Inferring Species Trees Directly from Biallelic Genetic Markers: Bypassing Gene Trees in a Full Coalescent Analysis

The multi-species coalescent provides an elegant theoretical framework for estimating species trees and species demographics from genetic markers. Practical applications of the multi-species coalescent model are, however, limited by the need to integrate or sample over all gene trees possible for each genetic marker. Here we describe a polynomial-time algorithm that computes the likelihood of a species tree directly from the markers under a finite-sites model of mutation, effectively integrating over all possible gene trees. The method applies to independent (unlinked) biallelic markers such as well-spaced single nucleotide polymorphisms (SNPs), and we have implemented it in SNAPP, a Markov chain Monte-Carlo sampler for inferring species trees, divergence dates, and population sizes. We report results from simulation experiments and from an analysis of 1997 amplified fragment length polymorphism (AFLP) loci in 69 individuals sampled from six species of {\em Ourisia} (New Zealand native foxglove)

Enhancing accuracy and precision of transparent synthetic soil modelling

Over recent years non-intrusive modelling techniques have been developed to investigate soil-structure interaction problems of increasingly complex geometry. This paper concerns the development of a small-scale, 1 g, modelling technique using a transparent analogue for soil with particle image velocimetry for internal displacement measurement. Larger model geometry achieved in this research using fine-grained transparent synthetic soils has led to an increased need for rigorous photogrammetric correction techniques. A correction framework, based upon a modified version of the pinhole camera model, is presented that corrects for lens and camera movement induced errors as well as scaling from image space to object space. An additional statistical approach is also developed to enhance the system precision, by minimising the impact of increased non-coplanarity between the photogrammetry control plane and the target plane. The enhanced data correction and statistical precision is demonstrated using a case study examining the failure mechanism around a double helical screw pile installed in transparent synthetic soil representative of a soft clay

Localisation of RNAs into the germ plasm of vitellogenic xenopus oocytes

We have studied the localisation of mRNAs in full-grown Xenopus laevis oocytes by injecting fluorescent RNAs, followed by confocal microscopy of the oocyte cortex. Concentrating on RNA encoding the Xenopus Nanos homologue, nanos1 (formerly Xcat2), we find that it consistently localised into aggregated germ plasm ribonucleoprotein (RNP) particles, independently of cytoskeletal integrity. This implies that a diffusion/entrapment-mediated mechanism is active, as previously reported for previtellogenic oocytes. Sometimes this was accompanied by localisation into scattered particles of the “late”, Vg1/VegT pathway; occasionally only late pathway localisation was seen. The Xpat RNA behaved in an identical fashion and for neither RNA was the localisation changed by any culture conditions tested. The identity of the labelled RNP aggregates as definitive germ plasm was confirmed by their inclusion of abundant mitochondria and co-localisation with the germ plasm protein Hermes. Further, the nanos1/Hermes RNP particles are interspersed with those containing the germ plasm protein Xpat. These aggregates may be followed into the germ plasm of unfertilized eggs, but with a notable reduction in its quantity, both in terms of injected molecules and endogenous structures. Our results conflict with previous reports that there is no RNA localisation in large oocytes, and that during mid-oogenesis even germ plasm RNAs localise exclusively by the late pathway. We find that in mid oogenesis nanos1 RNA also localises to germ plasm but also by the late pathway. Late pathway RNAs, Vg1 and VegT, also may localise into germ plasm. Our results support the view that mechanistically the two modes of localisation are extremely similar, and that in an injection experiment RNAs might utilise either pathway, the distinction in fates being very subtle and subject to variation. We discuss these results in relation to their biological significance and the results of others

Guidance and Ethical Considerations for Undertaking Transgender Health Research and Institutional Review Boards Adjudicating this Research

The purpose of this review is to create a set of provisional criteria for Institutional Review Boards (IRBs) to refer to when assessing the ethical orientation of transgender health research proposals. We began by searching for literature on this topic using databases and the reference lists of key articles, resulting in a preliminary set of criteria. We then collaborated to develop the following nine guidelines: (1) Whenever possible, research should be grounded, from inception to dissemination, in a meaningful collaboration with community stakeholders; (2) language and framing of transgender health research should be non-stigmatizing; (3) research should be disseminated back to the community; (4) the diversity of the transgender and gender diverse (TGGD) community should be accurately reflected and sensitively reflected; (5) informed consent must be meaningful, without coercion or undue influence; (6) the protection of participant confidentiality should be paramount; (7) alternative consent procedures should be considered for TGGD minors; (8) research should align with current professional standards that refute conversion, reorientation, or reparative therapy; and (9) IRBs should guard against the temptation to avoid, limit, or delay research on this subject

Analysis of a rapid load test on an instrumented bored pile in clay

Rapid load testing methods for piled foundations are generally easier and quicker to mobilise than classic static tests, and are less complex to analyse than dynamic load tests. A recently developed rapid load pile testing method known as the Statnamic test is seeing greater use in the UK for the assessment of piles. For foundation design, it is necessary to derive the equivalent static load-settlement curve from the rapid load test data by eliminating inertial and damping effects. Existing methods of test analysis generally provide good correlation with static tests for sands and gravels, but overpredict pile capacities by up to 50% for clays. In order to gain an insight into the behaviour of rapid load pile testing in clays, a full-scale pile instrumented with accelerometers, strain-gauged sister bars and a tip load cell was tested in a glacial lodgement till near Grimsby, UK. The soil around the pile was also instrumented with radially arrayed buried accelerometers. The test pile was subjected to rapid loading tests, the results of which were compared with constant rate of penetration and maintained load static tests on the same pile. Results from the field testing have been analysed using non-linear viscous parameters obtained from laboratory model and element tests to represent rate-dependent clay shear resistance in the post-yield phase of loading. Shaft frictions derived from the strain-gauged reinforcement in the pile have been compared with shear strains and stresses derived from accelerations in the surrounding soil to give an insight into the load transfer mechanisms for a rapidly loaded pile in clay.Permission is granted by ICE Publishing to print one copy for personal use. Any other use of these PDF files is subject to reprint fees.http://www.icevirtuallibrary.com/content/journal

The Middle Way: East Asian masters students’ perceptions of critical argumentation in U.K. universities.

The paper explores the learning experiences of East Asian masters students in dealing with Western academic norms of critical thinking in classroom debate and assignment writing. The research takes a cultural approach, and employs grounded theory and case study methodology, the aims being for students to explain their perceptions of their personal learning journeys. The data suggest that the majority of students interviewed rejected full academic acculturation into Western norms of argumentation. They instead opted for a ‘Middle Way’ that synergizes the traditional cultural academic values held by many East Asian students with those elements of Western academic norms that are perceived to be aligned with these. This is a relatively new area of research which represents a challenge for British lecturers and students

Speculation on the origins of accounting

A speculative historical or anthropological overview of the prehistory and early history of accounting from Cro-Magnon through the thirteenth century

Calculation of the properties of the rotational bands of 155,157^{155,157}Gd

We reexamine the long-standing problem of the microscopic derivation of a particle-core coupling model. We base our research on the Klein-Kerman approach, as amended by D\"onau and Frauendorf. We describe the formalism to calculate energy spectra and transition strengths in some detail. We apply our formalism to the rotational nuclei $^{155,157}$Gd, where recent experimental data requires an explanation. We find no clear evidence of a need for Coriolis attenuation.Comment: 27 pages, 13 uuencoded postscript figures. Uses epsf.st

Many Body Theory of Charge Transfer in Hyperthermal Atomic Scattering

We use the Newns-Anderson Hamiltonian to describe many-body electronic processes that occur when hyperthermal alkali atoms scatter off metallic surfaces. Following Brako and Newns, we expand the electronic many-body wavefunction in the number of particle-hole pairs (we keep terms up to and including a single particle-hole pair). We extend their earlier work by including level crossings, excited neutrals and negative ions. The full set of equations of motion are integrated numerically, without further approximations, to obtain the many-body amplitudes as a function of time. The velocity and work-function dependence of final state quantities such as the distribution of ion charges and excited atomic occupancies are compared with experiment. In particular, experiments that scatter alkali ions off clean Cu(001) surfaces in the energy range 5 to 1600 eV constrain the theory quantitatively. The neutralization probability of Na$^+$ ions shows a minimum at intermediate velocity in agreement with the theory. This behavior contrasts with that of K$^+$, which shows ... (7 figures, not included. Figure requests: [email protected])Comment: 43 pages, plain TeX, BUP-JBM-

Fluorofluorophores: Fluorescent Fluorous Chemical Tools Spanning the Visible Spectrum

“Fluoro” refers to both fluorescent and fluorinated compounds. Despite the shared prefix, there are very few fluorescent molecules that are soluble in perfluorinated solvents. This paucity is surprising, given that optical microscopy is a ubiquitous technique throughout the physical sciences and the orthogonality of fluorous materials is a commonly exploited strategy in synthetic chemistry, materials science, and chemical biology. We have addressed this shortage by synthesizing a panel of “fluorofluorophores,” fluorescent molecules containing high weight percent fluorine with optical properties spanning the visible spectrum. We demonstrate the utility of these fluorofluorophores by preparing fluorescent perfluorocarbon nanoemulsions.National Science Foundation (U.S.) (ECCS-0939514