CMB-S4 forecast on the primordial non-Gaussianity parameter of feature models

We present forecasts on the primordial non-Gaussianity parameter fNL of feature models for the future Cosmic Microwave Background Stage-4 (CMB-S4) experiments. The Fisher matrix of the bispectrum estimator was computed using noise covariances expected for preliminary CMB-S4 specifications including ones for the Simons Observatory. We introduce a novel method that improves the computation by orthonormalizing the covariance matrix. The most sensitive CMB-S4 experiment with 1' beam and 1 μK-arc min noise would yield a factor of 1.7-2.2 times more stringent constraints compared to Planck. Under the Simons Observatory baseline conditions the improvement would be about 1.3-1.6 times to Planck. We also thoroughly studied the effects of various model and experimental parameters on the forecast. Detailed analysis on the constraints coming from temperature and E-mode polarization, in particular, provided some insight into detecting oscillatory features in the CMB bispectrum.STF

Separable projection integrals for higher-order correlators of the cosmic microwave sky: Acceleration by factors exceeding 100

© 2016. We present a case study describing efforts to optimise and modernise "Modal", the simulation and analysis pipeline used by the Planck satellite experiment for constraining general non-Gaussian models of the early universe via the bispectrum (or three-point correlator) of the cosmic microwave background radiation. We focus on one particular element of the code: the projection of bispectra from the end of inflation to the spherical shell at decoupling, which defines the CMB we observe today. This code involves a three-dimensional inner product between two functions, one of which requires an integral, on a non-rectangular domain containing a sparse grid. We show that by employing separable methods this calculation can be reduced to a one-dimensional summation plus two integrations, reducing the overall dimensionality from four to three. The introduction of separable functions also solves the issue of the non-rectangular sparse grid. This separable method can become unstable in certain scenarios and so the slower non-separable integral must be calculated instead. We present a discussion of the optimisation of both approaches.We demonstrate significant speed-ups of ≈100×, arising from a combination of algorithmic improvements and architecture-aware optimisations targeted at improving thread and vectorisation behaviour. The resulting MPI/OpenMP hybrid code is capable of executing on clusters containing processors and/or coprocessors, with strong-scaling efficiency of 98.6% on up to 16 nodes. We find that a single coprocessor outperforms two processor sockets by a factor of 1.3× and that running the same code across a combination of both microarchitectures improves performance-per-node by a factor of 3.38×. By making bispectrum calculations competitive with those for the power spectrum (or two-point correlator) we are now able to consider joint analysis for cosmological science exploitation of new data.This research is supported by an STFC consolidated grant ST/L000636/1, and funded in part by the Intel R Parallel Computing Centre program. This work was undertaken on the COSMOS Shared Memory system at DAMTP, University of Cambridge operated on behalf of the STFC DiRAC HPC Facility. This equipment is funded by BIS National E-infrastructure capital grant ST/J005673/1 and STFC grants ST/H008586/1, ST/K00333X/1

Using inpainting to construct accurate cut-sky CMB estimators

The direct evaluation of manifestly optimal, cut-sky cosmic microwave background (CMB) power spectrum and bispectrum estimators is numerically very costly, due to the presence of inverse-covariance filtering operations. This justifies the investigation of alternative approaches. In this work, we mostly focus on an inpainting algorithm that was introduced in recent CMB analyses to cure cut-sky suboptimalities of bispectrum estimators. First, we show that inpainting can equally be applied to the problem of unbiased estimation of power spectra. We then compare the performance of a novel inpainted CMB temperature power spectrum estimator to the popular apodized pseudo-C$_{l}$ (PCL) method and demonstrate, both numerically and with analytic arguments, that inpainted power spectrum estimates significantly outperform PCL estimates. Finally, we study the case of cut-sky bispectrum estimators, comparing the performance of three different approaches: inpainting, apodization and a novel low-l leaning scheme. Providing an analytic argument of why the local shape is typically most affected we mainly focus on local-type non-Gaussianity. Our results show that inpainting allows us to achieve optimality also for bispectrum estimation, but interestingly also demonstrate that appropriate apodization, in conjunction with low-l cleaning, can lead to comparable accuracy.H. F. G. gratefully acknowledges the support of the Studienstiftung des deutschen Volkes, an Science and Technology Funding Council (STFC) studentship and a studentship of the Centre for Theoretical Cosmology (CTC), Department for Applied Mathematics and Theoretical Physics (DAMTP). This work was supported by an STFC consolidated Grant No. ST/L000636/1. It was undertaken on the COSMOS Shared Memory system at DAMTP, University of Cambridge, operated on behalf of the STFC Distributed Research utilising Advanced Computing (DiRAC) High Performance Computing (HPC) Facility. This equipment is funded by Business Innovation and Skills (BIS) National E-infrastructure capital Grant No. ST/J005673/1 and STFC Grants No. ST/H008586/1 and No. ST/K00333X/1

Primordial non-gaussianity and bispectrum measurements in the cosmic microwave background and large-scale structure

The most direct probe of non-Gaussian initial conditions has come from bispectrum measurements of temperature fluctuations in the Cosmic Microwave Background and of the matter and galaxy distribution at large scales. Such bispectrum estimators are expected to continue to provide the best constraints on the non-Gaussian parameters in future observations. We review and compare the theoretical and observational problems, current results and future prospects for the detection of a non-vanishing primordial component in the bispectrum of the Cosmic Microwave Background and large-scale structure, and the relation to specific predictions from different inflationary models.Peer Reviewe

Protocol for a collaborative meta-analysis of 5-HTTLPR, stress, and depression

Abstract Background Debate is ongoing about what role, if any, variation in the serotonin transporter linked polymorphic region (5-HTTLPR) plays in depression. Some studies report an interaction between 5-HTTLPR variation and stressful life events affecting the risk for depression, others report a main effect of 5-HTTLPR variation on depression, while others find no evidence for either a main or interaction effect. Meta-analyses of multiple studies have also reached differing conclusions. Methods/Design To improve understanding of the combined roles of 5-HTTLPR variation and stress in the development of depression, we are conducting a meta-analysis of multiple independent datasets. This coordinated approach utilizes new analyses performed with centrally-developed, standardized scripts. This publication documents the protocol for this collaborative, consortium-based meta-analysis of 5-HTTLPR variation, stress, and depression. Study eligibility criteria: Our goal is to invite all datasets, published or unpublished, with 5-HTTLPR genotype and assessments of stress and depression for at least 300 subjects. This inclusive approach is to minimize potential impact from publication bias. Data sources: This project currently includes investigators from 35 independent groups, providing data on at least N = 33,761 participants. The analytic plan was determined prior to starting data analysis. Analyses of individual study datasets will be performed by the investigators who collected the data using centrally-developed standardized analysis scripts to ensure a consistent analytical approach across sites. The consortium as a group will review and interpret the meta-analysis results. Discussion Variation in 5-HTTLPR is hypothesized to moderate the response to stress on depression. To test specific hypotheses about the role of 5-HTTLPR variation on depression, we will perform coordinated meta-analyses of de novo results obtained from all available data, using variables and analyses determined a priori. Primary analyses, based on the original 2003 report by Caspi and colleagues of a GxE interaction will be supplemented by secondary analyses to help interpret and clarify issues ranging from the mechanism of effect to heterogeneity among the contributing studies. Publication of this protocol serves to protect this project from biased reporting and to improve the ability of readers to interpret the results of this specific meta-analysis upon its completion.http://deepblue.lib.umich.edu/bitstream/2027.42/112319/1/12888_2013_Article_1474.pd

Use of psychotropic drugs before pregnancy and the risk for induced abortion: population-based register-data from Finland 1996-2006

<p>Abstract</p> <p>Background</p> <p>Some, though not all studies have reported an increased risk for mental health problems after an induced abortion. Problems with design and data have compromised these studies and the generalisation of their results.</p> <p>Methods</p> <p>The Finnish Medication and Pregnancy database (N = 622 671 births and 114 518 induced abortions for other than fetal reasons) in 1996-2006 was utilised to study the use of psychotropic drugs in the three months before a pregnancy ending in a birth or an induced abortion.</p> <p>Results</p> <p>In total 2.1% of women with a birth and 5.1% of women with an induced abortion had used a psychotropic medicine 0-3 months before pregnancy. Psychotropic drug users terminated their pregnancies (30.9%) more often than other pregnant women (15.5%). Adjustment for background characteristics explained one third of this elevated risk, but the risk remained significantly increased among users of psychotropic medicine (OR 1.94, 95% confidence intervals 1.87-2.02). A similar risk was found for first pregnancies (30.1% vs. 18.9%; adjusted OR 1.53, 95% confidence intervals 1.42-1.65). The rate for terminating pregnancy was the highest for women using hypnotics and sedatives (35.6% for all pregnancies and 29.1% for first pregnancies), followed by antipsychotics (33.9% and 36.0%) and antidepressants (32.0% and 32.1%).</p> <p>Conclusions</p> <p>The observed increased risk for induced abortion among women with psychotropic medication highlighs the importance to acknowledge the mental health needs of women seeking an induced abortion. Further studies are needed to establish the impact of pre-existing differences in mental health on mental health outcomes of induced abortions compared to outcomes of pregnancies ending in a birth.</p

The Perceptions on Male Circumcision as a Preventive Measure Against HIV Infection and Considerations in Scaling up of the Services: A Qualitative Study Among Police Officers in Dar es Salaam, Tanzania.

\ud In recent randomized controlled trials, male circumcision has been proven to complement the available biomedical interventions in decreasing HIV transmission from infected women to uninfected men. Consequently, Tanzania is striving to scale-up safe medical male circumcision to reduce HIV transmission. However, there is a need to investigate the perceptions of male circumcision in Tanzania using specific populations. The purpose of the present study was to assess the perceptions of male circumcision in a cohort of police officers that also served as a source of volunteers for a phase I/II HIV vaccine (HIVIS-03) trial in Dar es Salaam, Tanzania. In-depth interviews with 24 men and 10 women were conducted. Content analysis informed by the socio-ecological model was used to analyze the data. Informants perceived male circumcision as a health-promoting practice that may prevent HIV transmission and other sexually transmitted infections. They reported male circumcision promotes sexual pleasure, confidence and hygiene or sexual cleanliness. They added that it is a religious ritual and a cultural practice that enhances the recognition of manhood in the community. However, informants were concerned about the cost involved in male circumcision and cleanliness of instruments used in medical and traditional male circumcision. They also expressed confusion about the shame of undergoing circumcision at an advanced age and pain that could emanate after circumcision. The participants advocated for health policies that promote medical male circumcision at childhood, specifically along with the vaccination program. The perceived benefit of male circumcision as a preventive strategy to HIV and other sexually transmitted infections is important. However, there is a need to ensure that male circumcision is conducted under hygienic conditions. Integrating male circumcision service in the routine childhood vaccination program may increase its coverage at early childhood. The findings from this investigation provide contextual understanding that may assist in scaling-up male circumcision in Tanzania.\u

Protocol for a collaborative meta-analysis of 5-HTTLPR, stress, and depression

Background: Debate is ongoing about what role, if any, variation in the serotonin transporter linked polymorphic region (5-HTTLPR) plays in depression. Some studies report an interaction between 5-HTTLPR variation and stressful life events affecting the risk for depression, others report a main effect of 5-HTTLPR variation on depression, while others find no evidence for either a main or interaction effect. Meta-analyses of multiple studies have also reached differing conclusions.Methods/Design: To improve understanding of the combined roles of 5-HTTLPR variation and stress in the development of depression, we are conducting a meta-analysis of multiple independent datasets. This coordinated approach utilizes new analyses performed with centrally-developed, standardized scripts. This publication documents the protocol for this collaborative, consortium-based meta-analysis of 5-HTTLPR variation, stress, and depression.Study eligibility criteria: Our goal is to invite all datasets, published or unpublished, with 5-HTTLPR genotype and assessments of stress and depression for at least 300 subjects. This inclusive approach is to minimize potential impact from publication bias.Data sources: This project currently includes investigators from 35 independent groups, providing data on at least N = 33,761 participants.&nbsp; The analytic plan was determined prior to starting data analysis. Analyses of individual study datasets will be performed by the investigators who collected the data using centrally-developed standardized analysis scripts to ensure a consistent analytical approach across sites. The consortium as a group will review and interpret the meta-analysis results.Discussion: Variation in 5-HTTLPR is hypothesized to moderate the response to stress on depression. To test specific hypotheses about the role of 5-HTTLPR variation on depression, we will perform coordinated meta-analyses of de novo results obtained from all available data, using variables and analyses determined a priori. Primary analyses, based on the original 2003 report by Caspi and colleagues of a GxE interaction will be supplemented by secondary analyses to help interpret and clarify issues ranging from the mechanism of effect to heterogeneity among the contributing studies. Publication of this protocol serves to protect this project from biased reporting and to improve the ability of readers to interpret the results of this specific meta-analysis upon its completion

Prenatal and Postnatal Tobacco Exposure and Behavioral Problems in 10-Year-Old Children: Results from the GINI-plus Prospective Birth Cohort Study

BACKGROUND: Prenatal and postnatal tobacco exposure have been reported to be associated with behavioral problems. However, the magnitude of the association with tobacco exposure at specific periods of exposure is unclear. OBJECTIVE: We assessed the relative risk of behavioral problems in children who had been exposed to tobacco smoke in utero and postnatally. METHODS: We analyzed data from a prospective birth cohort study in two cities in Germany: the German Infant Nutrition Intervention. Our sample included 5,991 children born between 1995 and 1998 as well as their parents. We measured behavioral problems using the Strength and Difficulties Questionnaire (SDQ) at follow-up 10 years after birth. According to prespecified SDQ cutoff values, children were classified as &quot;normal,&quot; &quot;borderline,&quot; or &quot;abnormal&quot; according to the subscales &quot;emotional symptoms,&quot; &quot;conduct problems,&quot; &quot;hyperactivity/inattention,&quot; &quot;peer-relationship problems,&quot; and a total difficulties score. Smoke exposure and further covariates were assessed using parent questionnaires. RESULTS: Compared with children not exposed to tobacco smoke, children exposed both pre- and postnatally to tobacco smoke had twice the estimated risk [95% confidence interval (CI), 1.4-3.1] of being classified as abnormal according to the total difficulties score of the SDQ at 10 years of age. Children who were only prenatally exposed had a 90% higher relative risk (95% CI, 0.9-4.0), whereas children who were only postnatally exposed had a 30% higher relative risk (95% CI, 0.9-1.9). These results could not be explained by confounding by parental education, father&#39;s employment, child&#39;s time spent in front of computer or television screen, being a single father or mother, or mother&#39;s age. CONCLUSIONS: Prenatal exposure to tobacco smoke is associated with behavioral problems in school-age children. Although our findings do not preclude the influence of postnatal exposure, prenatal exposure seems to be more important

Modular Approach to Therapy for Anxiety, Depression, Trauma, or Conduct Problems in outpatient child and adolescent mental health services in New Zealand: study protocol for a randomized controlled trial

Background: Mental health disorders are common and disabling for young people because of the potential to disrupt key developmental tasks. Implementation of evidence-based psychosocial therapies in New Zealand is limited, owing to the inaccessibility, length, and cost of training in these therapies. Furthermore, most therapies address one problem area at a time, although comorbidity and changing clinical needs commonly occur in practice. A more flexible approach is needed. The Modular Approach to Therapy for Children with Anxiety, Depression, Trauma, or Conduct Problems (MATCH-ADTC) is designed to overcome these challenges; it provides a range of treatment modules addressing different problems, within a single training program. A clinical trial of MATCH-ADTC in the USA showed that MATCH-ADTC outperformed usual care and standard evidence-based treatment on several clinical measures. We aim to replicate these findings and evaluate the impact of providing training and supervision in MATCH-ADTC to: (1) improve clinical outcomes for youth attending mental health services; (2) increase the amount of evidence-based therapy content; (3) increase the efficiency of service delivery. Methods: This is an assessor-blinded multi-site effectiveness randomized controlled trial. Randomization occurs at two levels: (1) clinicians (≥60) are randomized to intervention or usual care; (2) youth participants (7–14 years old) accepted for treatment in child and adolescent mental health services (with a primary disorder that includes anxiety, depression, trauma-related symptoms, or disruptive behavior) are randomly allocated to receive MATCH-ADTC or usual care. Youth participants are recruited from ‘mainstream’, Māori-specific, and Pacific-specific child and adolescent mental health services. We originally planned to recruit 400 youth participants, but this has been revised to 200 participants. Centralized computer randomization ensures allocation concealment. The primary outcome measures are: (i) the difference in trajectory of change of clinical severity between groups (using the parent-rated Brief Problem Monitor); (ii) clinicians’ use of evidence-based treatment procedures during therapy sessions; (iii) total time spent by clinicians delivering therapy. Discussion: If MATCH-ADTC demonstrates effectiveness it could offer a practical efficient method to increase access to evidence-based therapies, and improve outcomes for youth attending secondary care services