A straightforward multiallelic significance test for the Hardy-Weinberg equilibrium law

Much forensic inference based upon DNA evidence is made assuming Hardy-Weinberg Equilibrium (HWE) for the genetic loci being used. Several statistical tests to detect and measure deviation from HWE have been devised, and their limitations become more obvious when testing for deviation within multiallelic DNA loci. The most popular methods-Chi-square and Likelihood-ratio tests-are based on asymptotic results and cannot guarantee a good performance in the presence of low frequency genotypes. Since the parameter space dimension increases at a quadratic rate on the number of alleles, some authors suggest applying sequential methods, where the multiallelic case is reformulated as a sequence of “biallelic” tests. However, in this approach it is not obvious how to assess the general evidence of the original hypothesis; nor is it clear how to establish the significance level for its acceptance/rejection. In this work, we introduce a straightforward method for the multiallelic HWE test, which overcomes the aforementioned issues of sequential methods. The core theory for the proposed method is given by the Full Bayesian Significance Test (FBST), an intuitive Bayesian approach which does not assign positive probabilities to zero measure sets when testing sharp hypotheses. We compare FBST performance to Chi-square, Likelihood-ratio and Markov chain tests, in three numerical experiments. The results suggest that FBST is a robust and high performance method for the HWE test, even in the presence of several alleles and small sample sizes

The politicisation of evaluation: constructing and contesting EU policy performance

Although systematic policy evaluation has been conducted for decades and has been growing strongly within the European Union (EU) institutions and in the member states, it remains largely underexplored in political science literatures. Extant work in political science and public policy typically focuses on elements such as agenda setting, policy shaping, decision making, or implementation rather than evaluation. Although individual pieces of research on evaluation in the EU have started to emerge, most often regarding policy “effectiveness” (one criterion among many in evaluation), a more structured approach is currently missing. This special issue aims to address this gap in political science by focusing on four key focal points: evaluation institutions (including rules and cultures), evaluation actors and interests (including competencies, power, roles and tasks), evaluation design (including research methods and theories, and their impact on policy design and legislation), and finally, evaluation purpose and use (including the relationships between discourse and scientific evidence, political attitudes and strategic use). The special issue considers how each of these elements contributes to an evolving governance system in the EU, where evaluation is playing an increasingly important role in decision making

Controlling spin relaxation with a cavity

Spontaneous emission of radiation is one of the fundamental mechanisms by which an excited quantum system returns to equilibrium. For spins, however, spontaneous emission is generally negligible compared to other non-radiative relaxation processes because of the weak coupling between the magnetic dipole and the electromagnetic field. In 1946, Purcell realized that the spontaneous emission rate can be strongly enhanced by placing the quantum system in a resonant cavity -an effect which has since been used extensively to control the lifetime of atoms and semiconducting heterostructures coupled to microwave or optical cavities, underpinning single-photon sources. Here we report the first application of these ideas to spins in solids. By coupling donor spins in silicon to a superconducting microwave cavity of high quality factor and small mode volume, we reach for the first time the regime where spontaneous emission constitutes the dominant spin relaxation mechanism. The relaxation rate is increased by three orders of magnitude when the spins are tuned to the cavity resonance, showing that energy relaxation can be engineered and controlled on-demand. Our results provide a novel and general way to initialise spin systems into their ground state, with applications in magnetic resonance and quantum information processing. They also demonstrate that, contrary to popular belief, the coupling between the magnetic dipole of a spin and the electromagnetic field can be enhanced up to the point where quantum fluctuations have a dramatic effect on the spin dynamics; as such our work represents an important step towards the coherent magnetic coupling of individual spins to microwave photons.Comment: 8 pages, 6 figures, 1 tabl

Neurolymphomatosis mimicking neurosarcoidosis: a case report

<p>Abstract</p> <p>Introduction</p> <p>Both neurosarcoidosis and central nervous system lymphoma can be very difficult to diagnose. We describe the case of a patient in whom neurosarcoidosis was strongly suspected, but who was eventually found to have lymphoma. We believe the case to be of interest and practical value to neurologists, oncologists and internists with an interest in inflammatory diseases.</p> <p>Case presentation</p> <p>A diagnosis of neurosarcoidosis was considered in a 49-year-old Caucasian man on the basis of the following symptoms and indications: a cough, bilateral hilar lymphadenopathy confirmed by thoracic computed tomography, the development of an S1 radiculopathy, cerebrospinal fluid abnormalities (raised protein level), bilateral lung hilar and lachrymal gland uptake on a gallium scan, and erythema nodosum confirmed with skin biopsy. These were followed by the development of multiple cranial neuropathies, including seventh nerve palsy. Exhaustive further investigations yielded no evidence for an alternative diagnosis. Treatments with steroids, cyclophosphamide, intravenous immunoglobulin and finally infliximab were of no benefit. He eventually developed cutaneous nodules, a biopsy of which revealed lymphoma that proved resistant to therapy.</p> <p>Conclusion</p> <p>Constant diagnostic vigilance is required in disorders such as neurosarcoidosis.</p

Cognitive dysfunction in naturally occurring canine idiopathic epilepsy

Globally, epilepsy is a common serious brain disorder. In addition to seizure activity, epilepsy is associated with cognitive impairments including static cognitive impairments present at onset, progressive seizure-induced impairments and co-morbid dementia. Epilepsy occurs naturally in domestic dogs but its impact on canine cognition has yet to be studied, despite canine cognitive dysfunction (CCD) recognised as a spontaneous model of dementia. Here we use data from a psychometrically validated tool, the canine cognitive dysfunction rating (CCDR) scale, to compare cognitive dysfunction in dogs diagnosed with idiopathic epilepsy (IE) with controls while accounting for age. An online cross-sectional study resulted in a sample of 4051 dogs, of which n = 286 had been diagnosed with IE. Four factors were significantly associated with a diagnosis of CCD (above the diagnostic cut-off of CCDR ≥50): (i) epilepsy diagnosis: dogs with epilepsy were at higher risk; (ii) age: older dogs were at higher risk; (iii) weight: lighter dogs (kg) were at higher risk; (iv) training history: dogs with more exposure to training activities were at lower risk. Impairments in memory were most common in dogs with IE, but progression of impairments was not observed compared to controls. A significant interaction between epilepsy and age was identified, with IE dogs exhibiting a higher risk of CCD at a young age, while control dogs followed the expected pattern of low-risk throughout middle age, with risk increasing exponentially in geriatric years. Within the IE sub-population, dogs with a history of cluster seizures and high seizure frequency had higher CCDR scores. The age of onset, nature and progression of cognitive impairment in the current IE dogs appear divergent from those classically seen in CCD. Longitudinal monitoring of cognitive function from seizure onset is required to further characterise these impairments

Molecular evolution of HoxA13 and the multiple origins of limbless morphologies in amphibians and reptiles

Developmental processes and their results, morphological characters, are inherited through transmission of genes regulating development. While there is ample evidence that cis-regulatory elements tend to be modular, with sequence segments dedicated to different roles, the situation for proteins is less clear, being particularly complex for transcription factors with multiple functions. Some motifs mediating protein-protein interactions may be exclusive to particular developmental roles, but it is also possible that motifs are mostly shared among different processes. Here we focus on HoxA13, a protein essential for limb development. We asked whether the HoxA13 amino acid sequence evolved similarly in three limbless clades: Gymnophiona, Amphisbaenia and Serpentes. We explored variation in ω (dN/dS) using a maximum-likelihood framework and HoxA13sequences from 47 species. Comparisons of evolutionary models provided low ω global values and no evidence that HoxA13 experienced relaxed selection in limbless clades. Branch-site models failed to detect evidence for positive selection acting on any site along branches of Amphisbaena and Gymnophiona, while three sites were identified in Serpentes. Examination of alignments did not reveal consistent sequence differences between limbed and limbless species. We conclude that HoxA13 has no modules exclusive to limb development, which may be explained by its involvement in multiple developmental processes

Magnetic resonance imaging of the erector spinae muscles in Duchenne muscular dystrophy: implication for scoliotic deformities

<p>Abstract</p> <p>Background</p> <p>In Duchenne muscular dystrophy (DMD), the muscular degeneration often leads to the development of scoliosis. Our objective was to investigate how anatomical changes in back muscles can lead to scoliosis. Muscular volume and the level of fat infiltration in those muscles were thus evaluated, in non-scoliotic, pre-scoliotic and scoliotic patients. The overlying skin thickness over the apex level of scoliotic deformations was also measured to facilitate the interpretation of electromyographic signals when recorded on the skin surface.</p> <p>Methods</p> <p>In 8 DMD patients and two healthy controls with no known muscular deficiencies, magnetic resonance imaging (MRI) was used to measure continuously at 3 mm intervals the distribution of the erector spinae (ES) muscle in the T8-L4 region as well as fat infiltration in the muscle and overlying skin thickness: four patients were non-scoliotic (NS), two were pre-scoliotic (PS, Cobb angle < 15°) and two were scoliotic (S, Cobb angle ≥ 15°). For each subject, 63 images 3 mm thick of the ES muscle were obtained in the T8-L4 region on both sides of the spine. The pixel dimension was 0.39 × 0.39 mm. With a commercial software, on each 12 bits image, the ES contour on the left and on the right sides of the spine were manually determined as well as those of its constituents i.e., the iliocostalis (IL), the longissimus (LO) and the spinalis (SP) muscles. Following this segmentation, the surfaces within the contours were determined, the muscles volume were obtained, the amount of fat infiltration inside each muscle was evaluated and the overlying skin thickness measured.</p> <p>Findings</p> <p>The volume of the ES muscle of our S and PS patients was found smaller on the convex side relative to the concave one by 5.3 ± 0.7% and 2.8 ± 0.2% respectively. For the 4 NS patients, the volume difference of this muscle between right and left sides was 2.1 ± 1.5% and for the 2 controls, it was 1.4 ± 1.2%. Fat infiltration for the S and the PS patients was larger on the convex side than on the concave one (4.4 ± 1.6% and 4.5 ± 0.7% respectively) and the difference was more important near the apex. Infiltration was more important in the lateral IL muscle than in the medial SP and it was always larger near L2 than at any other spinal level. Fat infiltration was much more important in the ES for the DMD patients (49.9% ± 1.6%) than for the two controls (2.6 ± 0.8%). As for the overlying skin thickness measured near the deformity of the patients, it was larger on the concave than on the convex side: 14.8 ± 6.1 vs 13.5 ± 5.7 mm for the S and 10.3 ± 6.3 vs 9.8 ± 5.6 mm for the PS.</p> <p>Interpretation</p> <p>In DMD patients, our results indicate that a larger replacement of muscles fibers by fat infiltration on one side of the spine is a factor that can lead to the development of scoliosis. Efforts to slow such an infiltration on the most affected side of the spine could thus be beneficial to those patients by delaying the apparition of the scoliotic deformation. In addition to anatomical considerations, results obtained from the same patients but in experiments dealing with electromyography recordings, point to differences in the muscular contraction mechanisms and/or of the neural input to back muscles. This is similar to the adolescent idiopathic scoliosis (AIS) where a role of the nervous system in the development of the deformation has also been suggested.</p

X-Ray Spectroscopy of Stars

(abridged) Non-degenerate stars of essentially all spectral classes are soft X-ray sources. Low-mass stars on the cooler part of the main sequence and their pre-main sequence predecessors define the dominant stellar population in the galaxy by number. Their X-ray spectra are reminiscent, in the broadest sense, of X-ray spectra from the solar corona. X-ray emission from cool stars is indeed ascribed to magnetically trapped hot gas analogous to the solar coronal plasma. Coronal structure, its thermal stratification and geometric extent can be interpreted based on various spectral diagnostics. New features have been identified in pre-main sequence stars; some of these may be related to accretion shocks on the stellar surface, fluorescence on circumstellar disks due to X-ray irradiation, or shock heating in stellar outflows. Massive, hot stars clearly dominate the interaction with the galactic interstellar medium: they are the main sources of ionizing radiation, mechanical energy and chemical enrichment in galaxies. High-energy emission permits to probe some of the most important processes at work in these stars, and put constraints on their most peculiar feature: the stellar wind. Here, we review recent advances in our understanding of cool and hot stars through the study of X-ray spectra, in particular high-resolution spectra now available from XMM-Newton and Chandra. We address issues related to coronal structure, flares, the composition of coronal plasma, X-ray production in accretion streams and outflows, X-rays from single OB-type stars, massive binaries, magnetic hot objects and evolved WR stars.Comment: accepted for Astron. Astrophys. Rev., 98 journal pages, 30 figures (partly multiple); some corrections made after proof stag

Layered convection as the origin of Saturn's luminosity anomaly

As they keep cooling and contracting, Solar System giant planets radiate more energy than they receive from the Sun. Applying the first and second principles of thermodynamics, one can determine their cooling rate, luminosity, and temperature at a given age. Measurements of Saturn's infrared intrinsic luminosity, however, reveal that this planet is significantly brighter than predicted for its age. This excess luminosity is usually attributed to the immiscibility of helium in the hydrogen-rich envelope, leading to "rains" of helium-rich droplets. Existing evolution calculations, however, suggest that the energy released by this sedimentation process may not be sufficient to resolve the puzzle. Here, we demonstrate using planetary evolution models that the presence of layered convection in Saturn's interior, generated, like in some parts of Earth oceans, by the presence of a compositional gradient, significantly reduces its cooling. It can explain the planet's present luminosity for a wide range of configurations without invoking any additional source of energy. This suggests a revision of the conventional homogeneous adiabatic interior paradigm for giant planets, and questions our ability to assess their heavy element content. This reinforces the possibility for layered convection to help explaining the anomalously large observed radii of extrasolar giant planets.Comment: Published in Nature Geoscience. Online publication date: April 21st, 2013. Accepted version before journal editing and with Supplementary Informatio

Primary care and pattern of skin diseases in a mediterranean island

BACKGROUND: In Greece where primary health care services are not fully developed, patients with simple or minor conditions have to attend to hospitals to be treated. We analysed the data of patients with cutaneous disorders attending the tertiary referral hospital on the Island of Crete, with the aim to identify the most common conditions that patients complain of, in order to define the areas where the education of General Practitioners in Dermatology must focus. METHODS: All patients attending the Dermatology ambulatory office in the Emergency Department of the University General Hospital of Heraklion from January 2003 to December 2003 were included in this retrospective analysis. The medical records of the patients (history, physical examination and laboratory investigations) were analysed to ascertain the diagnosis and the management of cases. All patients were evaluated by qualified dermatologists. RESULTS: A total of 3715 patients attended the Dermatology Clinic. Most patients were young adults in the age group 21–40 years (38.4%), and the male to female ratio was 1 to 1.2. Allergic skin diseases, mostly dermatitis and urticaria (35.7%) were the most common for attendance, followed by infectious diseases (26.1%) and insect bites (10.2%). Inflammatory and autoimmune disorders accounted for 7.9% of the cases. Pruritus of unknown origin was diagnosed in 6.3% of patients. Skin tumors were detected in 2.7%. The management of the vast majority of cases (85.0%) consisted of advice with or without a prescription, while only 4.8% of patients required admission. CONCLUSION: Allergic and infectious skin diseases were the most common cutaneous diseases in patients attending this tertiary University hospital, while the management of most patients did not require specialised care. On the basis of the present data, the training of primary health care providers in Dermatology should emphasize these common conditions, with the aim of improving primary care and alleviating the burden on hospital care