Sensitivity of genomic selection to using different prior distributions

Genomic selection describes a selection strategy based on genomic estimated breeding values (GEBV) predicted from dense genetic markers such as single nucleotide polymorphism (SNP) data. Different Bayesian models have been suggested to derive the prediction equation, with the main difference centred around the specification of the prior distributions

Genome position specific priors for genomic prediction

<p>Abstract</p> <p>Background</p> <p>The accuracy of genomic prediction is highly dependent on the size of the reference population. For small populations, including information from other populations could improve this accuracy. The usual strategy is to pool data from different populations; however, this has not proven as successful as hoped for with distantly related breeds. BayesRS is a novel approach to share information across populations for genomic predictions. The approach allows information to be captured even where the phase of SNP alleles and casuative mutation alleles are reversed across populations, or the actual casuative mutation is different between the populations but affects the same gene. Proportions of a four-distribution mixture for SNP effects in segments of fixed size along the genome are derived from one population and set as location specific prior proportions of distributions of SNP effects for the target population. The model was tested using dairy cattle populations of different breeds: 540 Australian Jersey bulls, 2297 Australian Holstein bulls and 5214 Nordic Holstein bulls. The traits studied were protein-, fat- and milk yield. Genotypic data was Illumina 777K SNPs, real or imputed.</p> <p>Results</p> <p>Results showed an increase in accuracy of up to 3.5% for the Jersey population when using BayesRS with a prior derived from Australian Holstein compared to a model without location specific priors. The increase in accuracy was however lower than was achieved when reference populations were combined to estimate SNP effects, except in the case of fat yield. The small size of the Jersey validation set meant that these improvements in accuracy were not significant using a Hotelling-Williams t-test at the 5% level. An increase in accuracy of 1-2% for all traits was observed in the Australian Holstein population when using a prior derived from the Nordic Holstein population compared to using no prior information. These improvements were significant (P<0.05) using the Hotelling Williams t-test for protein- and fat yield.</p> <p>Conclusion</p> <p>For some traits the method might be advantageous compared to pooling of reference data for distantly related populations, but further investigation is needed to confirm the results. For closely related populations the method does not perform better than pooling reference data. However, it does give an increased accuracy compared to analysis based on only one reference population, without an increased computational burden. The approach described here provides a general setup for inclusion of location specific priors: the approach could be used to include biological information in genomic predictions.</p

Primary Sjögren's Syndrome: health experiences and predictors of health quality among patients in the United States

<p>Abstract</p> <p>Objective</p> <p>To assess the health related quality of life of patients with primary Sjögren's Syndrome (PSS) in a large US sample.</p> <p>Methods</p> <p>Questionnaires were mailed to 547 patients with a confirmed diagnosis of PSS (PhysR-PSS) and all active members of the Sjögren's Syndrome Foundation USA (SSF-PSS), half of whom identified a friend without PSS to also complete the survey.</p> <p>Results</p> <p>277 PhysR-PSS patients were compared to 606 controls. The mean age was 62 years in the PhysR-PSS group and 61 years in the control group. 90% in both groups were women. Time from first symptom to diagnosis of PSS was a mean of 7 years. Sicca related morbidity, fatigue severity, depression and pain (assessed by validated questionnaires, PROFAD-SSI, FACIT-F, CES-D, BPI) were significantly greater, and all eight SF-36 domains were significantly diminished, in patients compared to controls. Somatic fatigue was the dominant predictor of physical function and of general health. Depression was the dominant predictor of emotional well being. Health care utilization was higher in patients than controls, including out of pocket dental expenses (mean: PhysR-PSS = $1473.3, controls =$503.6), dental visits (mean: PhysR-PSS = 4.0, controls = 2.3), current treatments (mean: PhysR-PSS = 6.6, controls = 2.5), and hospitalizations (53% PhysR-PSS, vs. 40% controls).</p> <p>Conclusion</p> <p>Diminished health quality and excess health costs are prevalent among PSS patients. Health experiences and functional impact of PSS is similar among US and European patients. Delayed diagnosis, sicca related morbidity, fatigue, pain and depression are substantial suggesting unmet health needs and the importance of earlier recognition of PSS.</p

3D Hydrodynamic Simulations of Relativistic Extragalactic Jets

We describe a new numerical 3D relativistic hydrodynamical code, the results of validation tests, and a comparison with earlier, 2D studies. The 3D code has been used to study the deflection and precession of relativistic flows. We find that even quite fast jets (gamma~10) can be significantly influenced by impinging on an oblique density gradient, exhibiting a rotation of the Mach disk in the jet's head. The flow is bent via a potentially strong, oblique internal shock that arises due to asymmetric perturbation of the flow by its cocoon. In extreme cases this cocoon can form a marginally relativistic flow orthogonal to the jet, leading to large scale dynamics quite unlike that normally associated with astrophysical jets. Exploration of a gamma=5 flow subject to a large amplitude precession (semi-angle 11.25dg) shows that it retains its integrity, with modest reduction in Lorentz factor and momentum flux, for almost 50 jet-radii, but thereafter, the collimated flow is disrupted. The flow is approximately ballistic, with velocity vectors not aligned with the local jet `wall'. We consider simple estimators of the flow emissivity in each case and conclude that a) while the oblique internal shocks which mediate a small change in the direction of the deflected flows have little impact on the global dynamics, significantly enhanced flow emission (by a factor of 2-3) may be associated with such regions; and b) the convolution of rest frame emissivity and Doppler boost in the case of the precessed jet invariably leads to a core-jet-like structure, but that intensity fluctuations in the jet cannot be uniquely associated with either change in internal conditions or Doppler boost alone, but in general are a combination of both factors.Comment: 41 pages, including 15 figures. Submitted to ApJ. Version with complete abstract. and full resolution, color figures available from http://www.astro.lsa.umich.edu/users/hughes/icon_dir/cfd.htm

High-fidelity phase and amplitude control of phase-only computer generated holograms using conjugate gradient minimisation

Funding: Leverhulme Trust (RPG-2013-074); EPSRC (EP/G03673X/1; EP/L015110/1).We demonstrate simultaneous control of both the phase and amplitude of light using a conjugate gradient minimisation-based hologram calculation technique and a single phase-only spatial light modulator (SLM). A cost function, which incorporates the inner product of the light field with a chosen target field within a defined measure region, is efficiently minimised to create high fidelity patterns in the Fourier plane of the SLM. A fidelity of F = 0.999997 is achieved for a pattern resembling an LG01 mode with a calculated light-usage efficiency of 41.5%. Possible applications of our method in optical trapping and ultracold atoms are presented and we show uncorrected experimental realisation of our patterns with F = 0.97 and 7.8% light efficiency.Publisher PDFPeer reviewe

Fatally entangled right whales can die extremely slowly

Author Posting. © IEEE, 2006. This article is posted here by permission of IEEE for personal use, not for redistribution. The definitive version was published in Proceedings Oceans 2006, Boston, MA, USA, 3 pp, doi:10.1109/OCEANS.2006.306792.Unlike smaller marine mammals that lack the mass and power to break free from serious entanglements in fixed fishing gear, right whales can do so, but they are not always rope free. The remaining rope can gradually constrict one or more body parts and the resulting debilitation and ultimate death can take many months. Thus the practices that lead to these mortalities need to be viewed not only as a conflict between the cultural and socioeconomic value of a fishery versus a potential species extinction process, but also in terms of an extreme animal welfare issue.Supported by NOAA NA04NMF4720392, Woods Hole Oceanographic Institution Ocean Life Institute, and the North Pond Foundation

A powerful intervention: general practitioners' use of sickness certification in depression

&lt;b&gt;Background&lt;/b&gt; Depression is frequently cited as the reason for sickness absence, and it is estimated that sickness certificates are issued in one third of consultations for depression. Previous research has considered GP views of sickness certification but not specifically in relation to depression. This study aimed to explore GPs views of sickness certification in relation to depression.&lt;p&gt;&lt;/p&gt; &lt;b&gt;Methods&lt;/b&gt; A purposive sample of GP practices across Scotland was selected to reflect variations in levels of incapacity claimants and antidepressant prescribing. Qualitative interviews were carried out between 2008 and 2009.&lt;p&gt;&lt;/p&gt; &lt;b&gt;Results&lt;/b&gt; A total of 30 GPs were interviewed. A number of common themes emerged including the perceived importance of GP advocacy on behalf of their patients, the tensions between stakeholders involved in the sickness certification system, the need to respond flexibly to patients who present with depression and the therapeutic nature of time away from work as well as the benefits of work. GPs reported that most patients with depression returned to work after a short period of absence and that it was often difficult to predict which patients would struggle to return to work.&lt;p&gt;&lt;/p&gt; &lt;b&gt;Conclusions&lt;/b&gt; GPs reported that dealing with sickness certification and depression presents distinct challenges. Sickness certificates are often viewed as powerful interventions, the effectiveness of time away from work for those with depression should be subject to robust enquiry

Mapping Cosmic Dawn and Reionization: Challenges and Synergies

Cosmic dawn and the Epoch of Reionization (EoR) are among the least explored observational eras in cosmology: a time at which the first galaxies and supermassive black holes formed and reionized the cold, neutral Universe of the post-recombination era. With current instruments, only a handful of the brightest galaxies and quasars from that time are detectable as individual objects, due to their extreme distances. Fortunately, a multitude of multi-wavelength intensity mapping measurements, ranging from the redshifted 21 cm background in the radio to the unresolved X-ray background, contain a plethora of synergistic information about this elusive era. The coming decade will likely see direct detections of inhomogenous reionization with CMB and 21 cm observations, and a slew of other probes covering overlapping areas and complementary physical processes will provide crucial additional information and cross-validation. To maximize scientific discovery and return on investment, coordinated survey planning and joint data analysis should be a high priority, closely coupled to computational models and theoretical predictions.Comment: 5 pages, 1 figure, submitted to the Astro2020 Decadal Survey Science White Paper cal

Recreating blood-brain barrier physiology and structure on chip: A novel neurovascular microfluidic bioreactor

The blood-brain barrier (BBB) is a critical structure that serves as the gatekeeper between the central nervous system and the rest of the body. It is the responsibility of the BBB to facilitate the entry of required nutrients into the brain and to exclude potentially harmful compounds; however, this complex structure has remained difficult to model faithfully in vitro. Accurate in vitro models are necessary for understanding how the BBB forms and functions, as well as for evaluating drug and toxin penetration across the barrier. Many previous models have failed to support all the cell types involved in the BBB formation and/or lacked the flow-created shear forces needed for mature tight junction formation. To address these issues and to help establish a more faithful in vitro model of the BBB, we have designed and fabricated a microfluidic device that is comprised of both a vascular chamber and a brain chamber separated by a porous membrane. This design allows for cell-to-cell communication between endothelial cells, astrocytes, and pericytes and independent perfusion of both compartments separated by the membrane. This NeuroVascular Unit (NVU) represents approximately one-millionth of the human brain, and hence, has sufficient cell mass to support a breadth of analytical measurements. The NVU has been validated with both fluorescein isothiocyanate (FITC)-dextran diffusion and transendothelial electrical resistance. The NVU has enabled in vitro modeling of the BBB using all human cell types and sampling effluent from both sides of the barrier

Immunotherapy for neuroblastoma using syngeneic fibroblasts transfected with IL-2 and IL-12

Cytokine-modified tumour cells have been used in clinical trials for immunotherapy of neuroblastoma, but primary tumour cells from surgical biopsies are difficult to culture. Autologous fibroblasts, however, are straightforward to manipulate in culture and easy to transfect using nonviral or viral vectors. Here we have compared the antitumour effect of fibroblasts and tumour cells transfected ex vivo to coexpress interleukin-2 (IL-2) and IL-12 in a syngeneic mouse model of neuroblastoma. Coinjection of cytokine-modified fibroblasts with Neuro-2A tumour cells abolished their in vivo tumorigenicity. Treatment of established tumours with three intratumoral doses of transfected fibroblasts showed a significant therapeutic effect with reduced growth or complete eradication of tumours in 90% of mice, associated with extensive leukocyte infiltration. Splenocytes recovered from vaccinated mice showed enhanced IL-2 production following Neuro-2A coculture, and increased cytotoxicity against Neuro-2A targets compared with controls. Furthermore, 100% of the tumour-free mice exhibited immune memory against tumour cells when rechallenged three months later. The potency of transfected fibroblasts was equivalent to that of tumour cells in all experiments. We conclude that syngeneic fibroblasts cotransfected with IL-2 and IL-12 mediate therapeutic effects against established disease, and are capable of generating immunological memory. Furthermore, as they are easier to recover and manipulate than autologous tumour cells, fibroblasts provide an attractive alternative immunotherapeutic strategy for the treatment of neuroblastoma