Combining Multi-Fidelity Modelling and Asynchronous Batch Bayesian Optimization

Bayesian Optimization is a useful tool for experiment design. Unfortunately, the classical, sequential setting of Bayesian Optimization does not translate well into laboratory experiments, for instance battery design, where measurements may come from different sources and their evaluations may require significant waiting times. Multi-fidelity Bayesian Optimization addresses the setting with measurements from different sources. Asynchronous batch Bayesian Optimization provides a framework to select new experiments before the results of the prior experiments are revealed. This paper proposes an algorithm combining multi-fidelity and asynchronous batch methods. We empirically study the algorithm behavior, and show it can outperform single-fidelity batch methods and multi-fidelity sequential methods. As an application, we consider designing electrode materials for optimal performance in pouch cells using experiments with coin cells to approximate battery performance

Cooperative coupling of ultracold atoms and surface plasmons

Cooperative coupling between optical emitters and light fields is one of the outstanding goals in quantum technology. It is both fundamentally interesting for the extraordinary radiation properties of the participating emitters and has many potential applications in photonics. While this goal has been achieved using high-finesse optical cavities, cavity-free approaches that are broadband and easy to build have attracted much attention recently. Here we demonstrate cooperative coupling of ultracold atoms with surface plasmons propagating on a plane gold surface. While the atoms are moving towards the surface they are excited by an external laser pulse. Excited surface plasmons are detected via leakage radiation into the substrate of the gold layer. A maximum Purcell factor of $\eta_\mathrm{P}=4.9$ is reached at an optimum distance of $z=250~\mathrm{nm}$ from the surface. The coupling leads to the observation of a Fano-like resonance in the spectrum.Comment: 9 pages, 4 figure

Retear of anterior cruciate ligament grafts in female basketball players: a case series

<p>Abstract</p> <p>Background</p> <p>Incidence of anterior cruciate ligament (ACL) injuries in young female basketball players is higher than that in male basketball players. Graft retears are more frequent with the increasing number of ACL reconstructions. The present study aimed to examine the incidence of retears in competitive female basketball players.</p> <p>Methods</p> <p>Sixty-four female basketball players (aged 12 to 29 years) who underwent primary anatomic double-bundle ACL reconstruction using hamstring grafts participated in the study. We investigated incidence, mechanism, and patient characteristics of ACL graft retears. Mann-Whitney <it>U </it>test was used for statistical analysis, and the level of significance was determined at <it>P </it>< 0.05.</p> <p>Results</p> <p>Six patients suffered from ACL graft retear (9.4%). Mean duration between primary ACL reconstruction and incidence of retears was 11.7 months. However, there were no other postoperative graft ruptures after 24 months. Primary injury and retear mechanisms varied by patient. At six months after the primary ACL reconstruction surgery, mean quadriceps and hamstring strengths were 81% and 87%, respectively, indicating favorable recovery of muscle strength. However, preoperative quadriceps and hamstring strength in the retear group were 65% and 71%, respectively. In particular, preoperative quadriceps strength in the retear group demonstrated a lower value than that in the uninjured group (<it>P </it>< 0.05).</p> <p>Conclusions</p> <p>We observed a high incidence of ACL graft retears in competitive female basketball players, as previously reported. Considering the timing of graft retear occurrences, an early return to playing basketball should be avoided following ACL reconstruction. Closer attention should be paid to player preoperative condition, as well as muscle strength and postoperative status.</p

Preoperative Behavioural Intervention versus standard care to Reduce Drinking before elective orthopaedic Surgery (PRE-OP BIRDS):Protocol for a multicentre pilot randomised controlled trial

Background Evidence suggests that increased preoperative alcohol consumption increases the risk of postoperative complications; therefore, a reduction or cessation in alcohol intake before surgery may reduce perioperative risk. Preoperative assessment presents an opportunity to intervene to optimise patients for surgery. This multicentre, two-arm, parallel group, individually randomised controlled trial will investigate whether a definitive trial of a brief behavioural intervention aimed at reducing preoperative alcohol consumption is feasible and acceptable to healthcare professionals responsible for its delivery and the preoperative elective orthopaedic patient population. Methods Screening will be conducted by trained healthcare professionals at three hospitals in the North East of England. Eligible patients (those aged 18 or over, listed for elective hip or knee arthroplasty surgery and scoring 5 or more or reporting consumption of six or more units on a single occasion at least weekly on the alcohol screening tool) who enrol in the trial will be randomised on a one-to-one non-blinded basis to either treatment as usual or brief behavioural intervention delivered in the pre-assessment clinic. Patients will be followed up 1–2 days pre-surgery, 1–5 days post-surgery (as an in-patient), 6 weeks post-surgery, and 6 months post intervention. Feasibility will be assessed through rates of screening, eligibility, recruitment, and retention to 6-month follow-up. An embedded qualitative study will explore the acceptability of study methods to patients and staff. Discussion This pilot randomised controlled trial will establish the feasibility and acceptability of trial procedures reducing uncertainties ahead of a definitive randomised controlled trial to establish the effectiveness of brief behavioural intervention to reduce alcohol consumption in the preoperative period and the potential impact on perioperative complications

Inference of gene regulatory networks from time series by Tsallis entropy

Background: The inference of gene regulatory networks (GRNs) from large-scale expression profiles is one of the most challenging problems of Systems Biology nowadays. Many techniques and models have been proposed for this task. However, it is not generally possible to recover the original topology with great accuracy, mainly due to the short time series data in face of the high complexity of the networks and the intrinsic noise of the expression measurements. In order to improve the accuracy of GRNs inference methods based on entropy (mutual information), a new criterion function is here proposed. Results: In this paper we introduce the use of generalized entropy proposed by Tsallis, for the inference of GRNs from time series expression profiles. The inference process is based on a feature selection approach and the conditional entropy is applied as criterion function. In order to assess the proposed methodology, the algorithm is applied to recover the network topology from temporal expressions generated by an artificial gene network (AGN) model as well as from the DREAM challenge. The adopted AGN is based on theoretical models of complex networks and its gene transference function is obtained from random drawing on the set of possible Boolean functions, thus creating its dynamics. On the other hand, DREAM time series data presents variation of network size and its topologies are based on real networks. The dynamics are generated by continuous differential equations with noise and perturbation. By adopting both data sources, it is possible to estimate the average quality of the inference with respect to different network topologies, transfer functions and network sizes. Conclusions: A remarkable improvement of accuracy was observed in the experimental results by reducing the number of false connections in the inferred topology by the non-Shannon entropy. The obtained best free parameter of the Tsallis entropy was on average in the range 2.5 <= q <= 3.5 (hence, subextensive entropy), which opens new perspectives for GRNs inference methods based on information theory and for investigation of the nonextensivity of such networks. The inference algorithm and criterion function proposed here were implemented and included in the DimReduction software, which is freely available at http://sourceforge.net/projects/dimreduction and http://code.google.com/p/dimreduction/.Fundacao de Amparo e Amparo a Pesquisa do Estado de Sao Paulo (FAPESP)Coordenacao de Aperfeicofamento de Pessoal de Nivel Superior (CAPES)Conselho Nacional de Desenvolvimento Cientifico e Tecnologico (CNPq

Genome-Wide Detection of Allele Specific Copy Number Variation Associated with Insulin Resistance in African Americans from the HyperGEN Study

African Americans have been understudied in genome wide association studies of diabetes and related traits. In the current study, we examined the joint association of single nucleotide polymorphisms (SNPs) and copy number variants (CNVs) with fasting insulin and an index of insulin resistance (HOMA-IR) in the HyperGEN study, a family based study with proband ascertainment for hypertension. This analysis is restricted to 1,040 African Americans without diabetes. We generated allele specific CNV genotypes at 872,243 autosomal loci using Birdsuite, a freely available multi-stage program. Joint tests of association for SNPs and CNVs were performed using linear mixed models adjusting for covariates and familial relationships. Our results highlight SNPs associated with fasting insulin and HOMA-IR (rs6576507 and rs8026527, 3.7*10−7≤P≤1.1*10−5) near ATPase, class V, type 10A (ATP10A), and the L Type voltage dependent calcium channel (CACNA1D, rs1401492, P≤5.2*10−6). ATP10A belongs to a family of aminophospholipid-transporting ATPases and has been associated with type 2 diabetes in mice. CACNA1D has been linked to pancreatic beta cell generation in mice. The two most significant copy variable markers (rs10277702 and rs361367; P<2.0*10−4) were in the beta variable region of the T-cell receptor gene (TCRVB). Human and mouse TCR has been shown to mimic insulin and its receptor and could contribute to insulin resistance. Our findings differ from genome wide association studies of fasting insulin and other diabetes related traits in European populations, highlighting the continued need to investigate unique genetic influences for understudied populations such as African Americans

Landscape structure, human disturbance and crop management affect foraging ground selection by migrating geese

It is well known that agricultural intensification has caused severe population declines among bird species which use farmland for breeding and overwintering, while migrating bird species may benefit from intensive farming, but in turn damage crops. Knowledge of the habitat selection of migrating birds is important from both a conservation and agro-economic point of view. We investigated the habitat preferences of three common migrating goose species: White-fronted Goose Anser albifrons, Bean Goose A. fabalis and Greylag Goose A. anser during the autumn of 2009 in western Poland. A total of 24 flocks of these species were identified. Geese preferred large, elevated fields that were remote from forests and human settlements but in close proximity to a lake. Geese selected maize stubbles and avoided winter cereals. They selected sites in landscapes with a lower diversity of crops. Flock size was negatively correlated with the proportion of pastures in the landscape, but it increased with field size, distance to forest and distance to town. Our results are in contrast with the paradigm that less intensive farmland positively influences habitat use by birds during foraging. We advise the delayed ploughing of stubbles with the aim of creating appropriate foraging habitats for geese and minimizing damage to cereal crops

Effectiveness of interventions to improve the health and housing status of homeless people: a rapid systematic review

Background: Research on interventions to positively impact health and housing status of people who are homeless has received substantially increased attention over the past 5 years. This rapid review examines recent evidence regarding interventions that have been shown to improve the health of homeless people, with particular focus on the effect of these interventions on housing status. Methods: A total of 1,546 articles were identified by a structured search of five electronic databases, a hand search of grey literature and relevant journals, and contact with experts. Two reviewers independently screened the first 10% of titles and abstracts for relevance. Inter-rater reliability was high and as a result only one reviewer screened the remaining titles and abstracts. Articles were included if they were published between January 2004 and December 2009 and examined the effectiveness of an intervention to improve the health or healthcare utilization of people who were homeless, marginally housed, or at risk of homelessness. Two reviewers independently scored all relevant articles for quality. Results: Eighty-four relevant studies were identified; none were of strong quality while ten were rated of moderate quality. For homeless people with mental illness, provision of housing upon hospital discharge was effective in improving sustained housing. For homeless people with substance abuse issues or concurrent disorders, provision of housing was associated with decreased substance use, relapses from periods of substance abstinence, and health services utilization, and increased housing tenure. Abstinent dependent housing was more effective in supporting housing status, substance abstinence, and improved psychiatric outcomes than non-abstinence dependent housing or no housing. Provision of housing also improved health outcomes among homeless populations with HIV. Health promotion programs can decrease risk behaviours among homeless populations. Conclusions: These studies provide important new evidence regarding interventions to improve health, housing status, and access to healthcare for homeless populations. The additional studies included in this current review provide further support for earlier evidence which found that coordinated treatment programs for homeless persons with concurrent mental illness and substance misuse issues usually result in better health and access to healthcare than usual care. This review also provides a synthesis of existing evidence regarding interventions that specifically support homeless populations with HIV.Partial funding for this paper was provided to the Effective Public Health Practice Project by the Region of Peel, Canada

What Do We Know About Neuropsychological Aspects Of Schizophrenia?

Application of a neuropsychological perspective to the study of schizophrenia has established a number of important facts about this disorder. Some of the key findings from the existing literature are that, while neurocognitive impairment is present in most, if not all, persons with schizophrenia, there is both substantial interpatient heterogeneity and remarkable within-patient stability of cognitive function over the long-term course of the illness. Such findings have contributed to the firm establishment of neurobiologic models of schizophrenia, and thereby help to reduce the social stigma that was sometimes associated with purely psychogenic models popular during parts of the 20th century. Neuropsychological studies in recent decades have established the primacy of cognitive functions over psychopathologic symptoms as determinants of functional capacity and independence in everyday functioning. Although the cognitive benefits of both conventional and even second generation antipsychotic medications appear marginal at best, recognition of the primacy of cognitive deficits as determinants of functional disability in schizophrenia has catalyzed recent efforts to develop targeted treatments for the cognitive deficits of this disorder. Despite these accomplishments, however, some issues remain to be resolved. Efforts to firmly establish the specific neurocognitive/neuropathologic systems responsible for schizophrenia remain elusive, as do efforts to definitively demonstrate the specific cognitive deficits underlying specific forms of functional impairment. Further progress may be fostered by recent initiatives to integrate neuropsychological studies with experimental neuroscience, perhaps leading to measures of deficits in cognitive processes more clearly associated with specific, identifiable brain systems