into the Design of Decision Support for Beta-Blocker Titration for Heart Failure

BACKGROUND

The recognition of and response to undertreatment of heart failure (HF) patients can be complicated. A clinical reminder can facilitate use of guideline-concordant β-blocker titration for HF patients with depressed ejection fraction. However, the design must consider the cognitive demands on the providers and the context of the work.

OBJECTIVE

This study's purpose is to develop requirements for a clinical decision support tool (a clinical reminder) by analyzing the cognitive demands of the task along with the factors in the Cabana framework of physician adherence to guidelines, the health information technology (HIT) sociotechnical framework, and the Promoting Action on Research Implementation in Health Services (PARIHS) framework of health services implementation. It utilizes a tool that extracts information from medical records (including ejection fraction in free text reports) to identify qualifying patients at risk of undertreatment.

METHODS

We conducted interviews with 17 primary care providers, 5 PharmDs, and 5 Registered Nurses across three Veterans Health Administration outpatient clinics. The interviews were based on cognitive task analysis (CTA) methods and enhanced through the inclusion of the Cabana, HIT sociotechnical, and PARIHS frameworks. The analysis of the interview data led to the development of requirements and a prototype design for a clinical reminder. We conducted a small pilot usability assessment of the clinical reminder using realistic clinical scenarios.

RESULTS

We identified organizational challenges (such as time pressures and underuse of pharmacists), knowledge issues regarding the guideline, and information needs regarding patient history and treatment status. We based the design of the clinical reminder on how to best address these challenges. The usability assessment indicated the tool could help the decision and titration processes.

CONCLUSION

Through the use of CTA methods enhanced with adherence, sociotechnical, and implementation frameworks, we designed a decision support tool that considers important challenges in the decision and execution of β-blocker titration for qualifying HF patients at risk of undertreatment.

Test results management and distributed cognition in electronic health record-enabled primary care

Managing abnormal test results in primary care involves coordination across various settings. This study identifies how primary care teams manage test results in a large, computerized healthcare system in order to inform health information technology requirements for test results management and other distributed healthcare services. At five US Veterans Health Administration facilities, we interviewed 37 primary care team members, including 16 primary care providers, 12 registered nurses, and 9 licensed practical nurses. We performed content analysis using a distributed cognition approach, identifying patterns of information transmission across people and artifacts (e.g. electronic health records). Results illustrate challenges (e.g. information overload) as well as strategies used to overcome challenges. Various communication paths were used. Some team members served as intermediaries, processing information before relaying it. Artifacts were used as memory aids. Health information technology should address the risks of distributed work by supporting awareness of team and task status for reliable management of results.

Polymorphisms in genes related to inflammation and obesity and colorectal adenoma risk

We previously investigated the association between single nucleotide polymorphisms (SNPs) in genes related to obesity and inflammation and colorectal cancer in the CLUE II cohort. However, the relationships between these SNPs and colorectal adenomas have not been well evaluated. In a nested case-control study of 135 incident adenoma cases and 269 matched controls in the CLUE II cohort (1989-2000), we genotyped 17 candidate SNPs in 12 genes (PPARG, TCF7L2, ADIPOQ, LEP, IL10, CRP, TLR4, IL6, IL1B, IL8, TNF, RNASEL) and 19 tagSNPs in three genes (IL10, CRP, and TLR4). Conditional logistic regression was used to calculate odds ratios (OR) for adenomas (overall and by size, histology, location, number). Polymorphisms in the inflammatory-related genes CRP, ADIPOQ, IL6, and TLR4 were observed to be associated with adenoma risk. At rs1205 in CRP, T (minor allele) carriers had a higher risk (OR 1.67, 95%CI 1.07-2.60; reference: CC) of adenomas overall and adenomas with aggressive characteristics. At rs1201299 in ADIPOQ, the AC genotype had a higher risk (OR 1.58, 95%CI 1.00-2.49) of adenomas, while the minor AA genotype had a borderline inverse association (OR 0.44, 95%CI 0.18-1.08; reference: CC). At rs1800797 in IL6, the AA genotype had a borderline inverse association (OR 0.53, 95%CI 0.27-1.05; reference: GG). Three TLR4 tagSNPs (rs10116253, rs1927911, rs7873784) were associated with adenomas among obese participants. None of these SNPs were associated with colorectal cancer in our prior study in CLUE II, possibly suggesting a different genetic etiology for early colorectal neoplasia.

BIOCHEMICAL GENETICS OF MOSQUITOFISH. IV. CHANGES OF ALLELE FREQUENCIES THROUGH TIME AND SPACE

Gene frequency data from samples of Gambusia affinis populations at 76 localities across the Savannah River drainage were used to investigate temporal and spatial patterns in population genetic structure. Localities in the Par Pond system on the Savannah River Plant were sampled in 1971, 1977, and 1979. Allelic frequencies in these populations were generally stable through time, although significant temporal changes were observed among samples from Pond C, an impoundment receiving thermal effluent. Significant spatial heterogeneity in allele frequencies was observed on both microgeographic and regional scales. Populations within the Par Pond system were spatially subdivided at four of the five loci surveyed (mean F_ST = 0.051). Subdivision was even more pronounced when samples from across the Savannah River drainage were compared (mean F_ST = 0.196). A hierarchial analysis of gene diversity (G_ST ) demonstrated that most of the genic diversity across the drainage exists as within-subdivision diversity. Even when populations from such contrasting habitats as rivers, creeks, ponds, and reservoirs are compared, an average of only 13% of the total gene diversity was attributed to between-group diversity. Greatest between-group gene diversity was observed when reservoirs were compared with one another. This general pattern of low between-habitat diversity suggests that differential selection pressures are not playing a major role in producing the observed levels of subdivision. In the Par Pond system, neither single locus nor multilocus genetic distances were significantly associated with geographic distance or with its reciprocal. For samples from over the Savannah River drainage, significant correlations between genetic and geographic distance were observed only for the Gpi-2 and Pgm-2 loci. Thus, there was a general lack of concordance between genetic and geographic distances. Spatial autocorrelation demonstrated patterns consistent with Wright's isolation by distance model. Significant positive correlations in allelic frequencies among neighboring populations were observed for five of six alleles; allelic frequencies in more distantly separated populations were typically not correlated.

Severity of Scab and its Effects on Fruit Weight in Mechanically Hedge-Pruned and Topped Pecan Trees

Scab is the most damaging disease of pecan in the southeastern United States. Pecan trees can attain 44 m in height, so managing disease in the upper canopy is a problem. Fungicide is ordinarily applied using ground-based air-blast sprayers. Although mechanical hedge-pruning and topping of pecan is done for several reasons, improved management of scab is an important reason in the humid, wet Southeast. Resulting shoot growth on cut limbs of susceptible cultivars could lead to more severe scab. In three experiments over three years, we explored the effect of hedge-pruning trees to ∼12 to 14 m compared with non-hedge-pruned trees. All trees received fungicide treatments (air-blast sprays and ≤3 aerial applications). Hedge-pruning either had no effect, or increased or decreased scab severity only slightly on leaflets, immature, or mature fruit (a -9.95 to +14.63% difference in scab severity compared with the control). However, height in the canopy invariably had a large and significant effect on scab severity, and amounted to a 0.05 to 73.77% difference in severity between the lowest and highest sample in the canopy. Fruit weight depended on sample height, with fruit most often weighing less when collected at greater sample heights. A robust relationship between fruit weight and scab severity was found at the highest sample heights where scab was also most often severe (R² = 0.21 to 0.67, P < 0.0001). Hedge-pruning and topping pecan tree canopies to manage tree size will enable better fungicide coverage, reducing risk of a scab epidemic as more of the canopy is assured efficacious fungicide spray coverage.

A Single-Cell Roadmap of Lineage Bifurcation in Human ESC Models of Embryonic Brain Development

During human brain development, multiple signaling pathways generate diverse cell types with varied regional identities. Here, we integrate single-cell RNA sequencing and clonal analyses to reveal lineage trees and molecular signals underlying early forebrain and mid/hindbrain cell differentiation from human embryonic stem cells (hESCs). Clustering single-cell transcriptomic data identified 41 distinct populations of progenitor, neuronal, and non-neural cells across our differentiation time course. Comparisons with primary mouse and human gene expression data demonstrated rostral and caudal progenitor and neuronal identities from early brain development. Bayesian analyses inferred a unified cell-type lineage tree that bifurcates between cortical and mid/hindbrain cell types. Two methods of clonal analyses confirmed these findings and further revealed the importance of Wnt/β-catenin signaling in controlling this lineage decision. Together, these findings provide a rich transcriptome-based lineage map for studying human brain development and modeling developmental disorders.

Selecting SNPs informative for African, American Indian and European Ancestry: application to the Family Investigation of Nephropathy and Diabetes (FIND)

Background

The presence of population structure in a sample may confound the search for important genetic loci associated with disease. Our four samples in the Family Investigation of Nephropathy and Diabetes (FIND), European Americans, Mexican Americans, African Americans, and American Indians are part of a genome- wide association study in which population structure might be particularly important. We therefore decided to study in detail one component of this, individual genetic ancestry (IGA). From SNPs present on the Affymetrix 6.0 Human SNP array, we identified 3 sets of ancestry informative markers (AIMs), each maximized for the information in one the three contrasts among ancestral populations: Europeans (HAPMAP, CEU), Africans (HAPMAP, YRI and LWK), and Native Americans (full heritage Pima Indians). We estimate IGA and present an algorithm for their standard errors, compare IGA to principal components, emphasize the importance of balancing information in the ancestry informative markers (AIMs), and test the association of IGA with diabetic nephropathy in the combined sample.

Results

A fixed parental allele maximum likelihood algorithm was applied to the FIND to estimate IGA in four samples: 869 American Indians; 1385 African Americans; 1451 Mexican Americans; and 826 European Americans. When the information in the AIMs is unbalanced, the estimates are incorrect with large error. Individual genetic admixture is highly correlated with principle components for capturing population structure. It takes ~700 SNPs to reduce the average standard error of individual admixture below 0.01. When the samples are combined, the resulting population structure creates associations between IGA and diabetic nephropathy.

Conclusions

The identified set of AIMs, which include American Indian parental allele frequencies, may be particularly useful for estimating genetic admixture in populations from the Americas. Failure to balance information in maximum likelihood, poly-ancestry models creates biased estimates of individual admixture with large error. This also occurs when estimating IGA using the Bayesian clustering method as implemented in the program STRUCTURE. Odds ratios for the associations of IGA with disease are consistent with what is known about the incidence and prevalence of diabetic nephropathy in these populations.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-2654-x) contains supplementary material, which is available to authorized users.

Genome-Wide Association and Trans-ethnic Meta-Analysis for Advanced Diabetic Kidney Disease: Family Investigation of Nephropathy and Diabetes (FIND)

Diabetic kidney disease (DKD) is the most common etiology of chronic kidney disease (CKD) in the industrialized world and accounts for much of the excess mortality in patients with diabetes mellitus. Approximately 45% of U.S. patients with incident end-stage kidney disease (ESKD) have DKD. Independent of glycemic control, DKD aggregates in families and has higher incidence rates in African, Mexican, and American Indian ancestral groups relative to European populations. The Family Investigation of Nephropathy and Diabetes (FIND) performed a genome-wide association study (GWAS) contrasting 6,197 unrelated individuals with advanced DKD with healthy and diabetic individuals lacking nephropathy of European American, African American, Mexican American, or American Indian ancestry. A large-scale replication and trans-ethnic meta-analysis included 7,539 additional European American, African American and American Indian DKD cases and non-nephropathy controls. Within ethnic group meta-analysis of discovery GWAS and replication set results identified genome-wide significant evidence for association between DKD and rs12523822 on chromosome 6q25.2 in American Indians (P = 5.74x10^-9). The strongest signal of association in the trans-ethnic meta-analysis was with a SNP in strong linkage disequilibrium with rs12523822 (rs955333; P = 1.31x10^-8), with directionally consistent results across ethnic groups. These 6q25.2 SNPs are located between the SCAF8 and CNKSR3 genes, a region with DKD relevant changes in gene expression and an eQTL with IPCEF1, a gene co-translated with CNKSR3. Several other SNPs demonstrated suggestive evidence of association with DKD, within and across populations. These data identify a novel DKD susceptibility locus with consistent directions of effect across diverse ancestral groups and provide insight into the genetic architecture of DKD.

Type 2 diabetes is the most common cause of severe kidney disease worldwide and diabetic kidney disease (DKD) associates with premature death. Individuals of non-European ancestry have the highest burden of type 2 DKD; hence understanding the causes of DKD remains critical to reducing health disparities. Family studies demonstrate that genes regulate the onset and progression of DKD; however, identifying these genes has proven to be challenging. The Family Investigation of Diabetes and Nephropathy consortium (FIND) recruited a large multi-ethnic collection of individuals with type 2 diabetes with and without kidney disease in order to detect genes associated with DKD. FIND discovered and replicated a DKD-associated genetic locus on human chromosome 6q25.2 (rs955333) between the SCAF8 and CNKSR genes. Findings were supported by significantly different expression of genes in this region from kidney tissue of subjects with, versus without DKD. The present findings identify a novel kidney disease susceptibility locus in individuals with type 2 diabetes which is consistent across subjects of differing ancestries. In addition, FIND results provide a rich catalogue of genetic variation in DKD patients for future research on the genetic architecture regulating this common and devastating disease.

Graphical display of diagnostic test results in electronic health records: a comparison of 8 systems

Accurate display and interpretation of clinical laboratory test results is essential for safe and effective diagnosis and treatment. In an attempt to ascertain how well current electronic health records (EHRs) facilitated these processes, we evaluated the graphical displays of laboratory test results in eight EHRs using objective criteria for optimal graphs based on literature and expert opinion. None of the EHRs met all 11 criteria; the magnitude of deficiency ranged from one EHR meeting 10 of 11 criteria to three EHRs meeting only 5 of 11 criteria. One criterion (i.e., the EHR has a graph with y-axis labels that display both the name of the measured variable and the units of measure) was absent from all EHRs. One EHR system graphed results in reverse chronological order. One EHR system plotted data collected at unequally-spaced points in time using equally-spaced data points, which had the effect of erroneously depicting the visual slope perception between data points. This deficiency could have a significant, negative impact on patient safety. Only two EHR systems allowed users to see, hover-over, or click on a data point to see the precise values of the x-y coordinates. Our study suggests that many current EHR-generated graphs do not meet evidence-based criteria aimed at improving laboratory data comprehension.

Loss of δ-catenin function in severe autism

Autism is a multifactorial neurodevelopmental disorder affecting more males than females; consequently, under a multifactorial genetic hypothesis, females are affected only when they cross a higher biological threshold. We hypothesize that deleterious variants at conserved residues are enriched in severely affected patients arising from FEMFs (female-enriched multiplex families) with severe disease, enhancing the detection of key autism genes in modest numbers of cases. We show the utility of this strategy by identifying missense and dosage sequence variants in the gene encoding the adhesive junction-associated delta catenin protein (CTNND2) in FEMFs and demonstrating their loss-of-function effect by functional analyses in zebrafish embryos and cultured hippocampal neurons from wildtype and Ctnnd2 null mouse embryos. Finally, through gene expression and network analyses, we highlight a critical role for CTNND2 in neuronal development and an intimate connection to chromatin biology. Our data contribute to the understanding of the genetic architecture of autism and suggest that genetic analyses of phenotypic extremes, such as FEMFs, are of innate value in multifactorial disorders.

How context affects electronic health record-based test result follow-up: a mixed-methods evaluation

OBJECTIVES

Electronic health record (EHR)-based alerts can facilitate transmission of test results to healthcare providers, helping ensure timely and appropriate follow-up. However, failure to follow-up on abnormal test results (missed test results) persists in EHR-enabled healthcare settings. We aimed to identify contextual factors associated with facility-level variation in missed test results within the Veterans Affairs (VA) health system.

DESIGN, SETTING AND PARTICIPANTS

Based on a previous survey, we categorised VA facilities according to primary care providers' (PCPs') perceptions of low (n=20) versus high (n=20) risk of missed test results. We interviewed facility representatives to collect data on several contextual factors derived from a sociotechnical conceptual model of safe and effective EHR use. We compared these factors between facilities categorised as low and high perceived risk, adjusting for structural characteristics.

RESULTS

Facilities with low perceived risk were significantly more likely to use specific strategies to prevent alerts from being lost to follow-up (p=0.0114). Qualitative analysis identified three high-risk scenarios for missed test results: alerts on tests ordered by trainees, alerts 'handed off' to another covering clinician (surrogate clinician), and alerts on patients not assigned in the EHR to a PCP. Test result management policies and procedures to address these high-risk situations varied considerably across facilities.

CONCLUSIONS

Our study identified several scenarios that pose a higher risk for missed test results in EHR-based healthcare systems. In addition to implementing provider-level strategies to prevent missed test results, healthcare organisations should consider implementing monitoring systems to track missed test results.

An analysis of electronic health record-related patient safety concerns

OBJECTIVE

A recent Institute of Medicine report called for attention to safety issues related to electronic health records (EHRs). We analyzed EHR-related safety concerns reported within a large, integrated healthcare system.

METHODS

The Informatics Patient Safety Office of the Veterans Health Administration (VA) maintains a non-punitive, voluntary reporting system to collect and investigate EHR-related safety concerns (ie, adverse events, potential events, and near misses). We analyzed completed investigations using an eight-dimension sociotechnical conceptual model that accounted for both technical and non-technical dimensions of safety. Using the framework analysis approach to qualitative data, we identified emergent and recurring safety concerns common to multiple reports.

RESULTS

We extracted 100 consecutive, unique, closed investigations between August 2009 and May 2013 from 344 reported incidents. Seventy-four involved unsafe technology and 25 involved unsafe use of technology. A majority (70%) involved two or more model dimensions. Most often, non-technical dimensions such as workflow, policies, and personnel interacted in a complex fashion with technical dimensions such as software/hardware, content, and user interface to produce safety concerns. Most (94%) safety concerns related to either unmet data-display needs in the EHR (ie, displayed information available to the end user failed to reduce uncertainty or led to increased potential for patient harm), software upgrades or modifications, data transmission between components of the EHR, or 'hidden dependencies' within the EHR.

DISCUSSION

EHR-related safety concerns involving both unsafe technology and unsafe use of technology persist long after 'go-live' and despite the sophisticated EHR infrastructure represented in our data source. Currently, few healthcare institutions have reporting and analysis capabilities similar to the VA.

CONCLUSIONS

Because EHR-related safety concerns have complex sociotechnical origins, institutions with long-standing as well as recent EHR implementations should build a robust infrastructure to monitor and learn from them.

Resilient Practices in Maintaining Safety of Health Information Technologies

Electronic health record systems (EHRs) can improve safety and reliability of health care, but they can also introduce new vulnerabilities by failing to accommodate changes within a dynamic EHR-enabled health care system. Continuous assessment and improvement is thus essential for achieving resilience in EHR-enabled health care systems. Given the rapid adoption of EHRs by many organizations that are still early in their experiences with EHR safety, it is important to understand practices for maintaining resilience used by organizations with a track record of success in EHR use. We conducted interviews about safety practices with 56 key informants (including information technology managers, chief medical information officers, physicians, and patient safety officers) at two large health care systems recognized as leaders in EHR use. We identified 156 references to resilience-related practices from 41 informants. Framework analysis generated five categories of resilient practices: (a) sensitivity to dynamics and interdependencies affecting risks, (b) basic monitoring and responding practices, (c) management of practices and resources for monitoring and responding, (d) sensitivity to risks beyond the horizon, and (e) reflecting on risks with the safety and quality control process itself. The categories reflect three functions that facilitate resilience: reflection, transcending boundaries, and involving sharp-end practitioners in safety management.

"Generalized osteoarthritis": a systematic review

OBJECTIVES

Given the conflicting definitions of "generalized osteoarthritis" (GOA) in the literature, we performed a systematic review of GOA definitions, risk factors, and outcomes.

METHODS

We searched the MEDLINE literature with the terms osteoarthritis, generalized, polyarticular, multiple joint, and multi-joint to obtain articles related to GOA, following evidence-based guidelines. Titles and abstracts of 948 articles were reviewed, with full-text review of 108. Data were extracted based on pre-specified criteria for 74 articles plus 24 identified through bibliographic review (n = 98).

RESULTS

Twenty-four large cohorts (n ~ 30,000) were represented along with numerous clinical series (n ~ 9000), across 22 countries and 60 years (1952-2012). No less than 15 definitions of GOA were given in 30 studies with a stated GOA definition; at least 6 groups used a summed score of joints or radiographic grades. Prevalence estimates based on these GOA definitions were 1-80%, although most were 5-25%. Increased risk and progression of GOA was associated with age, female sex, and genetic/familial factors. Associations with increased body mass index or bone mineral density were not consistent. A study estimated the heritability of GOA at 42%. Collagen biomarker levels increased with the number of involved joints. Increased OA burden was associated with increased mortality and disability, poorer health, and function.

CONCLUSION

While there remains no standard definition of GOA, this term is commonly used. The impact on health may be greater when OA is in more than one joint. A descriptive term, such as multi-joint or polyarticular OA, designating OA of multiple joints or joint groups is recommended.

A genome-wide search for linkage of estimated glomerular filtration rate (eGFR) in the Family Investigation of Nephropathy and Diabetes (FIND)

Objective

Estimated glomerular filtration rate (eGFR), a measure of kidney function, is heritable, suggesting that genes influence renal function. Genes that influence eGFR have been identified through genome-wide association studies. However, family-based linkage approaches may identify loci that explain a larger proportion of the heritability. This study used genome-wide linkage and association scans to identify quantitative trait loci (QTL) that influence eGFR.

Methods

Genome-wide linkage and sparse association scans of eGFR were performed in families ascertained by probands with advanced diabetic nephropathy (DN) from the multi-ethnic Family Investigation of Nephropathy and Diabetes (FIND) study. This study included 954 African Americans (AA), 781 American Indians (AI), 614 European Americans (EA) and 1,611 Mexican Americans (MA). A total of 3,960 FIND participants were genotyped for 6,000 single nucleotide polymorphisms (SNPs) using the Illumina Linkage IVb panel. GFR was estimated by the Modification of Diet in Renal Disease (MDRD) formula.

Results

The non-parametric linkage analysis, accounting for the effects of diabetes duration and BMI, identified the strongest evidence for linkage of eGFR on chromosome 20q11 (log of the odds [LOD] = 3.34; P = 4.4×10⁻⁵) in MA and chromosome 15q12 (LOD = 2.84; P = 1.5×10⁻⁴) in EA. In all subjects, the strongest linkage signal for eGFR was detected on chromosome 10p12 (P = 5.5×10⁻⁴) at 44 cM near marker rs1339048. A subsequent association scan in both ancestry-specific groups and the entire population identified several SNPs significantly associated with eGFR across the genome.

Conclusion

The present study describes the localization of QTL influencing eGFR on 20q11 in MA, 15q21 in EA and 10p12 in the combined ethnic groups participating in the FIND study. Identification of causal genes/variants influencing eGFR, within these linkage and association loci, will open new avenues for functional analyses and development of novel diagnostic markers for DN.

Resilient actions in the diagnostic process and system performance

OBJECTIVES

Systemic issues can adversely affect the diagnostic process. Many system-related barriers can be masked by 'resilient' actions of frontline providers (ie, actions supporting the safe delivery of care in the presence of pressures that the system cannot readily adapt to). We explored system barriers and resilient actions of primary care providers (PCPs) in the diagnostic evaluation of cancer.

METHODS

We conducted a secondary data analysis of interviews of PCPs involved in diagnostic evaluation of 29 lung and colorectal cancer cases. Cases covered a range of diagnostic timeliness and were analysed to identify barriers for rapid diagnostic evaluation, and PCPs' actions involving elements of resilience addressing those barriers. We rated these actions according to whether they were usual or extraordinary for typical PCP work.

RESULTS

Resilient actions and associated barriers were found in 59% of the cases, in all ranges of timeliness, with 40% involving actions rated as beyond typical. Most of the barriers were related to access to specialty services and coordination with patients. Many of the resilient actions involved using additional communication channels to solicit cooperation from other participants in the diagnostic process.

DISCUSSION

Diagnostic evaluation of cancer involves several resilient actions by PCPs targeted at system deficiencies. PCPs' actions can sometimes mitigate system barriers to diagnosis, and thereby impact the sensitivity of 'downstream' measures (eg, delays) in detecting barriers. While resilient actions might enable providers to mitigate system deficiencies in the short run, they can be resource intensive and potentially unsustainable. They complement, rather than substitute for, structural remedies to improve system performance. Measures to detect and fix system performance issues targeted by these resilient actions could facilitate diagnostic safety.

Performance of experienced versus less experienced paramedics in managing challenging scenarios: a cognitive task analysis study

STUDY OBJECTIVE

Out-of-hospital care is becoming more complex, thus placing greater reliance on the cognitive abilities of paramedics to manage difficult situations. In adapting to the challenges in their work, paramedics develop expertise. We study the cognitive strategies used by expert paramedics to contribute to understanding how paramedics and the EMS system can adapt to new challenges.

METHODS

We conducted a "staged-world" cognitive task analysis to explore paramedics' handling of cognitive challenges related to sense-making and to resource and task management. A mixed-fidelity simulation was used to present paramedics with 2 challenging scenarios: a pulmonary embolism initially presenting as a myocardial infarction and a 2-person shooting with limited resources available.

RESULTS

Participants were 10 paramedics, 6 more experienced and 4 less experienced. Analysis involved comparing the performance of the 2 groups to identify strategies associated with expertise. The more experienced paramedics made more assessments, explored a wider variety of presumptive diagnoses, and identified the pulmonary embolism earlier. They switched attention between the 2 shooting victims more, used their emergency medical technician-basic level partners more, and provided more advanced level care for both patients. Their patients arrived at the emergency department more prepared for specialized emergency care.

CONCLUSION

Our findings correspond to general cognitive attributes of expertise: greater cue gathering and inferential reasoning, and more functional and strategic thinking. These results suggest potential areas and methods to facilitate development of expertise, as well as ways to better support use of expertise. Future studies should expand on these findings through larger sample sizes and more complex scenarios.

Primary care practitioners' views on test result management in EHR-enabled health systems: a national survey

Context

Failure to notify patients of test results is common even when electronic health records (EHRs) are used to report results to practitioners. We sought to understand the broad range of social and technical factors that affect test result management in an integrated EHR-based health system.

Methods

Between June and November 2010, we conducted a cross-sectional, web-based survey of all primary care practitioners (PCPs) within the Department of Veterans Affairs nationwide. Survey development was guided by a socio-technical model describing multiple inter-related dimensions of EHR use.

Findings

Of 5001 PCPs invited, 2590 (51.8%) responded. 55.5% believed that the EHRs did not have convenient features for notifying patients of test results. Over a third (37.9%) reported having staff support needed for notifying patients of test results. Many relied on the patient's next visit to notify them for normal (46.1%) and abnormal results (20.1%). Only 45.7% reported receiving adequate training on using the EHR notification system and 35.1% reported having an assigned contact for technical assistance with the EHR; most received help from colleagues (60.4%). A majority (85.6%) stayed after hours or came in on weekends to address notifications; less than a third reported receiving protected time (30.1%). PCPs strongly endorsed several new features to improve test result management, including better tracking and visualization of result notifications.

Conclusions

Despite an advanced EHR, both social and technical challenges exist in ensuring notification of test results to practitioners and patients. Current EHR technology requires significant improvement in order to avoid similar challenges elsewhere.

DNA repair gene variants in relation to overall cancer risk: a population-based study

The hypothesis that germ-line polymorphisms in DNA repair genes influence cancer risk has previously been tested primarily on a cancer site-specific basis. The purpose of this study was to test the hypothesis that DNA repair gene allelic variants contribute to globally elevated cancer risk by measuring associations with risk of all cancers that occurred within a population-based cohort. In the CLUE II cohort study established in 1989 in Washington County, MD, this study was comprised of all 3619 cancer cases ascertained through 2007 compared with a sample of 2296 with no cancer. Associations were measured between 759 DNA repair gene single nucleotide polymorphisms (SNPs) and risk of all cancers. A SNP in O(6)-methylguanine-DNA methyltransferase, MGMT, (rs2296675) was significantly associated with overall cancer risk [per minor allele odds ratio (OR) 1.30, 95% confidence interval (CI) 1.19-1.43 and P-value: 4.1 × 10(-8)]. The association between rs2296675 and cancer risk was stronger among those aged ≤54 years old than those who were ≥55 years at baseline (P-for-(interaction) = 0.021). OR were in the direction of increased risk for all 15 categories of malignancies studied (P < 0.0001), ranging from 1.22 (P = 0.42) for ovarian cancer to 2.01 (P = 0.008) for urinary tract cancers; the smallest P-value was for breast cancer (OR 1.45, P = 0.0002). The results indicate that the minor allele of MGMT SNP rs2296675, a common genetic marker with 37% carriers, was significantly associated with increased risk of cancer across multiple tissues. Replication is needed to more definitively determine the scientific and public health significance of this observed association.

A population-based study of DNA repair gene variants in relation to non-melanoma skin cancer as a marker of a cancer-prone phenotype

For unknown reasons, non-melanoma skin cancer (NMSC) is associated with increased risk of other malignancies. Focusing solely on DNA repair or DNA repair-related genes, this study tested the hypothesis that DNA repair gene variants contribute to the increased cancer risk associated with a personal history of NMSC. From the parent CLUE II cohort study, established in 1989 in Washington County, MD, the study consisted of a cancer-free control group (n 5 2296) compared with three mutually exclusive groups of cancer cases ascertained through 2007: (i) Other (non-NMSC) cancer only (n 5 2349); (ii) NMSC only (n 5 694) and (iii) NMSC plus other cancer (n 5 577). The frequency of minor alleles in 759 DNA repair gene single nucleotide polymorphisms (SNPs) was compared in these four groups. Comparing those with both NMSC and other cancer versus those with no cancer, 10 SNPs had allelic trend P-values <0.01. The two top-ranked SNPs were both within the thymine DNA glycosylase gene (TDG). One was a non-synonymous coding SNP (rs2888805) [per allele odds ratio (OR) 1.40, 95% confidence interval (CI) 1.16-1.70; P-value 5 0.0006] and the other was an intronic SNP in high linkage disequilibrium with rs2888805 (rs4135150). None of the associations had a P-value <6.6310(-5), the threshold for statistical significance after correcting for multiple comparisons. The results pinpoint DNA repair genes most likely to contribute to the NMSC cancer-prone phenotype. A promising lead is genetic variants in TDG, important not only in base excision repair but also in regulating the epigenome and gene expression, which may contribute to the NMSC-associated increase in overall cancer risk.

A population-based study of hedgehog pathway gene variants in relation to the dual risk of basal cell carcinoma plus another cancer

INTRODUCTION

A personal history of basal cell carcinoma (BCC) is associated with increased risk of other malignancies, but the reason is unknown. The hedgehog pathway is critical to the etiology of BCC, and is also believed to contribute to susceptibility to other cancers. This study tested the hypothesis that hedgehog pathway and pathway-related gene variants contribute to the increased risk of subsequent cancers among those with a history of BCC.

METHODS

The study was nested within the ongoing CLUE II cohort study, established in 1989 in Washington County, Maryland, USA. The study consisted of a cancer-free control group (n=2296) compared to three different groups of cancer cases ascertained through 2007, those diagnosed with: (1) Other (non-BCC) cancer only (n=2349); (2) BCC only (n=534); and (3) BCC plus other cancer (n=446). The frequencies of variant alleles were compared among these four groups for 20 single nucleotide polymorphisms (SNPs) in 6 hedgehog pathway genes (SHH, IHH, PTCH2, SMO, GLI1, SUFU), and also 22 SNPs in VDR and 8 SNPs in FAS, which have cross-talk with the hedgehog pathway.

RESULTS

Comparing those with both BCC and other cancer versus those with no cancer, no significant associations were observed for any of the hedgehog pathway SNPs, or for the FAS SNPs. One VDR SNP was nominally significantly associated with the BCC cancer-prone phenotype, rs11574085 [per minor allele odds ratio (OR) 1.38, 95% confidence interval (CI) 1.05-1.82; p-value=0.02].

CONCLUSION

The hedgehog pathway gene SNPs studied, along with the VDR and FAS SNPs studied, are not strongly associated with the BCC cancer-prone phenotype.

Abstract 2639: A community-based study of nucleotide excision repair polymorphisms in relation to risk of non-melanoma skin cancer

Nucleotide excision repair (NER) is responsible for protecting DNA in skin cells against ultraviolet radiation-induced damage. Using a candidate pathway approach, a matched case-control study nested within a prospective, community-based cohort was carried out to test the hypothesis that single nucleotide polymorphisms (SNPs) in NER genes are associated with susceptibility to non-melanoma skin cancer (NMSC). Histologically-confirmed cases of NMSC (n=900) were matched to controls (n=900) on age, gender, and skin type. Associations were measured between NMSC and 221 SNPs in 26 NER genes. Using the additive model, two tightly linked functional SNPs in ERCC6 were significantly associated with increased risk of NMSC: rs2228527 (odds ratio (OR) 1.57, 95% confidence interval (CI) 1.20 - 2.05), and rs2228529 (OR 1.57, 95% CI 1.20 - 2.05). These associations were confined to basal cell carcinoma of the skin (BCC) (rs2228529, OR 1.78, 95% CI 1.30 - 2.44; rs2228527 OR 1.78, 95% CI 1.31 - 2.43). These novel, hypothesis-generating findings suggest functional variants in ERCC6 may be associated with an increased risk of NMSC that may be specific to BCC.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 2639. doi:1538-7445.AM2012-2639

BNNT-mediated irreversible electroporation: its potential on cancer cells

Irreversible lethal electroporation (IRE) is a new non-thermal ablation modality that uses short pulses of high amplitude static electric fields (up 1000 V/cm) to create irreversible pores in the cell membrane, thus, causing cell death. Recently, IRE has emerged as a promising clinical modality for cancer disease treatment. Here, we investigated the responses of tumour human HeLa cells when subjected to IRE in the presence of BNNTs. These consist of tiny tubes of B and N atoms (arranged in hexagons) with diameters ranging from a 1 to 3 nanometres and lengths < 2 μm. BNNTs have attracted wide attention because of their unique electrical properties. We speculate that BNNTs, when interacting with cells exposed to static electrical fields, amplify locally the electric field, leading to cell death. In this work, electroporation assays were performed with a commercial electroporator using the cell- specific protocol suggested by the supplier (exponential decay wave, time constant 20 ms) with the specific aim to compare IRE in absence and in presence of BNNTs. We observed that BNNTs have the capacity to decrease substantially the voltage required for IRE. When cells were pulsed at 800 V/cm, we observed a 2,2-fold reduction in cell survival in the presence of BNNTs compared to controls. We conclude that the death of the tumour cells exposed to IRE is strongly enhanced in the presence of BNNTs, indicating their potential therapeutic application.

Radial elasticity of multi-walled boron nitride nanotubes

We investigated the radial mechanical properties of multi-walled boron nitride nanotubes (MW-BNNTs) using atomic force microscopy. The employed MW-BNNTs were synthesized using pressurized vapor/condenser (PVC) methods and were dispersed in aqueous solution using ultrasonication methods with the aid of ionic surfactants. Our nanomechanical measurements reveal the elastic deformational behaviors of individual BNNTs with two to four tube walls in their transverse directions. Their effective radial elastic moduli were obtained through interpreting their measured radial deformation profiles using Hertzian contact mechanics models. Our results capture the dependences of the effective radial moduli of MW-BNNTs on both the tube outer diameter and the number of tube layers. The effective radial moduli of double-walled BNNTs are found to be several-fold higher than those of single-walled BNNTs within the same diameter range. Our work contributes directly to a complete understanding of the fundamental structural and mechanical properties of BNNTs and the pursuits of their novel structural and electronics applications.

In situ mechanical property measurements of amorphous carbon-boron nitride nanotube nanostructures

To understand the mechanical properties of amorphous carbon (a-C)/boron nitride nanotube (BNNT) nanostructures, in situ mechanical tests are conducted inside a transmission electron microscope equipped with an integrated atomic force microscope system. The nanotube structure is modified with amorphous carbon deposited by controlled electron beam irradiation. We demonstrate multiple in situ tensile, compressive, and lap shear tests with a-C/BNNT hybrid nanostructures. The tensile strength of the a-C/BNNT hybrid nanostructure is 5.29 GPa with about 90 vol% of a-C. The tensile strength and strain of the end-to-end joint structure with a-C welding is 0.8 GPa and 5.2% whereas the lap shear strength of the side-by-side joint structure with a-C is 0.25 GPa.

Radial mechanical properties of single-walled boron nitride nanotubes

The radial mechanical properties of single-walled boron nitride nanotubes (SW-BNNTs) are investigated by atomic force microscopy. Nanomechanical measurements reveal the radial deformation of individual SW-BNNTs in both elastic and plastic regimes. The measured effective radial elastic moduli of SW-BNNTs are found to follow a decreasing trend with an increase in tube diameter, ranging from 40.78 to 1.85 GPa for tube diameters of 0.58 to 2.38 nm. The results show that SW-BNNTs have relatively lower effective radial elastic moduli than single-walled carbon nanotubes (SWCNTs). The axially strong, but radially supple characteristics suggest that SW-BNNTs may be superior to SWCNTs as reinforcing additives for nanocomposite applications.

Exploring situational awareness in diagnostic errors in primary care

OBJECTIVE

Diagnostic errors in primary care are harmful but poorly studied. To facilitate the understanding of diagnostic errors in real-world primary care settings that use electronic health records (EHRs), this study explored the use of the situational awareness (SA) framework from aviation human factors research.

METHODS

A mixed-methods study was conducted involving reviews of EHR data followed by semi-structured interviews of selected providers from two institutions in the USA. The study population included 380 consecutive patients with colorectal and lung cancers diagnosed between February 2008 and January 2009. Using a pre-tested data collection instrument, trained physicians identified diagnostic errors, defined as lack of timely action on one or more established indications for diagnostic work-up for lung and colorectal cancers. Twenty-six providers involved in cases with and without errors were interviewed. Interviews probed for providers' lack of SA and how this may have influenced the diagnostic process.

RESULTS

Of 254 cases meeting inclusion criteria, errors were found in 30 of 92 (32.6%) lung cancer cases and 56 of 167 (33.5%) colorectal cancer cases. Analysis of interviews related to error cases revealed evidence of lack of one of four levels of SA applicable to primary care practice: information perception, information comprehension, forecasting future events, and choosing appropriate action based on the first three levels. In cases without error, application of the SA framework provided insight into processes involved in attention management.

CONCLUSIONS

A framework of SA can help analyse and understand diagnostic errors in primary care settings that use EHRs.

Genomewide linkage scan for diabetic renal failure and albuminuria: the FIND study

BACKGROUND

Diabetic nephropathy (DN) is a leading cause of mortality and morbidity in patients with type 1 and type 2 diabetes. The multicenter FIND consortium aims to identify genes for DN and its associated quantitative traits, e.g. the urine albumin:creatinine ratio (ACR). Herein, the results of whole-genome linkage analysis and a sparse association scan for ACR and a dichotomous DN phenotype are reported in diabetic individuals.

METHODS

A genomewide scan comprising more than 5,500 autosomal single nucleotide polymorphism markers (average spacing of 0.6 cM) was performed on 1,235 nuclear and extended pedigrees (3,972 diabetic participants) ascertained for DN from African-American (AA), American-Indian (AI), European-American (EA) and Mexican-American (MA) populations.

RESULTS

Strong evidence for linkage to DN was detected on chromosome 6p (p = 8.0 × 10(-5), LOD = 3.09) in EA families as well as suggestive evidence for linkage to chromosome 7p in AI families. Regions on chromosomes 3p in AA, 7q in EA, 16q in AA and 22q in MA displayed suggestive evidence of linkage for urine ACR. The linkage peak on chromosome 22q overlaps the MYH9/APOL1 gene region, previously implicated in AA diabetic and nondiabetic nephropathies.

CONCLUSION

These results strengthen the evidence for previously identified genomic regions and implicate several novel loci potentially involved in the pathogenesis of DN.

Admixture mapping comes of age

Admixture mapping is based on the hypothesis that differences in disease rates between populations are due in part to frequency differences in disease-causing genetic variants. In admixed populations, these genetic variants occur more often on chromosome segments inherited from the ancestral population with the higher disease variant frequency. A genome scan for disease association requires only enough markers to identify the ancestral chromosome segments; for recently admixed populations, such as African Americans, 1,500-2,500 ancestry-informative markers (AIMs) are sufficient. The method was proposed over 50 years ago, but the AIM panels and statistical methods required have only recently become available. Since the first admixture scan in 2005, the genetic bases for a range of diseases/traits have been identified by admixture mapping. Here, we provide a historical perspective, review AIM panels and software packages, and discuss recent successes and unexpected insights into human diseases that exhibit disparate rates across human populations.

Effect of host genetics on the development of cytomegalovirus retinitis in patients with AIDS

BACKGROUND

Cytomegalovirus (CMV) retinitis is a common opportunistic infection among patients with AIDS and still causes visual morbidity despite the wide spread usage of highly active antiretroviral therapy (HAART). The ubiquitous CMV pathogen contains a human interleukin-10 (IL-10) homolog in its genome and utilizes it to evade host immune reactions through an IL-10 receptor mediated immune-suppression pathway.

METHODS

Effects of IL-10R1, IL-10 and previously described AIDS restriction gene variants are investigated on the development of CMV retinitis in the Longitudinal Study of the Ocular Complications of AIDS (LSOCA) cohort (N = 1284).

RESULTS

In European Americans (n = 750), a haplotype carrying an amino acid changing variation in the cytoplasmic domain (S420L) of IL-10R1 can be protective (OR, 0.14; 95% CI, 0.02-0.94; P = .04) against, whereas another haplotype carrying an amino acid changing variation in the extracellular domain (I224V) of IL-10R1 can be more susceptible (OR, 6.21; 95% CI, 1.22- 31.54; P = .03) to CMV retinitis. In African Americans (n = 534), potential effects of IL-10 variants are observed.

CONCLUSION

Host genetics may have a role in the occurrence of CMV retinitis in patients infected with HIV.

Protein synthesis in the intestine of goldfish acclimatized to different temperatures

1. The incorporation of [(14)C]valine and [(3)H]threonine has been studied in mucosa of goldfish acclimatized to different temperatures. 2. [(14)C]Valine was incorporated more rapidly than [(3)H]threonine at acclimatization temperatures below 15 degrees ; this distinction disappeared at higher temperatures. 3. The rate of amino acid incorporation rose as the environmental temperature was increased. 4. The number of valine residues in mucosal protein fell and the number of methionine residues rose as the acclimatization temperature was raised. 5. The concentration of free methionine was closely related to the amount in protein in goldfish mucosa; both increased at higher acclimatization temperatures. 6. An attempt is made to show that these changes are integrated with possible homoeostatic mechanisms in the goldfish intestine.

Sodium-glucose interactions in the goldfish intestine

1. Everted sacs of goldfish intestine transfer glucose and water to their serosal surfaces and the total transfer is greater in the anterior intestine than in the intestinal bulb or rectum.2. Transmural potentials, with the serosa positive to the mucosa, were recorded from all parts of the goldfish intestine but were highest in the anterior intestine and the rectum. In both these areas the total potential was dependent partly upon the presence of glucose.3. Reducing the concentration of sodium bathing the mucosa of the anterior intestine reduced the glucose-evoked potential in a non-linear way. The steady-state potentials, with or without glucose, first increased and later decreased as the sodium concentration was further reduced.4. Reducing the concentration of glucose bathing the mucosa from 27 to 5 mM slightly increased the glucose-evoked potential. Further reduction of the glucose concentration caused the glucose-evoked potential to fall.5. Phlorrhizin inhibited the glucose-evoked potential. The degree of inhibition was proportional to the log concentration of phlorrhizin over the range 2 x 10(-7)-6 x 10(-5)M. The steady-state potential with glucose present was lower than when glucose was absent at phlorrhizin concentrations, 6 x 10(-6)-6 x 10(-5)M.6. The glucose-evoked potential increased rapidly over the temperature range 5-15 degrees C and more slowly from 15 to 30 degrees C. The steady-state potentials also increased with temperature, the rate of increase being greater when glucose was present. Below 15 degrees C the glucose-independent potential was higher and above 15 degrees C lower than the steady-state potential recorded with glucose present.7. These findings are discussed in terms of sodium-glucose interaction taking place at the luminal side of the mucosal cell, on the outside of the mucosal cell membrane.

Influence of cholecalciferol (vitamin D(3)) on the initial kinetics of the uptake of calcium ions by rat small-intestinal mucosa (Short Communication)

The uptake of Ca(2+) by isolated small-intestinal mucosa from vitamin D-depleted and -repleted rats was analysed for the effects of vitamin D on initial kinetics. The rapid association of Ca(2+) with the tissue, which is complete within 1min, was unaffected by the vitamin, whereas the subsequent, linear, uptake was significantly increased. Neither the tissue space accessible to inulin nor the permeability to thiourea was influenced by vitamin D treatment.

Influence of temperature acclimatization on the ionic activation of goldfish intestinal adenosine triphosphatase

1. An adenosine triphosphatase membrane system, dependent on Mg(2+) and activated further by Na(+)+K(+), was prepared from goldfish anterior intestine by differential centrifugation of homogenized intestinal scrapings. 2. The affinity of this preparation for Na(+) in the presence of K(+)+Mg(2+), for K(+) in the presence of Na(+)+Mg(2+) and for Mg(2+) alone, measured at 37 degrees , did not depend on the previous environmental temperature of the fish. When Na(+)+K(+) were added to preparations from 8 degrees -acclimatized fish the affinity for Mg(2+) increased; this was not seen with preparations from 30 degrees -acclimatized fish. 3. Part of the Mg(2+)-activated adenosine triphosphatase was inhibited by Na(+) and the amount of inhibition appeared to increase at high acclimatization temperatures. 4. This Na(+)-inhibited adenosine triphosphatase was separated from the (Na(+)+K(+))-activated enzyme by centrifugation on sucrose density gradients. 5. Preparations from 8 degrees -acclimatized fish contained less Mg(2+)-activated and more (Na(+)+K(+))-activated adenosine triphosphatase than did similar fractions from 30 degrees -acclimatized fish. 6. Acclimatization to different environmental temperatures might involve one form of adenosine triphosphatase changing to another. The origin of various membranes seen in microsomal fractions must, however, be established before this hypothesis can be tested further.

Intercalation as a means to suppress cyclization and promote polymerization of base-pairing oligonucleotides in a prebiotic world

The RNA world hypothesis proposes that nucleic acids were once responsible for both information storage and chemical catalysis, before the advent of coded protein synthesis. However, it is difficult to imagine how nucleic acid polymers first appeared, as the abiotic chemical formation of long nucleic acid polymers from mononucleotides or short oligonucleotides remains elusive, and barriers to achieving this goal are substantial. One specific obstacle to abiotic nucleic acid polymerization is strand cyclization. Chemically activated short oligonucleotides cyclize efficiently, which severely impairs polymer growth. We show that intercalation, which stabilizes and rigidifies nucleic acid duplexes, almost totally eliminates strand cyclization, allowing for chemical ligation of tetranucleotides into duplex polymers of up to 100 base pairs in length. In contrast, when these reactions are performed in the absence of intercalators, almost exclusively cyclic tetra- and octanucleotides are produced. Intercalator-free polymerization is not observed, even at tetranucleotide concentrations > 10,000-fold greater than those at which intercalators enable polymerization. We also demonstrate that intercalation-mediated polymerization is most favored if the size of the intercalator matches that of the base pair; intercalators that bind to Watson-Crick base pairs promote the polymerization of oligonucleotides that form these base pairs. Additionally, we demonstrate that intercalation-mediated polymerization is possible with an alternative, non-Watson-Crick-paired duplex that selectively binds a complementary intercalator. These results support the hypothesis that intercalators (acting as 'molecular midwives') could have facilitated the polymerization of the first nucleic acids and possibly helped select the first base pairs, even if only trace amounts of suitable oligomers were available.

Genome-wide scans for footprints of natural selection

Detecting recent selected ‘genomic footprints’ applies directly to the discovery of disease genes and in the imputation of the formative events that molded modern population genetic structure. The imprints of historic selection/adaptation episodes left in human and animal genomes allow one to interpret modern and ancestral gene origins and modifications. Current approaches to reveal selected regions applied in genome-wide selection scans (GWSSs) fall into eight principal categories: (I) phylogenetic footprinting, (II) detecting increased rates of functional mutations, (III) evaluating divergence versus polymorphism, (IV) detecting extended segments of linkage disequilibrium, (V) evaluating local reduction in genetic variation, (VI) detecting changes in the shape of the frequency distribution (spectrum) of genetic variation, (VII) assessing differentiating between populations (F_ST), and (VIII) detecting excess or decrease in admixture contribution from one population. Here, we review and compare these approaches using available human genome-wide datasets to provide independent verification (or not) of regions found by different methods and using different populations. The lessons learned from GWSSs will be applied to identify genome signatures of historic selective pressures on genes and gene regions in other species with emerging genome sequences. This would offer considerable potential for genome annotation in functional, developmental and evolutionary contexts.

Association of common polymorphisms in IL10, and in other genes related to inflammatory response and obesity with colorectal cancer

OBJECTIVE AND METHODS

The association of 17 candidate single nucleotide polymorphisms (SNPs) in IL10 and other immune response genes (CRP, TLR4, IL6, IL1B, IL8, TNF, RNASEL) and genes related to obesity (PPARG, TCF7L2, ADIPOQ, LEP) with colorectal cancer was investigated. Haplotype tagging SNPs were chosen for IL10, CRP, and TLR4. Incident colorectal cancer cases (n = 208) and matched controls (n = 381) were identified between baseline in 1989 and 2003 among participants in the CLUE II cohort. Odds ratios (OR) and 95% confidence intervals (95% CI) were estimated using conditional logistic regression.

RESULTS

Compared with the AA genotype at the candidate IL10-1082 locus (rs1800896), carrying one (OR, 0.79; 95% CI, 0.53-1.18) or two (OR, 0.58; 95% CI, 0.35-0.95) G alleles, a known higher producer of the anti-inflammatory cytokine IL-10, was associated with lower risk of colorectal cancer (p trend = 0.03). Statistically significant associations with colorectal cancer were observed for three tagSNPs in IL10 (rs1800890, rs3024496, rs3024498) and one common haplotype, but these associations were due to high linkage disequilibrium with IL10-1082. Two CRP haplotypes (global p = 0.04) and TLR4 tagSNPs (rs7873784, rs11536891), but not TLR4 haplotypes, were associated with colorectal cancer.

CONCLUSIONS

Our study suggests that polymorphisms in IL10, and also possibly in CRP and other genes related to immune response or obesity may be associated with colorectal cancer.

Very long single- and few-walled boron nitride nanotubes via the pressurized vapor/condenser method

A new method for producing long, small-diameter, single- and few-walled, boron nitride nanotubes (BNNTs) in macroscopic quantities is reported. The pressurized vapor/condenser (PVC) method produces, without catalysts, highly crystalline, very long, small-diameter, BNNTs. Palm-sized, cotton-like masses of BNNT raw material were grown by this technique and spun directly into centimeters-long yarn. Nanotube lengths were observed to be 100 times that of those grown by the most closely related method. Self-assembly and growth models for these long BNNTs are discussed.

Association of APOE polymorphism with chronic kidney disease in a nationally representative sample: a Third National Health and Nutrition Examination Survey (NHANES III) Genetic Study

Background

Apolipoprotein E polymorphisms (APOE) have been associated with lowered glomerular filtration rate (GFR) and chronic kidney disease (CKD) with e2 allele conferring risk and e4 providing protection. However, few data are available in non-European ethnic groups or in a population-based cohort.

Methods

The authors analyzed 5,583 individuals from the Third National Health and Nutrition Examination Survey (NHANES III) to determine association with estimated GFR by the Modification of Diet in Renal Disease (MDRD) equation and low-GFR cases. Low-GFR cases were defined as GFR <75 ml/min/1.73 m²; additionally, GFR was analyzed continuously.

Results

In univariate analysis, the e4 allele was negatively associated with low-GFR cases in non-Hispanic whites, odds ratio (OR): 0.76, 95% confidence interval (CI): 0.60, 0.97. In whites, there was a significant association between increasing APOE score (indicating greater number of e2 alleles) and higher prevalence of low-GFR cases (OR: 1.21, 95%CI: 1.01, 1.45). Analysis of continuous GFR in whites found the e4 allele was associated with higher levels of continuous GFR (β-coefficient: 2.57 ml/min/1.73 m², 95%CI: 0.005, 5.14); in non-Hispanic blacks the e2 allele was associated with lower levels of continuous GFR (β-coefficient: -3.73 ml/min/1.73 m², 95%CI: -6.61, -0.84). APOE e2 and e4 alleles were rare and not associated with low-GFR cases or continuous GFR in Mexican Americans.

Conclusion

In conclusion, the authors observed a weak association between the APOE e4 allele and low-GFR cases and continuous GFR in non-Hispanic whites, and the APOE e2 allele and continuous GFR in non-Hispanic blacks, but found no association with either measure of kidney function in Mexican Americans. Larger studies including multiethnic groups are needed to determine the significance of this association.

Hypothesis-driven candidate gene association studies: practical design and analytical considerations

Candidate gene association studies (CGAS) are a useful epidemiologic approach to drawing inferences about relations between genes and disease, especially when experimental data support the involvement of specific biochemical pathways. The value of CGAS is apparent when allele frequencies are low, effect sizes are small, or the study population is limited or unique. CGAS is also valuable for validating previous reports of genetic associations with disease in different populations. Despite the many advantages, the information generated from CGAS is sometimes compromised because of either inefficient study design or suboptimal analytical approaches. Here the authors discuss issues related to the study design and statistical analyses of CGAS that can help to optimize their usefulness and information content. These issues include judicious hypothesis-driven selection of biochemical pathways, genes, and single nucleotide polymorphisms, as well as appropriate quality control and analytical procedures for measuring main effects and for evaluating environmental exposure modifications and interactions. A study design algorithm using the example of DNA repair genes and cancer is presented for purposes of illustration.