Using XML and XSLT for flexible elicitation of mental-health risk knowledge

Current tools for assessing risks associated with mental-health problems require assessors to make high-level judgements based on clinical experience. This paper describes how new technologies can enhance qualitative research methods to identify lower-level cues underlying these judgements, which can be collected by people without a specialist mental-health background. Methods and evolving results: Content analysis of interviews with 46 multidisciplinary mental-health experts exposed the cues and their interrelationships, which were represented by a mind map using software that stores maps as XML. All 46 mind maps were integrated into a single XML knowledge structure and analysed by a Lisp program to generate quantitative information about the numbers of experts associated with each part of it. The knowledge was refined by the experts, using software developed in Flash to record their collective views within the XML itself. These views specified how the XML should be transformed by XSLT, a technology for rendering XML, which resulted in a validated hierarchical knowledge structure associating patient cues with risks. Conclusions: Changing knowledge elicitation requirements were accommodated by flexible transformations of XML data using XSLT, which also facilitated generation of multiple data-gathering tools suiting different assessment circumstances and levels of mental-health knowledge

On-microscope staging of live cells reveals changes in the dynamics of transcriptional bursting during differentiation

Determining the mechanisms by which genes are switched on and off during development is a key aim of current biomedical research. Gene transcription has been widely observed to occur in a discontinuous fashion, with short bursts of activity interspersed with periods of inactivity. It is currently not known if or how this dynamic behaviour changes as mammalian cells differentiate. To investigate this, using an on-microscope analysis, we monitored mouse α-globin transcription in live cells throughout erythropoiesis. We find that changes in the overall levels of α-globin transcription are most closely associated with changes in the fraction of time a gene spends in the active transcriptional state. We identify differences in the patterns of transcriptional bursting throughout differentiation, with maximal transcriptional activity occurring in the mid-phase of differentiation. Early in differentiation, we observe increased fluctuation in transcriptional activity whereas at the peak of gene expression, in early erythroblasts, transcription is relatively stable. Later during differentiation as α-globin expression declines, we again observe more variability in transcription within individual cells. We propose that the observed changes in transcriptional behaviour may reflect changes in the stability of active transcriptional compartments as gene expression is regulated during differentiation

Climate change mitigation and adaptation in the land use sector: from complementarity to synergy

Currently, mitigation and adaptation measures are handled separately, due to differences in priorities for the measures and segregated planning and implementation policies at international and national levels. There is a growing argument that synergistic approaches to adaptation and mitigation could bring substantial benefits at multiple scales in the land use sector. Nonetheless, efforts to implement synergies between adaptation and mitigation measures are rare due to the weak conceptual framing of the approach and constraining policy issues. In this paper, we explore the attributes of synergy and the necessary enabling conditions and discuss, as an example, experience with the Ngitili system in Tanzania that serves both adaptation and mitigation functions. An in-depth look into the current practices suggests that more emphasis is laid on complementarity—i.e., mitigation projects providing adaptation co-benefits and vice versa rather than on synergy. Unlike complementarity, synergy should emphasize functionally sustainable landscape systems in which adaptation and mitigation are optimized as part of multiple functions. We argue that the current practice of seeking co-benefits (complementarity) is a necessary but insufficient step toward addressing synergy. Moving forward from complementarity will require a paradigm shift from current compartmentalization between mitigation and adaptation to systems thinking at landscape scale. However, enabling policy, institutional, and investment conditions need to be developed at global, national, and local levels to achieve synergistic goals

Nanoscale potassium niobate crystal structure and phase transition

Nanoscale potassium niobate (KNbO3) powders of orthorhombic structure were synthesized using the sol-gel method. The heat-treatment temperature of the gels had a pronounced effect on KNbO3 particle size and morphology. Field emission scanning electron microscopy and transmission electron microscopy were used to determine particle size and morphology. The average KNbO3 grain size was estimated to be less than 100 nm, and transmission electron microscopy images indicated that KNbO3 particles had a brick-like morphology. Synchrotron X-ray diffraction was used to identify the room-temperature structures using Rietveld refinement. The ferroelectric orthorhombic phase was retained even for particles smaller than 50 nm. The orthorhombic to tetragonal and tetragonal to cubic phase transitions of nanocrystalline KNbO3 were investigated using temperature-dependent powder X-ray diffraction. Differential scanning calorimetry was used to examine the temperature dependence of KNbO3 phase transition. The Curie temperature and phase transition were independent of particle size, and Rietveld analyses showed increasing distortions with decreasing particle size

Vulnerability assessment and feasibility analysis of seismic strengthening of school buildings

The majority of structures in seismic-prone areas worldwide are structures that have been designed either without seismic design considerations, or using codes of practice that are seriously inadequate in the light of current seismic design principles. In Cyprus, after a series of earthquakes that occurred between 1995 and 1999, it was decided to carry out an unprecedented internationally seismic retrofitting of all school buildings, taking into account the sensitivity of the society towards these structures. In this paper representative school buildings are analysed in both their pristine condition and after applying retrofitting schemes typical of those implemented in the aforementioned large-scale strengthening programme. Non-linear analysis is conducted on calibrated analytical models of the selected buildings and fragility curves are derived for typical reinforced concrete and unreinforced masonry structures. These curves are then used to carry out a feasibility study, including both benefit-cost and life-cycle analysis, and evaluate the effectiveness of the strengthening programme

The reliability of evidence review methodology in environmental science and conservation

Given the proliferation of primary research articles, the importance of reliable environmental evidence reviews for informing policy and management decisions is increasing. Although conducting reviews is an efficient method of synthesising the fragmented primary evidence base, reviews that are of poor methodological reliability have the potential to misinform by not accurately reflecting the available evidence base. To assess the current value of evidence reviews for decision-making we appraised a systematic sample of articles published in early 2015 (N = 92) using the Collaboration for Environmental Evidence Synthesis Assessment Tool (CEESAT). CEESAT assesses the methodology of policy-relevant evidence reviews according to elements important for objectivity, transparency and comprehensiveness. Overall, reviews performed poorly with a median score of 2.5/39 and a modal score of zero (range 0–30, mean 5.8), and low scores were ubiquitous across subject areas. In general, reviews that applied meta-analytical techniques achieved higher scores than narrative syntheses (median 18.3 and 2.0 respectively), as a result of the latter consistently failing to adequately report methodology or how conclusions were drawn. However, some narrative syntheses achieved high scores, illustrating that the reliability of reviews should be assessed on a case-by-case basis. Given the potential importance of reviews for informing management and policy, as well as research, it is vital that overall methodological reliability is improved. Although the increasing number of systematic reviews and meta-analyses highlight that some progress is being made, our findings suggest little or no improvement in the last decade. To motivate progress, we recommend that an annual assessment of the methodological reliability of evidence reviews be conducted. To better serve the environmental policy and management communities we identify a requirement for independent critical appraisal of review methodology thus enabling decision-makers to select reviews that are most likely to accurately reflect the evidence base

Evaluating Knowledge to Support Climate Action: A Framework for Sustained Assessment. Report of an Independent Advisory Committee on Applied Climate Assessment

As states, cities, tribes, and private interests cope with climate damages and seek to increase preparedness and resilience, they will need to navigate myriad choices and options available to them. Making these choices in ways that identify pathways for climate action that support their development objectives will require constructive public dialogue, community participation, and flexible and ongoing access to science- and experience-based knowledge. In 2016, a Federal Advisory Committee (FAC) was convened to recommend how to conduct a sustained National Climate Assessment (NCA) to increase the relevance and usability of assessments for informing action. The FAC was disbanded in 2017, but members and additional experts reconvened to complete the report that is presented here. A key recommendation is establishing a new nonfederal "climate assessment consortium" to increase the role of state/local/tribal government and civil society in assessments. The expanded process would 1) focus on applied problems faced by practitioners, 2) organize sustained partnerships for collaborative learning across similar projects and case studies to identify effective tested practices, and 3) assess and improve knowledge-based methods for project implementation. Specific recommendations include evaluating climate models and data using user-defined metrics; improving benefit-cost assessment and supporting decision-making under uncertainty; and accelerating application of tools and methods such as citizen science, artificial intelligence, indicators, and geospatial analysis. The recommendations are the result of broad consultation and present an ambitious agenda for federal agencies, state/local/tribal jurisdictions, universities and the research sector, professional associations, nongovernmental and community-based organizations, and private-sector firms.New York State Energy Research and Development Authority [123416]; Columbia University's Earth Institute; American Meteorological Society; Kresge Foundation6 month embargo; published online: 21 May 2019This item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]

Identifying Determinants of Cullin Binding Specificity Among the Three Functionally Different Drosophila melanogaster Roc Proteins via Domain Swapping

BACKGROUND: Cullin-dependent E3 ubiquitin ligases (CDL) are key regulators of protein destruction that participate in a wide range of cell biological processes. The Roc subunit of CDL contains an evolutionarily conserved RING domain that binds ubiquitin charged E2 and is essential for ubiquitylation. Drosophila melanogaster contains three highly related Roc proteins: Roc1a and Roc2, which are conserved in vertebrates, and Roc1b, which is specific to Drosophila. Our previous genetic data analyzing Roc1a and Roc1b mutants suggested that Roc proteins are functionally distinct, but the molecular basis for this distinction is not known. METHODOLOGY/PRINCIPAL FINDINGS: Using co-immunoprecipitation studies we show that Drosophila Roc proteins bind specific Cullins: Roc1a binds Cul1-4, Roc1b binds Cul3, and Roc2 binds Cul5. Through domain swapping experiments, we demonstrate that Cullin binding specificity is strongly influenced by the Roc NH(2)-terminal domain, which forms an inter-molecular beta sheet with the Cullin. Substitution of the Roc1a RING domain with that of Roc1b results in a protein with similar Cullin binding properties to Roc1a that is active as an E3 ligase but cannot complement Roc1a mutant lethality, indicating that the identity of the RING domain can be an important determinant of CDL function. In contrast, the converse chimeric protein with a substitution of the Roc1b RING domain with that of Roc1a can rescue the male sterility of Roc1b mutants, but only when expressed from the endogenous Roc1b promoter. We also identified mutations of Roc2 and Cul5 and show that they cause no overt developmental phenotype, consistent with our finding that Roc2 and Cul5 proteins are exclusive binding partners, which others have observed in human cells as well. CONCLUSIONS: The Drosophila Roc proteins are highly similar, but have diverged during evolution to bind a distinct set of Cullins and to utilize RING domains that have overlapping, but not identical, function in vivo

ATRX dysfunction Induces replication defects in primary mouse cells

The chromatin remodeling protein ATRX, which targets tandem repetitive DNA, has been shown to be required for expression of the alpha globin genes, for proliferation of a variety of cellular progenitors, for chromosome congression and for the maintenance of telomeres. Mutations in ATRX have recently been identified in tumours which maintain their telomeres by a telomerase independent pathway involving homologous recombination thought to be triggered by DNA damage. It is as yet unknown whether there is a central underlying mechanism associated with ATRX dysfunction which can explain the numerous cellular phenomena observed. There is, however, growing evidence for its role in the replication of various repetitive DNA templates which are thought to have a propensity to form secondary structures. Using a mouse knockout model we demonstrate that ATRX plays a direct role in facilitating DNA replication. Ablation of ATRX alone, although leading to a DNA damage response at telomeres, is not sufficient to trigger the alternative lengthening of telomere pathway in mouse embryonic stem cells