A Target Restricted Assembly Method (TRAM) for Phylogenomics

While next generation sequencing technology can produce sequences covering the entire genome, assembly and annotation are still prohibitive steps for many phylogenomics applications. Here we describe a method of Target Restricted Assembly (TRAM) of a single lane of Illumina sequences for genes of relevance to phylogeny reconstruction, i.e. single copy protein-coding genes. This method has the potential to produce a data set of hundreds of genes using only one Illumina lane per taxon

Scotin, a novel p53-inducible proapoptotic protein located in the ER and the nuclear membrane

p53 is a transcription factor that induces growth arrest or apoptosis in response to cellular stress. To identify new p53-inducible proapoptotic genes, we compared, by differential display, the expression of genes in spleen or thymus of normal and p53 nullizygote mice after γ-irradiation of whole animals. We report the identification and characterization of human and mouse Scotin homologues, a novel gene directly transactivated by p53. The Scotin protein is localized to the ER and the nuclear membrane. Scotin can induce apoptosis in a caspase-dependent manner. Inhibition of endogenous Scotin expression increases resistance to p53-dependent apoptosis induced by DNA damage, suggesting that Scotin plays a role in p53-dependent apoptosis. The discovery of Scotin brings to light a role of the ER in p53-dependent apoptosis

Mott g-Ratios in Rbx(NH3)1-x and Oxidation state of Rubidium Compounds from XAS

The x-ray absorption spectra (XAS) of Rb metal, Rh,( JH,J, ,, 2H-NbSe2Rb111x and RbBr near the Rb K-edge have been used to ascertain that the oxidation state V of rubidium dissolved in ammonia and intt:rcalated in the layer compound is in the range 0 \u3c V \u3c I. Theobservededge shifts with temperature for semimctals are explainedin terms of the population of band states, and the ratio of the density states near the mobility edge over that calculated for a free electron model, i.e. the Mott ratio g, is ascertained using a semiempirical relation developed for the x-ray absorbance from Is levels to empty states ncar the mobility edge

Estimation of Seismic Compression in Dry Soils Using the CPT

A popular method to evaluate earthquake induced settlements in dry sands is the approach proposed by Pradel (1998) which was based on standard penetration test (SPT) results and is only applicable to clean sands. A simple modification of the Pradel (1998) method is proposed based on cone penetration test (CPT) results and is extended to cover a wide range of unsaturated soils. A key parameter in the method by Pradel (1998) is the small strain shear modulus, Go, which can be estimated from the CPT or measured using the seismic CPT. The CPT can provide a continuous evaluation of seismic compression that allows the expeditious analysis of complicated soil profiles and a framework for sensitivity analyses. Soil parameters, such as soil type, fines content, and equivalent SPT blow count interpolated from CPTs, were compared with adjacent borings and related laboratory test results from a ground improvement site. Both vibro-stone columns and compaction grouting were adopted to mitigate the site seismic settlement. The proposed simple modification of the Pradel method provided a valuable tool to evaluate the effectiveness of ground improvement work

Are osseous artefacts a window to perishable material culture? Implications of an unusually complex bone tool from the Late Pleistocene of East Timor

We report the discovery of an unusually complex and regionally unique bone artefact in a Late Pleistocene archaeological assemblage (c. 35 ka [thousands of years ago]) from the site of Matja Kuru 2 on the island of Timor, in Wallacea. The artefact is interpreted as the broken butt of a formerly hafted projectile point, and it preserves evidence of a complex hafting mechanism including insertion into a shaped or split shaft, a complex pattern of binding including lateral stabilization of the cordage within a bilateral series of notches, and the application of mastic at several stages in the hafting process. The artefact provides the earliest direct evidence for the use of this combination of hafting technologies in the wider region of Southeast Asia, Wallacea, Melanesia and Australasia, and is morphologically unparallelled in deposits of any age. By contrast, it bears a close morphological resemblance to certain bone artefacts from the Middle Stone Age of Africa and South Asia. Examination of ethnographic projectile technology from the region of Melanesia and Australasia shows that all of the technological elements observed in the Matja Kuru 2 artefact were in use historically in the region, including the unusual feature of bilateral notching to stabilize a hafted point. This artefact challenges the notion that complex bone-working and hafting technologies were a relatively late innovation in this part of the world. Moreover, its regional uniqueness encourages us to abandon the perception of bone artefacts as a discrete class of material culture, and to adopt a new interpretative framework in which they are treated as manifestations of a more general class of artefacts that more typically were produced on perishable raw materials including wood

Transport theory yields renormalization group equations

We show that dissipative transport and renormalization can be described in a single theoretical framework. The appropriate mathematical tool is the Nakajima-Zwanzig projection technique. We illustrate our result in the case of interacting quantum gases, where we use the Nakajima-Zwanzig approach to investigate the renormalization group flow of the effective two-body interaction.Comment: 11 pages REVTeX, twocolumn, no figures; revised version with additional examples, to appear in Phys. Rev.

A possible mechanism of ultrafast amorphization in phase-change memory alloys: an ion slingshot from the crystalline to amorphous position

We propose that the driving force of an ultrafast crystalline-to-amorphous transition in phase-change memory alloys are strained bonds existing in the (metastable) crystalline phase. For the prototypical example of GST, we demonstrate that upon breaking of long Ge-Te bond by photoexcitation Ge ion shot from an octahedral crystalline to a tetrahedral amorphous position by the uncompensated force of strained short bonds. Subsequent lattice relaxation stabilizes the tetrahedral surroundings of the Ge atoms and ensures the long-term stability of the optically induced phase.Comment: 6 pages, 3 figure

Could health information systems enhance the quality of Aboriginal health promotion? A retrospective audit of Aboriginal health programs in the Northern Territory of Australia.

BACKGROUND:In Australia, health services are seeking innovative ways to utilize data stored in health information systems to report on, and improve, health care quality and health system performance for Aboriginal Australians. However, there is little research about the use of health information systems in the context of Aboriginal health promotion. In 2008, the Northern Territory's publicly funded healthcare system introduced the quality improvement program planning system (QIPPS) as the centralized online system for recording information about health promotion programs. The purpose of this study was to explore the potential for utilizing data stored in QIPPS to report on quality of Aboriginal health promotion, using chronic disease prevention programs as exemplars. We identify the potential benefits and limitations of health information systems for enhancing Aboriginal health promotion. METHODS:A retrospective audit was undertaken on a sample of health promotion projects delivered between 2013 and 2016. A validated, paper-based audit tool was used to extract information stored in the QIPPS online system and report on Aboriginal health promotion quality. Simple frequency counts were calculated for dichotomous and categorical items. Text was extracted and thematically analyzed to describe community participation processes and strategies used in Aboriginal health promotion. RESULTS:39 Aboriginal health promotion projects were included in the analysis. 34/39 projects recorded information pertaining to the health promotion planning phases, such as statements of project goals, 'needs assessment' findings, and processes for consulting Aboriginal people in the community. Evaluation findings were reported in approximately one third of projects and mostly limited to a recording of numbers of participants. For almost half of the projects analyzed, community participation strategies were not recorded. CONCLUSION:This is the first Australian study to shed light on the feasibility of utilizing data stored in a purposefully designed health promotion information system. Data availability and quality were limiting factors for reporting on Aboriginal health promotion quality. Based on our learnings of QIPPS, strategies to improve the quality and accuracy of data entry together with the use of quality improvement approaches are needed to reap the potential benefits of future health promotion information systems

Comparing proxy rated quality of life of people living with dementia in care homes

Background: Improving quality of life (QOL) for people with dementia is a priority. In care homes, we often rely on proxy ratings from staff and family but we do not know if, or how, they differ in care homes. Methods: We compared 1056 pairs of staff and family DEMQOL-Proxy ratings from 86 care homes across England. We explored factors associated with ratings quantitatively using multilevel modelling and, qualitatively, through thematic analysis of 12 staff and 12 relative interviews. Results: Staff and family ratings were weakly correlated (ρs = 0.35). Median staff scores were higher than family's (104 v. 101; p < 0.001). Family were more likely than staff to rate resident QOL as ‘Poor’ (χ2 = 55.91, p < 0.001). Staff and family rated QOL higher when residents had fewer neuropsychiatric symptoms and severe dementia. Staff rated QOL higher in homes with lower staff:resident ratios and when staff were native English speakers. Family rated QOL higher when the resident had spent longer living in the care home and was a native English. Spouses rated residents’ QOL higher than other relatives. Qualitative results suggest differences arise because staff felt good care provided high QOL but families compared the present to the past. Family judgements centre on loss and are complicated by decisions about care home placement and their understandings of dementia. Conclusion: Proxy reports differ systematically between staff and family. Reports are influenced by the rater:staff and family may conceptualise QOL differently