Speech perception in MRI scanner noise by persons with aphasia

Purpose. To examine reductions in performance on auditory tasks by aphasic and neurologically-intact individuals as a result of concomitant MRI scanner noise. Methods. Four tasks together forming a continuum of linguistic complexity were developed. They included complex-tone pitch discrimination, same/different discrimination of minimal pair syllables, lexical decision, and sentence plausibility. Each task was performed by persons with aphasia (PWA) and by controls. The stimuli were presented in silence and also in the noise recorded from within the bore of a 3T MRI scanner at three signal-to-noise ratios (S/Ns). Results. Across the four tasks, the PWA scored lower than the controls and performance fell as a function of decreased S/N. However, the rate at which performance fell was not different across the two listener groups in any task. Conclusions. Depending upon the relative levels of the signals and noise, the intense noise accompanying MRI scanning has the potential to severely disrupt performance. However, PWA are no more susceptible to the disruptive influence of this noise than are unimpaired individuals usually employed as controls. Thus, fMRI data from aphasic and control individuals may be interpreted without complications associated with large interactions between scanner noise and performance reduction

Origins of Hidden Sector Dark Matter I: Cosmology

We present a systematic cosmological study of a universe in which the visible sector is coupled, albeit very weakly, to a hidden sector comprised of its own set of particles and interactions. Assuming that dark matter (DM) resides in the hidden sector and is charged under a stabilizing symmetry shared by both sectors, we determine all possible origins of weak-scale DM allowed within this broad framework. We show that DM can arise only through a handful of mechanisms, lending particular focus to Freeze-Out and Decay and Freeze-In, as well as their variations involving late time re-annihilations of DM and DM particle anti-particle asymmetries. Much like standard Freeze-Out, where the abundance of DM depends only on the annihilation cross-section of the DM particle, these mechanisms depend only on a very small subset of physical parameters, many of which may be measured directly at the LHC. In particular, we show that each DM production mechanism is associated with a distinctive window in lifetimes and cross-sections for particles which may be produced in the near future. We evaluate prospects for employing the LHC to definitively reconstruct the origin of DM in a companion paper.Comment: 32 pages, 19 figures; v2: references added, published versio

Porosities of building limestones: using the solid density to assess data quality

A good knowledge of the volume-fraction porosity is essential in any technical work on porous materials. In construction materials the porosity is commonly measured by the Archimedes buoyancy method, from which the bulk density of the test specimen is also obtained. The porosity and the bulk density together fix the solid density of the specimen, as only two of the three quantities are independent. The solid density, although rarely discussed, is determined by the mineralogy of the specimen, and therefore can provide a valuable check on the accuracy of porosity and bulk density measurements. Our analysis of published data on calcitic limestones shows that the solid density is generally close to the ideal crystallographic density of calcite. Small deviations can often be traced to variations in mineral composition. However some published porosity–density data are inconsistent with the known mineralogy. Deviations which cannot be ascribed to composition may be assumed to arise from measurement errors. We show the value of using the solid density as a quality check on the measured porosity. We recommend that the solid density should always be calculated for this purpose when the Archimedes method is used. This check can be useful also when porosities are measured by helium pycnometry or by mercury intrusion porosimetry

Systems analysis of transcription factor activities in environments with stable and dynamic oxygen concentrations.

Understanding gene regulation requires knowledge of changes in transcription factor (TF) activities. Simultaneous direct measurement of numerous TF activities is currently impossible. Nevertheless, statistical approaches to infer TF activities have yielded non-trivial and verifiable predictions for individual TFs. Here, global statistical modelling identifies changes in TF activities from transcript profiles of Escherichia coli growing in stable (fixed oxygen availabilities) and dynamic (changing oxygen availability) environments. A core oxygen-responsive TF network, supplemented by additional TFs acting under specific conditions, was identified. The activities of the cytoplasmic oxygen-responsive TF, FNR, and the membrane-bound terminal oxidases implied that, even on the scale of the bacterial cell, spatial effects significantly influence oxygen-sensing. Several transcripts exhibited asymmetrical patterns of abundance in aerobic to anaerobic and anaerobic to aerobic transitions. One of these transcripts, ndh, encodes a major component of the aerobic respiratory chain and is regulated by oxygen-responsive TFs ArcA and FNR. Kinetic modelling indicated that ArcA and FNR behaviour could not explain the ndh transcript profile, leading to the identification of another TF, PdhR, as the source of the asymmetry. Thus, this approach illustrates how systematic examination of regulatory responses in stable and dynamic environments yields new mechanistic insights into adaptive processes

Improving Phrap-Based Assembly of the Rat Using “Reliable” Overlaps

The assembly methods used for whole-genome shotgun (WGS) data have a major impact on the quality of resulting draft genomes. We present a novel algorithm to generate a set of “reliable” overlaps based on identifying repeat k-mers. To demonstrate the benefits of using reliable overlaps, we have created a version of the Phrap assembly program that uses only overlaps from a specific list. We call this version PhrapUMD. Integrating PhrapUMD and our “reliable-overlap” algorithm with the Baylor College of Medicine assembler, Atlas, we assemble the BACs from the Rattus norvegicus genome project. Starting with the same data as the Nov. 2002 Atlas assembly, we compare our results and the Atlas assembly to the 4.3 Mb of rat sequence in the 21 BACs that have been finished. Our version of the draft assembly of the 21 BACs increases the coverage of finished sequence from 93.4% to 96.3%, while simultaneously reducing the base error rate from 4.5 to 1.1 errors per 10,000 bases. There are a number of ways of assessing the relative merits of assemblies when the finished sequence is available. If one views the overall quality of an assembly as proportional to the inverse of the product of the error rate and sequence missed, then the assembly presented here is seven times better. The UMD Overlapper with options for reliable overlaps is available from the authors at http://www.genome.umd.edu. We also provide the changes to the Phrap source code enabling it to use only the reliable overlaps

mmView: a web-based viewer of the mmCIF format

<p>Abstract</p> <p>Background</p> <p>Structural biomolecular data are commonly stored in the PDB format. The PDB format is widely supported by software vendors because of its simplicity and readability. However, the PDB format cannot fully address many informatics challenges related to the growing amount of structural data. To overcome the limitations of the PDB format, a new textual format mmCIF was released in June 1997 in its version 1.0. mmCIF provides extra information which has the advantage of being in a computer readable form. However, this advantage becomes a disadvantage if a human must read and understand the stored data. While software tools exist to help to prepare mmCIF files, the number of available systems simplifying the comprehension and interpretation of the mmCIF files is limited.</p> <p>Findings</p> <p>In this paper we present mmView - a cross-platform web-based application that allows to explore comfortably the structural data of biomacromolecules stored in the mmCIF format. The mmCIF categories can be easily browsed in a tree-like structure, and the corresponding data are presented in a well arranged tabular form. The application also allows to display and investigate biomolecular structures via an integrated Java application Jmol.</p> <p>Conclusions</p> <p>The mmView software system is primarily intended for educational purposes, but it can also serve as a useful research tool. The mmView application is offered in two flavors: as an open-source stand-alone application (available from <url>http://sourceforge.net/projects/mmview</url>) that can be installed on the user's computer, and as a publicly available web server.</p

A Brownian particle in a microscopic periodic potential

We study a model for a massive test particle in a microscopic periodic potential and interacting with a reservoir of light particles. In the regime considered, the fluctuations in the test particle's momentum resulting from collisions typically outweigh the shifts in momentum generated by the periodic force, and so the force is effectively a perturbative contribution. The mathematical starting point is an idealized reduced dynamics for the test particle given by a linear Boltzmann equation. In the limit that the mass ratio of a single reservoir particle to the test particle tends to zero, we show that there is convergence to the Ornstein-Uhlenbeck process under the standard normalizations for the test particle variables. Our analysis is primarily directed towards bounding the perturbative effect of the periodic potential on the particle's momentum.Comment: 60 pages. We reorganized the article and made a few simplifications of the conten

A risk prediction model for the assessment and triage of women with hypertensive disorders of pregnancy in low-resourced settings: the miniPIERS (Pre-eclampsia Integrated Estimate of RiSk) multi-country prospective cohort study.

BACKGROUND: Pre-eclampsia/eclampsia are leading causes of maternal mortality and morbidity, particularly in low- and middle- income countries (LMICs). We developed the miniPIERS risk prediction model to provide a simple, evidence-based tool to identify pregnant women in LMICs at increased risk of death or major hypertensive-related complications. METHODS AND FINDINGS: From 1 July 2008 to 31 March 2012, in five LMICs, data were collected prospectively on 2,081 women with any hypertensive disorder of pregnancy admitted to a participating centre. Candidate predictors collected within 24 hours of admission were entered into a step-wise backward elimination logistic regression model to predict a composite adverse maternal outcome within 48 hours of admission. Model internal validation was accomplished by bootstrapping and external validation was completed using data from 1,300 women in the Pre-eclampsia Integrated Estimate of RiSk (fullPIERS) dataset. Predictive performance was assessed for calibration, discrimination, and stratification capacity. The final miniPIERS model included: parity (nulliparous versus multiparous); gestational age on admission; headache/visual disturbances; chest pain/dyspnoea; vaginal bleeding with abdominal pain; systolic blood pressure; and dipstick proteinuria. The miniPIERS model was well-calibrated and had an area under the receiver operating characteristic curve (AUC ROC) of 0.768 (95% CI 0.735-0.801) with an average optimism of 0.037. External validation AUC ROC was 0.713 (95% CI 0.658-0.768). A predicted probability ≥25% to define a positive test classified women with 85.5% accuracy. Limitations of this study include the composite outcome and the broad inclusion criteria of any hypertensive disorder of pregnancy. This broad approach was used to optimize model generalizability. CONCLUSIONS: The miniPIERS model shows reasonable ability to identify women at increased risk of adverse maternal outcomes associated with the hypertensive disorders of pregnancy. It could be used in LMICs to identify women who would benefit most from interventions such as magnesium sulphate, antihypertensives, or transportation to a higher level of care

‘Content to be sad’ or ‘runaway apprentice’? The psychological contract and career agency of young scientists in the entrepreneurial university

This article examines employee agency in psychological contracts by exploring how young scientists proactively shape their careers in response to unmet expectations induced by academic entrepreneurialism. It uses the lens of social exchange to examine their relationships with the professors engaged in two types of activities: collaborative research characterized by diffuse/reciprocal exchange, and commercial ventures, by restricted/negotiated exchange. These two categories show how career agency varies in orientation, form and behavioural outcome depending on the relational context within which their psychological contracts evolve. Those involved in collaborative research experienced a relational psychological contract and responded to unfulfilled career promises by ‘extended investment’ in their current jobs. They use ‘proxy agency’ by enlisting the support of their professors. However, some become ‘trapped’ in perennial temporary employment and are ‘content to be sad’. By contrast, those involved in research commercialization experienced a transactional contract and assert ‘personal agency’ by crafting their own entrepreneurial careers. They are ‘runaways’ who seek autonomy. The evidence is based on interviews with 24 doctoral/postdoctoral researchers and 16 professors from three leading UK universities. The study extends psychological contract theory by incorporating career agency and sheds new light on changing academic careers

Troubling "understanding mathematics-in-depth": Its role in the identity work of student-teachers in England

Copyright @ The Author(s) 2013. This article is published with open access at Springerlink.comThis article has been made available through the Brunel Open Access Publishing Fund.In this paper, we focus on an initiative in England devised to prepare non-mathematics graduates to train as secondary mathematics teachers through a 6-month Mathematics Enhancement Course (MEC) to boost their subject knowledge. The course documentation focuses on the need to develop “understanding mathematics in-depth” in students in order for them to become successful mathematics teachers. We take a poststructural approach, so we are not interested in asking what such an understanding is, about the value of this approach or about the effectiveness of the MECs in developing this understanding in their participants. Instead we explore what positions this discourse of “understanding mathematics in-depth” makes available to MEC students. We do this by looking in detail at the “identity work” of two students, analysing how they use and are used by this discourse to position themselves as future mathematics teachers. In doing so, we show how even benign-looking social practices such as “understanding mathematics in-depth” are implicated in practices of inclusion and exclusion. We show this through detailed readings of interviews with two participants, one of whom fits with the dominant discourses in the MEC and the other who, despite passing the MEC, experiences tensions between her national identity work and MEC discourses. We argue that it is vital to explore “identity work” within teacher education contexts to ensure that becoming a successful mathematics teacher is equally available to all.King’s College Londo