Barriers and Strategies to an Iterative Model of Advance Care Planning Communication

Background: Early and repeated patient–provider conversations about advance care planning (ACP) are now widely recommended. We sought to characterize barriers and strategies for realizing an iterative model of ACP patient–provider communication. Methods: A total of 2 multidisciplinary focus groups and 3 semistructured interviews with 20 providers at a large Veterans Affairs medical center. Thematic analysis was employed to identify salient themes. Results: Barriers included variation among providers in approaches to ACP, lack of useful information about patient values to guide decision making, and ineffective communication between providers across settings. Strategies included eliciting patient values rather than specific treatment choices and an increased role for primary care in the ACP process. Conclusions: Greater attention to connecting providers across the continuum, maximizing the potential of the electronic health record, and linking patient experiences to their values may help to connect ACP communication across the continuum.Keywords: patient preference, primary health care, goals of care, continuity of care, advance care planning, electronic health recordKeywords: patient preference, primary health care, goals of care, continuity of care, advance care planning, electronic health recor

Developing an Informatics Tool To Advance Supportive Care: The Veterans Health Care Administration Palliative Care National Clinical Template

BACKGROUND: Increasing emphasis in performance-based payment, public reporting, and quality improvement (QI) has led to widespread interest in measuring and improving the quality of care. By 2014, hospice programs will be required to report quality data to the federal government or incur financial penalties. With this increased interest in quality reporting comes an opportunity to develop informatics tools to capture data that reflect the complex practices involved in palliative care (PC). Therefore, there is a need to disseminate information on developing tools that facilitate capturing data and fostering improved performance. The Veterans Health Care Administration, a national leader in health information technology (HIT) and PC, established the Quality Improvement Resource Center (QuIRC) to develop innovative HIT tools to standardize and improve PC practices throughout the 153 Department of Veterans Affairs (VA) medical centers nationwide. OBJECTIVE: The aim of the paper is to describe the development of the Palliative Care-National Clinical Template (PC-NCT) for documenting initial PC consults. RESULTS: Domains of quality of life provided the foundation for this template. Principles of user-centered informatics design guided development activities. A national consensus panel of PC experts prioritized quality indicators as targets for QI. An interdisciplinary team of PC providers identified desired aspects of template functionality. QuIRC balanced PC providers' desired aspects of functionality against the feasibility within the VA HIT system. Formal pilot and usability testing contributed to numerous iterations of the PC-NCT currently piloted in five geographically distributed sites. CONCLUSION: This paper presents a robust approach to developing an informatics tool for PC practice. Data collected via the PC-NCT will bring variations in current practice into view and assist in directing resources at "important targets" for QI. Although the development of HIT tools to quantify PC practice is complex, there is enormous potential to improve the quality of care for patients and families facing serious illnesses

Machine learning integrates genomic signatures for subclassification beyond primary and secondary acute myeloid leukemia

Although genomic alterations drive the pathogenesis of acute myeloid leukemia (AML), traditional classifications are largely based on morphology, and prototypic genetic founder lesions define only a small proportion of AML patients. The historical subdivision of primary/de novo AML and secondary AML has shown to variably correlate with genetic patterns. The combinatorial complexity and heterogeneity of AML genomic architecture may have thus far precluded genomic-based subclassification to identify distinct molecularly defined subtypes more reflective of shared pathogenesis. We integrated cytogenetic and gene sequencing data from a multicenter cohort of 6788 AML patients that were analyzed using standard and machine learning methods to generate a novel AML molecular subclassification with biologic correlates corresponding to underlying pathogenesis. Standard supervised analyses resulted in modest cross-validation accuracy when attempting to use molecular patterns to predict traditional pathomorphologic AML classifications. We performed unsupervised analysis by applying the Bayesian latent class method that identified 4 unique genomic clusters of distinct prognoses. Invariant genomic features driving each cluster were extracted and resulted in 97% cross-validation accuracy when used for genomic subclassification. Subclasses of AML defined by molecular signatures overlapped current pathomorphologic and clinically defined AML subtypes. We internally and externally validated our results and share an open-access molecular classification scheme for AML patients. Although the heterogeneity inherent in the genomic changes across nearly 7000 AML patients was too vast for traditional prediction methods, machine learning methods allowed for the definition of novel genomic AML subclasses, indicating that traditional pathomorphologic definitions may be less reflective of overlapping pathogenesis

Disturbance and Plant Succession in the Mojave and Sonoran Deserts of the American Southwest

Disturbances such as fire, land clearing, and road building remove vegetation and can have major influences on public health through effects on air quality, aesthetics, recreational opportunities, natural resource availability, and economics. Plant recovery and succession following disturbance are poorly understood in arid lands relative to more temperate regions. This study quantitatively reviewed vegetation reestablishment following a variety of disturbances in the Mojave and Sonoran Deserts of southwestern North America. A total of 47 studies met inclusion criteria for the review. The time estimated by 29 individual studies for full reestablishment of total perennial plant cover was 76 years. Although long, this time was shorter than an estimated 215 years (among 31 individual studies) required for the recovery of species composition typical of undisturbed areas, assuming that recovery remains linear following the longest time since disturbance measurement made by the studies

Aircraft Regional-Scale Flux Measurements over Complex Landscapes of Mangroves, Desert, and Marine Ecosystems of Magdalena Bay, Mexico

Natural ecosystems are rarely structurally simple or functionally homogeneous. This is true for the complex coastal region of Magdalena Bay, Baja California Sur, Mexico, where the spatial variability in ecosystem fluxes from the Pacific coastal ocean, eutrophic lagoon, mangroves, and desert were studied. The Sky Arrow 650TCN environmental research aircraft proved to be an effective tool in characterizing land–atmosphere fluxes of energy, CO2, and water vapor across a heterogeneous landscape at the scale of 1 km. The aircraft was capable of discriminating fluxes from all ecosystem types, as well as between nearshore and coastal areas a few kilometers distant. Aircraft-derived average midday CO2 fluxes from the desert showed a slight uptake of −1.32 μmol CO2 m−2 s−1, the coastal ocean also showed an uptake of −3.48 μmol CO2 m−2 s−1, and the lagoon mangroves showed the highest uptake of −8.11 μmol CO2 m−2 s−1. Additional simultaneous measurements of the normalized difference vegetation index (NDVI) allowed simple linear modeling of CO2 flux as a function of NDVI for the mangroves of the Magdalena Bay region. Aircraft approaches can, therefore, be instrumental in determining regional CO2 fluxes and can be pivotal in calculating and verifying ecosystem carbon sequestration regionally when coupled with satellite-derived products and ecosystem models

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Iceberg melting substantially modifies oceanic heat flux towards a major Greenlandic tidewater glacier

Fjord dynamics influence oceanic heat flux to the Greenland ice sheet. Submarine iceberg melting releases large volumes of freshwater within Greenland’s fjords, yet its impact on fjord dynamics remains unclear. We modify an ocean model to simulate submarine iceberg melting in Sermilik Fjord, east Greenland. Here we find that submarine iceberg melting cools and freshens the fjord by up to ~5 °C and 0.7 psu in the upper 100-200 m. The release of freshwater from icebergs drives an overturning circulation, resulting in a ~10% increase in net up-fjord heat flux. In addition, we find that submarine iceberg melting accounts for over 95% of heat used for ice melt in Sermilik Fjord. Our results highlight the substantial impact that icebergs have on the dynamics of a major Greenlandic fjord, demonstrating the importance of including related processes in studies that seek to quantify interactions between the ice sheet and the ocean

Evolution of reproductive mode in the scaly-winged bark louse Echmepteryx hageni

The origin and maintenance of sexual reproduction has long been of interest to evolutionary biologists. While the relationship between genetic diversity and asexuality has received recent attention, the precise nature of this relationship is dependent on the physiological mechanism (e.g. automixis vs. apomixes) and the details of the origin (e.g. endosymbiont infection or hybridogenesis) of asexual reproduction. Most of the work explicitly exploring the links between reproductive mode and genetic diversity has been theoretical in nature and has only modeled asexuality as clonal reproduction. Thus, the applicability of these studies beyond apomictic species is questionable. Empirical studies are necessary to understand the full breadth of the relationship, and ideal systems to do so are species with sexual and asexual forms co-existing. A common pattern of co-existence of reproductive mode is geographic parthenogenesis. This pattern is characterized by sexual populations occupying the central part of the species’ range, while asexual populations are found in peripheral or marginal habitats. There is an alternative pattern of sexual-asexual co-existence that is present in several species of bark lice (Insecta: Psocoptera), an inconspicuous and under-studied group of insects that scrape lichen and other organic matter off a substrate, often bark, dead branches, rock outcroppings, or leaf litter. It is in many ways the inverse of geographic parthenogenesis. The asexual form of these species occupy the central part of the range, while sexual populations are restricted to peripheral or highly isolated localities. One such species is the scaly winged bark louse, Echmepteryx hageni, which is found through eastern North America, but sexual populations are known only from a few rock outcroppings in southern Illinois and eastern Kentucky. There is a strong disparity in mitochondrial genetic diversity between the reproductive forms of E. hageni, with the parthenogenetic form exhibiting very high haplotypic and nucleotide diversity while the sexual populations are virtually homogenous. In Chapter 1, I show that the disparity in genetic diversity is also present at nuclear loci, though not as strongly as at the mitochondrial markers. A demographic signal of rapid range expansion in the asexual form of E. hageni previously observed in mitochondrial data is also present at three of four nuclear loci. However, there are contrasting patterns of genetic structure and population differentiation between the two genomic regions. Finally, I outline three hypotheses that might explain the disparity in genetic diversity between the sexual and asexual forms present in the mitochondrial (and to a lesser extent the nuclear) genetic data: (1) sexuals are derived from the asexuals and are recent in origin, (2) asexual E. hageni have a greater per-year mutation rate due to life history differences, (3) conversion of a genetically diverse sexual species to a primarily asexual species. I test the first and third hypotheses in Chapter 2, both of which involve the question of the direction of evolution in reproductive mode in E. hageni. Hypothesis 1 is based on sexuality being a recently derived trait in E. hageni, while Hypothesis 3 posits a recent conversion of the species from sexual to primarily asexual reproduction. The derived position of sexual E. hageni observed in maximum parsimony analyses of mtDNA (Shreve et al 2011) is confirmed by maximum likelihood analysis, though with different root placement. However, outgroup randomization tests cast doubt on the ability of phylogenetic outgroups to accurately root the E. hageni tree. Once the evolutionary relatedness of mitochondrial haplotypes was taken into account via nesting of haplotype groups, measures of cytonuclear disequilibria at the four nuclear loci are consistent with the relatively recent conversion of a diverse, sexual species to parthenogenetic reproduction, consistent with Hypothesis 3. However, a secondary assumption of Hypothesis 3, that parthenogenesis is the result of an endosymbiont infection, is not supported. Both Wolbachia and Rickettsia are found in some E. hageni, but infection does not appear to be correlated with asexual reproduction. Chapter 3 compares patterns of mitochondrial genetic diversity in E. hageni with another bark louse species, Peripsocus subfasciatus, in order to test Hypothesis 2. The multivoltine sexual form of P. subfasciatus has significantly greater haplotypic and nucleotide diversity than the univoline sexual E. hageni. In addition, unlike E. hageni, the genetic diversity of sexual P. subfasciatus is slightly but statistically greater than in the asexual form of the species. These results are consistent with the hypothesis that life history differences between the multivoltine asexual form and the univoltine sexual form of E. hageni are at least partially responsible for the disparity in genetic diversity between the two reproductive forms of this species. Asexual genetic diversity is elevated in P. subfasciatus in a manner similar to E. hageni, suggesting that this may be a common pattern in the restricted-sexuality distribution. However, additional studies of other bark lice with this pattern are necessary to verify the trend. Chapter 4 examines the extreme range disjunctions present in P. subfasciatus from a phylogeographic and population genetic perspective. P. subfasciatus is found in eastern North America, the Pacific coast of the western North America, and also in Europe. In addition, sexuality is restricted to western North America and isolated populations in eastern North America. There are two mitochondrial clades with a mean sequence divergence between them of 1.8%, but this genetic break does not correspond to reproductive mode or to geography. In fact, reproductive mode has virtually no association with genetic structure at all. On the contrary, analysis of mitochondrial and nuclear data finds that grouping western North American and European populations versus eastern North American populations explains more of the genetic variation within P. subfasciatus than any other grouping scheme. European and western North American population may therefore have historically connected via the Bering land bridge, but phylogeographic history of the eastern North American-European split remains unclear. The experiments and analyses carried out as part of the dissertation have variously both supported and contradicted each of the three hypotheses. As a result, the evolutionary processes shaping genetic diversity and distributional patterns in E. hageni remain unclear. The three hypotheses are not all mutually exclusive, and it is possible that life history differences have worked in conjunction with other evolutionary and ecological processes to shape genetic diversity within E. hageni. One plausible sequence of events is that a rapid conversion from sexual to asexual reproduction in E. hageni resulted in a majority of the standing genetic diversity being preserved in the parthenogenetic lineages. At this point, the life history differences between the sexual and asexual forms and their differences in effective population size could have worked together to maintain and exacerbate the differences in genetic diversity between the reproductive forms