mbs: modifying Hudson's ms software to generate samples of DNA sequences with a biallelic site under selection

<p>Abstract</p> <p>Background</p> <p>The pattern of single nucleotide polymorphisms, or SNPs, contains a tremendous amount of information with respect to the mechanisms of the micro-evolutionary process of a species. The inference of the roles of these mechanisms, including natural selection, relies heavily on computer simulations. A coalescent simulation is extremely powerful in generating a large number of samples of DNA sequences from a population (species) when all mutations are neutral, and Hudson's <b>ms </b>software is frequently used for this purpose.</p> <p>However, it has been difficult to incorporate natural selection into the coalescent framework.</p> <p>Results</p> <p>We herein present a software application to generate samples of DNA sequences when there is a biallelic site targeted by selection. This software application, referred to as <b>mbs</b>, is developed by modifying Hudson's <b>ms</b>. The <b>mbs </b>software is so flexible that it can incorporate any arbitrary histories of population size changes and any mode of selection as long as selection is operating on a biallelic site.</p> <p>Conclusion</p> <p><b>mbs </b>provides opportunities to investigate the effect of any mode of selection on the pattern of SNPs under various demography.</p

A New Normal: Integrating Lived Experience Into Scientific Data Syntheses

status: publishe

Gender equality and girls education: Investigating frameworks, disjunctures and meanings of quality education

The article draws on qualitative educational research across a diversity of low-income countries to examine the gendered inequalities in education as complex, multi-faceted and situated rather than a series of barriers to be overcome through linear input–output processes focused on isolated dimensions of quality. It argues that frameworks for thinking about educational quality often result in analyses of gender inequalities that are fragmented and incomplete. However, by considering education quality more broadly as a terrain of quality it investigates questions of educational transitions, teacher supply and community participation, and develops understandings of how education is experienced by learners and teachers in their gendered lives and their teaching practices. By taking an approach based on theories of human development the article identifies dynamics of power underpinning gender inequalities in the literature and played out in diverse contexts and influenced by social, cultural and historical contexts. The review and discussion indicate that attaining gender equitable quality education requires recognition and understanding of the ways in which inequalities intersect and interrelate in order to seek out multi-faceted strategies that address not only different dimensions of girls’ and women’s lives, but understand gendered relationships and structurally entrenched inequalities between women and men, girls and boys

Clades and clans: a comparison study of two evolutionary models

The Yule-Harding-Kingman (YHK) model and the proportional to distinguishable arrangements (PDA) model are two binary tree generating models that are widely used in evolutionary biology. Understanding the distributions of clade sizes under these two models provides valuable insights into macro-evolutionary processes, and is important in hypothesis testing and Bayesian analyses in phylogenetics. Here we show that these distributions are log-convex, which implies that very large clades or very small clades are more likely to occur under these two models. Moreover, we prove that there exists a critical value $\kappa(n)$ for each $n\geqslant 4$ such that for a given clade with size $k$, the probability that this clade is contained in a random tree with $n$ leaves generated under the YHK model is higher than that under the PDA model if $1<k<\kappa(n)$, and lower if $\kappa(n)<k<n$. Finally, we extend our results to binary unrooted trees, and obtain similar results for the distributions of clan sizes.Comment: 21page

An enhanced static-list scheduling algorithm for temporal partitioning onto RPUs

This paper presents a novel algorithm for temporal partitioning of graphs representing a behavioral description. The algorithm is based on an extension of the traditional static-list scheduling that tailors it to resolve both scheduling and temporal partitioning. The nodes to be mapped into a partition are selected based on a statically computed cost model. The cost for each node integrates communication effects, the critical path length, and the possibility of the critical path to hide the delay of parallel nodes. In order to alleviate the runtime there is no dynamic update of the costs. A comparison of the algorithm to other schedulers and with close-to-optimum results obtained with a simulated annealing approach is shown. The presented algorithm has been implemented and the results show that it is robust, effective, and efficient, and when compared to other methods finds very good results in small amounts of CPU time

Imaging the Two Gaps of the High-TC Superconductor Pb-Bi2Sr2CuO6+x

The nature of the pseudogap state, observed above the superconducting transition temperature TC in many high temperature superconductors, is the center of much debate. Recently, this discussion has focused on the number of energy gaps in these materials. Some experiments indicate a single energy gap, implying that the pseudogap is a precursor state. Others indicate two, suggesting that it is a competing or coexisting phase. Here we report on temperature dependent scanning tunneling spectroscopy of Pb-Bi2Sr2CuO6+x. We have found a new, narrow, homogeneous gap that vanishes near TC, superimposed on the typically observed, inhomogeneous, broad gap, which is only weakly temperature dependent. These results not only support the two gap picture, but also explain previously troubling differences between scanning tunneling microscopy and other experimental measurements.Comment: 6 page

Inferring introduction routes of invasive species using approximate Bayesian computation on microsatellite data

Determining the routes of introduction provides not only information about the history of an invasion process, but also information about the origin and construction of the genetic composition of the invading population. It remains difficult, however, to infer introduction routes from molecular data because of a lack of appropriate methods. We evaluate here the use of an approximate Bayesian computation (ABC) method for estimating the probabilities of introduction routes of invasive populations based on microsatellite data. We considered the crucial case of a single source population from which two invasive populations originated either serially from a single introduction event or from two independent introduction events. Using simulated datasets, we found that the method gave correct inferences and was robust to many erroneous beliefs. The method was also more efficient than traditional methods based on raw values of statistics such as assignment likelihood or pairwise F(ST). We illustrate some of the features of our ABC method, using real microsatellite datasets obtained for invasive populations of the western corn rootworm, Diabrotica virgifera virgifera. Most computations were performed with the DIYABC program (http://www1.montpellier.inra.fr/CBGP/diyabc/)

Coherent electrical control of a single high-spin nucleus in silicon

Nuclear spins are highly coherent quantum objects. In large ensembles, their control and detection via magnetic resonance is widely exploited, for example, in chemistry, medicine, materials science and mining. Nuclear spins also featured in early proposals for solid-state quantum computers1 and demonstrations of quantum search2 and factoring3 algorithms. Scaling up such concepts requires controlling individual nuclei, which can be detected when coupled to an electron4–6. However, the need to address the nuclei via oscillating magnetic fields complicates their integration in multi-spin nanoscale devices, because the field cannot be localized or screened. Control via electric fields would resolve this problem, but previous methods7–9 relied on transducing electric signals into magnetic fields via the electron–nuclear hyperfine interaction, which severely affects nuclear coherence. Here we demonstrate the coherent quantum control of a single 123Sb (spin-7/2) nucleus using localized electric fields produced within a silicon nanoelectronic device. The method exploits an idea proposed in 196110 but not previously realized experimentally with a single nucleus. Our results are quantitatively supported by a microscopic theoretical model that reveals how the purely electrical modulation of the nuclear electric quadrupole interaction results in coherent nuclear spin transitions that are uniquely addressable owing to lattice strain. The spin dephasing time, 0.1 seconds, is orders of magnitude longer than those obtained by methods that require a coupled electron spin to achieve electrical driving. These results show that high-spin quadrupolar nuclei could be deployed as chaotic models, strain sensors and hybrid spin-mechanical quantum systems using all-electrical controls. Integrating electrically controllable nuclei with quantum dots11,12 could pave the way to scalable, nuclear- and electron-spin-based quantum computers in silicon that operate without the need for oscillating magnetic fields

Ultracold dense gas of deeply bound heteronuclear molecules

Recently, the quest for an ultracold and dense ensemble of polar molecules has attracted strong interest. Polar molecules have bright prospects for novel quantum gases with long-range and anisotropic interactions, for quantum information science, and for precision measurements. However, high-density clouds of ultracold polar molecules have so far not been produced. Here, we report a key step towards this goal. Starting from an ultracold dense gas of heteronuclear 40K-87Rb Feshbach molecules with typical binding energies of a few hundred kHz and a negligible dipole moment, we coherently transfer these molecules into a vibrational level of the ground-state molecular potential bound by >10 GHz. We thereby increase the binding energy and the expected dipole moment of the 40K-87Rb molecules by more than four orders of magnitude in a single transfer step. Starting with a single initial state prepared with Feshbach association, we achieve a transfer efficiency of 84%. While dipolar effects are not yet observable, the presented technique can be extended to access much more deeply bound vibrational levels and ultimately those exhibiting a significant dipole moment. The preparation of an ultracold quantum gas of polar molecules might therefore come within experimental reach.Comment: 5 pages, 5 figure

A nurse-led, preventive, psychological intervention to reduce PTSD symptom severity in critically ill patients: the POPPI feasibility study and cluster RCT

BACKGROUND: High numbers of patients experience severe acute stress in critical care units. Acute stress has been linked to post-critical care psychological morbidity, including post-traumatic stress disorder (PTSD). Previously, a preventive, complex psychological intervention [Psychological Outcomes following a nurse-led Preventative Psychological Intervention for critically ill patients (POPPI)] was developed by this research team, to be led by nurses, to reduce the development of PTSD symptom severity at 6 months. OBJECTIVES: The objectives were to (1) standardise and refine the POPPI intervention, and, if feasible, (2) evaluate it in a cluster randomised clinical trial (RCT). DESIGN: Two designs were used – (1) two feasibility studies to test the delivery and acceptability (to patients and staff) of the intervention, education package and support tools, and to test the trial procedures (i.e. recruitment and retention), and (2) a multicentre, parallel-group, cluster RCT with a baseline period and staggered roll-out of the intervention. SETTING: This study was set in NHS adult, general critical care units. PARTICIPANTS: The participants were adult patients who were > 48 hours in a critical care unit, receiving level 3 care and able to consent. INTERVENTIONS: The intervention comprised three elements – (1) creating a therapeutic environment in critical care, (2) three stress support sessions for patients identified as acutely stressed and (3) a relaxation and recovery programme for patients identified as acutely stressed. MAIN OUTCOMES MEASURES: Primary outcome – patient-reported symptom severity using the PTSD Symptom Scale – Self Report (PSS-SR) questionnaire (to measure clinical effectiveness) and incremental costs, quality-adjusted life-years (QALYs) and net monetary benefit at 6 months (to measure cost-effectiveness). Secondary outcomes – days alive and free from sedation to day 30; duration of critical care unit stay; PSS-SR score of > 18 points; depression, anxiety and health-related quality of life at 6 months; and lifetime cost-effectiveness. RESULTS: (1) A total of 127 participants were recruited to the intervention feasibility study from two sites and 86 were recruited to the RCT procedures feasibility study from another two sites. The education package, support tools and intervention were refined. (2) A total of 24 sites were randomised to the intervention or control arms. A total of 1458 participants were recruited. Twelve sites delivered the intervention during the intervention period: > 80% of patients received two or more stress support sessions and all 12 sites achieved the target of > 80% of clinical staff completing the POPPI online training. There was, however, variation in delivery across sites. There was little difference between baseline and intervention periods in the development of PTSD symptom severity (measured by mean PSS-SR score) at 6 months for surviving patients in either the intervention or the control group: treatment effect estimate −0.03, 95% confidence interval (CI) −2.58 to 2.52; p = 0.98. On average, the intervention decreased costs and slightly improved QALYs, leading to a positive incremental net benefit at 6 months (£835, 95% CI −£4322 to £5992), but with considerable statistical uncertainty surrounding these results. There were no significant differences between the groups in any of the secondary outcomes or in the prespecified subgroup analyses. LIMITATIONS: There was a risk of bias because different consent processes were used and as a result of the lack of blinding, which was mitigated as far as possible within the study design. The intervention started later than anticipated. Patients were not routinely monitored for delirium. CONCLUSIONS: Among level 3 patients who stayed > 48 hours in critical care, the delivery of a preventive, complex psychological intervention, led by nurses, did not reduce the development of PTSD symptom severity at 6 months, when compared with usual care. FUTURE WORK: Prior to development and evaluation of subsequent psychological interventions, there is much to learn from post hoc analyses of the cluster RCT rich quantitative and qualitative data. TRIAL REGISTRATION: This trial is registered as ISRCTN61088114 and ISRCTN53448131. FUNDING: This project was funded by the National Institute for Health Research (NIHR) Health Services and Delivery Research programme and will be published in full in Health Services and Delivery Research; Vol. 23, No. 30. See the NIHR Journals Library website for further project information