Unsupervised machine learning for detection of phase transitions in off-lattice systems II. Applications

We outline how principal component analysis (PCA) can be applied to particle configuration data to detect a variety of phase transitions in off-lattice systems, both in and out of equilibrium. Specifically, we discuss its application to study 1) the nonequilibrium random organization (RandOrg) model that exhibits a phase transition from quiescent to steady-state behavior as a function of density, 2) orientationally and positionally driven equilibrium phase transitions for hard ellipses, and 3) compositionally driven demixing transitions in the non-additive binary Widom-Rowlinson mixture

Aluminum tolerance in maize is associated with higher MATE1 gene copy number

Genome structure variation, including copy number variation and presence/absence variation, comprises a large extent of maize genetic diversity; however, its effect on phenotypes remains largely unexplored. Here, we describe how copy number variation underlies a rare allele that contributes to maize aluminum (Al) tolerance. Al toxicity is the primary limitation for crop production on acid soils, which make up 50% of the world's potentially arable lands. In a recombinant inbred line mapping population, copy number variation of the Al tolerance gene multidrug and toxic compound extrusion 1 (MATE1) is the basis for the quantitative trait locus of largest effect on phenotypic variation. This expansion in MATE1 copy number is associated with higher MATE1 expression, which in turn results in superior Al tolerance. The three MATE1 copies are identical and are part of a tandem triplication. Only three maize inbred lines carrying the three-copy allele were identified from maize and teosinte diversity panels, indicating that copy number variation for MATE1 is a rare, and quite likely recent, event. These maize lines with higher MATE1 copy number are also Al-tolerant, have high MATE1 expression, and originate from regions of highly acidic soils. Our findings show a role for copy number variation in the adaptation of maize to acidic soils in the tropics and suggest that genome structural changes may be a rapid evolutionary response to new environments

Role of "external facilitation" in implementation of research findings: a qualitative evaluation of facilitation experiences in the Veterans Health Administration

BACKGROUND: Facilitation has been identified in the literature as a potentially key component of successful implementation. It has not, however, either been well-defined or well-studied. Significant questions remain about the operational definition of facilitation and about the relationship of facilitation to other interventions, especially to other change agent roles when used in multi-faceted implementation projects. Researchers who are part of the Quality Enhancement Research Initiative (QUERI) are actively exploring various approaches and processes, including facilitation, to enable implementation of best practices in the Veterans Health Administration health care system – the largest integrated healthcare system in the United States. This paper describes a systematic, retrospective evaluation of implementation-related facilitation experiences within QUERI, a quality improvement program developed by the US Department of Veterans Affairs. METHODS: A post-hoc evaluation was conducted through a series of semi-structured interviews to examine the concept of facilitation across several multi-site QUERI implementation studies. The interview process is based on a technique developed in the field of education, which systematically enhances learning through experience by stimulating recall and reflection regarding past complex activities. An iterative content analysis approach relative to a set of conceptually-based interview questions was used for data analysis. FINDINGS: Findings suggest that facilitation, within an implementation study initiated by a central change agency, is a deliberate and valued process of interactive problem solving and support that occurs in the context of a recognized need for improvement and a supportive interpersonal relationship. Facilitation was described primarily as a distinct role with a number of potentially crucial behaviors and activities. Data further suggest that external facilitators were likely to use or integrate other implementation interventions, while performing this problem-solving and supportive role. PRELIMINARY CONCLUSIONS: This evaluation provides evidence to suggest that facilitation could be considered a distinct implementation intervention, just as audit and feedback, educational outreach, or similar methods are considered to be discrete interventions. As such, facilitation should be well-defined and explicitly evaluated for its perceived usefulness within multi-intervention implementation projects. Additionally, researchers should better define the specific contribution of facilitation to the success of implementation in different types of projects, different types of sites, and with evidence and innovations of varying levels of strength and complexity

Orientationally ordered silicon nanocrystal cuboctahedra in superlattices

This is an open access article published under an ACS AuthorChoice License. See Standard ACS AuthorChoice/Editors' Choice Usage Agreement - https://pubs.acs.org/page/policy/authorchoice_termsofuse.htmlUniform silicon nanocrystals were synthesized with cuboctahedral shape and passivated with 1-dodecene capping ligands. Transmission electron microscopy, electron diffraction, and grazing incidence wide-angle and small-angle X-ray scattering show that these soft cuboctahedra assemble into face-centered cubic superlattices with orientational order. The preferred nanocrystal orientation was found to depend on the orientation of the superlattices on the substrate, indicating that the interactions with the substrate and assembly kinetics can influence the orientation of faceted nanocrystals in superlattices

Data for improvement and clinical excellence: protocol for an audit with feedback intervention in long-term care

<p>Abstract</p> <p>Background</p> <p>There is considerable evidence about the effectiveness of audit coupled with feedback, although few audit with feedback interventions have been conducted in long-term care (LTC) settings to date. In general, the effects have been found to be modest at best, although in settings where there has been little history of audit and feedback, the effects may be greater, at least initially. The primary purpose of the Data for Improvement and Clinical Excellence (DICE) Long-Term Care project is to assess the effects of an audit with feedback intervention delivered monthly over 13 months in four LTC facilities. The research questions we addressed are:</p> <p indent="1">1. What effects do feedback reports have on processes and outcomes over time?</p> <p indent="1">2. How do different provider groups in LTC and home care respond to feedback reports based on data targeted at improving quality of care?</p> <p>Methods/design</p> <p>The research team conducting this study comprises researchers and decision makers in continuing care in the province of Alberta, Canada. The intervention consists of monthly feedback reports in nine LTC units in four facilities in Edmonton, Alberta. Data for the feedback reports comes from the Resident Assessment Instrument Minimum Data Set (RAI) version 2.0, a standardized instrument mandated for use in LTC facilities throughout Alberta. Feedback reports consist of one page, front and back, presenting both graphic and textual information. Reports are delivered to all staff working in the four LTC facilities. The primary evaluation uses a controlled interrupted time series design both adjusted and unadjusted for covariates. The concurrent process evaluation uses observation and self-report to assess uptake of the feedback reports. Following the project phase described in this protocol, a similar intervention will be conducted in home care settings in Alberta. Depending on project findings, if they are judged useful by decision makers participating in this research team, we plan dissemination and spread of the feedback report approach throughout Alberta.</p

The association between clinical integration of care and transfer of veterans with acute coronary syndromes from primary care VHA hospitals

BACKGROUND: Few studies report on the effect of organizational factors facilitating transfer between primary and tertiary care hospitals either within an integrated health care system or outside it. In this paper, we report on the relationship between degree of clinical integration of cardiology services and transfer rates of acute coronary syndrome (ACS) patients from primary to tertiary hospitals within and outside the Veterans Health Administration (VHA) system. METHODS: Prospective cohort study. Transfer rates were obtained for all patients with ACS diagnoses admitted to 12 primary VHA hospitals between 1998 and 1999. Binary variables measuring clinical integration were constructed for each primary VHA hospital reflecting: presence of on-site VHA cardiologist; referral coordinator at the associated tertiary VHA hospital; and/or referral coordinator at the primary VHA hospital. We assessed the association between the integration variables and overall transfer from primary to tertiary hospitals, using random effects logistic regression, controlling for clustering at two levels and adjusting for patient characteristics. RESULTS: Three of twelve hospitals had a VHA cardiologist on site, six had a referral coordinator at the tertiary VHA hospital, and four had a referral coordinator at the primary hospital. Presence of a VHA staff cardiologist on site and a referral coordinator at the tertiary VHA hospital decreased the likelihood of any transfer (OR 0.45, 95% CI 0.27–0.77, and 0.46, p = 0.002, CI 0.27–0.78). Conversely, having a referral coordinator at the primary VHA hospital increased the likelihood of transfer (OR 6.28, CI 2.92–13.48). CONCLUSIONS: Elements of clinical integration are associated with transfer, an important process in the care of ACS patients. In promoting optimal patient care, clinical integration factors should be considered in addition to patient characteristics

12-Lipoxygenase governs the innate immune pathogenesis of islet inflammation and autoimmune diabetes

Macrophages and related myeloid cells are innate immune cells that participate in the early islet inflammation of type 1 diabetes (T1D). The enzyme 12-lipoxygenase (12-LOX) catalyzes the formation of proinflammatory eicosanoids, but its role and mechanisms in myeloid cells in the pathogenesis of islet inflammation have not been elucidated. Leveraging a model of islet inflammation in zebrafish, we show here that macrophages contribute significantly to the loss of β cells and the subsequent development of hyperglycemia. The depletion or inhibition of 12-LOX in this model resulted in reduced macrophage infiltration into islets and the preservation of β cell mass. In NOD mice, the deletion of the gene encoding 12-LOX in the myeloid lineage resulted in reduced insulitis with reductions in proinflammatory macrophages, a suppressed T cell response, preserved β cell mass, and almost complete protection from the development of T1D. 12-LOX depletion caused a defect in myeloid cell migration, a function required for immune surveillance and tissue injury responses. This effect on migration resulted from the loss of the chemokine receptor CXCR3. Transgenic expression of the gene encoding CXCR3 rescued the migratory defect in zebrafish 12-LOX morphants. Taken together, our results reveal a formative role for innate immune cells in the early pathogenesis of T1D and identify 12-LOX as an enzyme required to promote their prodiabetogenic phenotype in the context of autoimmunity