Reproducibility in the absence of selective reporting : An illustration from large-scale brain asymmetry research

Altres ajuts: Max Planck Society (Germany).The problem of poor reproducibility of scientific findings has received much attention over recent years, in a variety of fields including psychology and neuroscience. The problem has been partly attributed to publication bias and unwanted practices such as p-hacking. Low statistical power in individual studies is also understood to be an important factor. In a recent multisite collaborative study, we mapped brain anatomical left-right asymmetries for regional measures of surface area and cortical thickness, in 99 MRI datasets from around the world, for a total of over 17,000 participants. In the present study, we revisited these hemispheric effects from the perspective of reproducibility. Within each dataset, we considered that an effect had been reproduced when it matched the meta-analytic effect from the 98 other datasets, in terms of effect direction and significance threshold. In this sense, the results within each dataset were viewed as coming from separate studies in an "ideal publishing environment," that is, free from selective reporting and p hacking. We found an average reproducibility rate of 63.2% (SD = 22.9%, min = 22.2%, max = 97.0%). As expected, reproducibility was higher for larger effects and in larger datasets. Reproducibility was not obviously related to the age of participants, scanner field strength, FreeSurfer software version, cortical regional measurement reliability, or regional size. These findings constitute an empirical illustration of reproducibility in the absence of publication bias or p hacking, when assessing realistic biological effects in heterogeneous neuroscience data, and given typically-used sample sizes

The genetic architecture of the human cerebral cortex

INTRODUCTION The cerebral cortex underlies our complex cognitive capabilities. Variations in human cortical surface area and thickness are associated with neurological, psychological, and behavioral traits and can be measured in vivo by magnetic resonance imaging (MRI). Studies in model organisms have identified genes that influence cortical structure, but little is known about common genetic variants that affect human cortical structure. RATIONALE To identify genetic variants associated with human cortical structure at both global and regional levels, we conducted a genome-wide association meta-analysis of brain MRI data from 51,665 individuals across 60 cohorts. We analyzed the surface area and average thickness of the whole cortex and 34 cortical regions with known functional specializations. RESULTS We identified 306 nominally genome-wide significant loci (P < 5 × 10−8) associated with cortical structure in a discovery sample of 33,992 participants of European ancestry. Of the 299 loci for which replication data were available, 241 loci influencing surface area and 14 influencing thickness remained significant after replication, with 199 loci passing multiple testing correction (P < 8.3 × 10−10; 187 influencing surface area and 12 influencing thickness). Common genetic variants explained 34% (SE = 3%) of the variation in total surface area and 26% (SE = 2%) in average thickness; surface area and thickness showed a negative genetic correlation (rG = −0.32, SE = 0.05, P = 6.5 × 10−12), which suggests that genetic influences have opposing effects on surface area and thickness. Bioinformatic analyses showed that total surface area is influenced by genetic variants that alter gene regulatory activity in neural progenitor cells during fetal development. By contrast, average thickness is influenced by active regulatory elements in adult brain samples, which may reflect processes that occur after mid-fetal development, such as myelination, branching, or pruning. When considered together, these results support the radial unit hypothesis that different developmental mechanisms promote surface area expansion and increases in thickness. To identify specific genetic influences on individual cortical regions, we controlled for global measures (total surface area or average thickness) in the regional analyses. After multiple testing correction, we identified 175 loci that influence regional surface area and 10 that influence regional thickness. Loci that affect regional surface area cluster near genes involved in the Wnt signaling pathway, which is known to influence areal identity. We observed significant positive genetic correlations and evidence of bidirectional causation of total surface area with both general cognitive functioning and educational attainment. We found additional positive genetic correlations between total surface area and Parkinson’s disease but did not find evidence of causation. Negative genetic correlations were evident between total surface area and insomnia, attention deficit hyperactivity disorder, depressive symptoms, major depressive disorder, and neuroticism. CONCLUSION This large-scale collaborative work enhances our understanding of the genetic architecture of the human cerebral cortex and its regional patterning. The highly polygenic architecture of the cortex suggests that distinct genes are involved in the development of specific cortical areas. Moreover, we find evidence that brain structure is a key phenotype along the causal pathway that leads from genetic variation to differences in general cognitive function

TRY plant trait database – enhanced coverage and open access

Plant traits—the morphological, anatomical, physiological, biochemical and phenological characteristics of plants—determine how plants respond to environmental factors, affect other trophic levels, and influence ecosystem properties and their benefits and detriments to people. Plant trait data thus represent the basis for a vast area of research spanning from evolutionary biology, community and functional ecology, to biodiversity conservation, ecosystem and landscape management, restoration, biogeography and earth system modelling. Since its foundation in 2007, the TRY database of plant traits has grown continuously. It now provides unprecedented data coverage under an open access data policy and is the main plant trait database used by the research community worldwide. Increasingly, the TRY database also supports new frontiers of trait‐based plant research, including the identification of data gaps and the subsequent mobilization or measurement of new data. To support this development, in this article we evaluate the extent of the trait data compiled in TRY and analyse emerging patterns of data coverage and representativeness. Best species coverage is achieved for categorical traits—almost complete coverage for ‘plant growth form’. However, most traits relevant for ecology and vegetation modelling are characterized by continuous intraspecific variation and trait–environmental relationships. These traits have to be measured on individual plants in their respective environment. Despite unprecedented data coverage, we observe a humbling lack of completeness and representativeness of these continuous traits in many aspects. We, therefore, conclude that reducing data gaps and biases in the TRY database remains a key challenge and requires a coordinated approach to data mobilization and trait measurements. This can only be achieved in collaboration with other initiatives

Risk profiles and one-year outcomes of patients with newly diagnosed atrial fibrillation in India: Insights from the GARFIELD-AF Registry.

BACKGROUND: The Global Anticoagulant Registry in the FIELD-Atrial Fibrillation (GARFIELD-AF) is an ongoing prospective noninterventional registry, which is providing important information on the baseline characteristics, treatment patterns, and 1-year outcomes in patients with newly diagnosed non-valvular atrial fibrillation (NVAF). This report describes data from Indian patients recruited in this registry. METHODS AND RESULTS: A total of 52,014 patients with newly diagnosed AF were enrolled globally; of these, 1388 patients were recruited from 26 sites within India (2012-2016). In India, the mean age was 65.8 years at diagnosis of NVAF. Hypertension was the most prevalent risk factor for AF, present in 68.5% of patients from India and in 76.3% of patients globally (P < 0.001). Diabetes and coronary artery disease (CAD) were prevalent in 36.2% and 28.1% of patients as compared with global prevalence of 22.2% and 21.6%, respectively (P < 0.001 for both). Antiplatelet therapy was the most common antithrombotic treatment in India. With increasing stroke risk, however, patients were more likely to receive oral anticoagulant therapy [mainly vitamin K antagonist (VKA)], but average international normalized ratio (INR) was lower among Indian patients [median INR value 1.6 (interquartile range {IQR}: 1.3-2.3) versus 2.3 (IQR 1.8-2.8) (P < 0.001)]. Compared with other countries, patients from India had markedly higher rates of all-cause mortality [7.68 per 100 person-years (95% confidence interval 6.32-9.35) vs 4.34 (4.16-4.53), P < 0.0001], while rates of stroke/systemic embolism and major bleeding were lower after 1 year of follow-up. CONCLUSION: Compared to previously published registries from India, the GARFIELD-AF registry describes clinical profiles and outcomes in Indian patients with AF of a different etiology. The registry data show that compared to the rest of the world, Indian AF patients are younger in age and have more diabetes and CAD. Patients with a higher stroke risk are more likely to receive anticoagulation therapy with VKA but are underdosed compared with the global average in the GARFIELD-AF. CLINICAL TRIAL REGISTRATION-URL: http://www.clinicaltrials.gov. Unique identifier: NCT01090362

Conceptual Design Report for a Fast Muon Trigger

This document is a Conceptual Design Report for a fast muon trigger for the PHENIX experiment that will enable the study of flavor separated quark and anti-quark spin polarizations in the proton. A powerful way of measuring these polarizations is via single spin asymmetries for W boson production in polarized proton-proton reactions. The measurement is done by tagging W{sup +} and W{sup -} via their decay into high transverse momentum leptons in the forward directions. The PHENIX experiment is capable of measuring high momentum muons at forward rapidity, but the current online trigger does not have sufficient rejection to sample the rare leptons fromW decay at the highest luminosities at the Relativistic Heavy Ion Collider (RHIC). This Report details the goals, design, R&amp;D, and schedule for building new detectors and trigger electronics to use the full RHIC luminosity to make this critical measurement. The idea for W boson measurements in polarized proton-proton collisions at RHIC was first suggested by Jacques Soffer and Claude Bourrely in 1995. This prompted the RIKEN institute in Japan to supply funds to build a second muon arm for PHENIX (south muon arm). The existence of both a north and south muon arm makes it possible to utilize a Z{sup 0} sample to study and control systematic uncertainties which arise in the reconstruction of high momentum muons. This document has its origins in recommendations made by a NSAC Subcommittee that reviewed the U.S. Heavy Ion Physics Program in June 2004. Part of their Recommendation 1 was to 'Invest in near-term detector upgrades of the two large experiments, PHENIX and STAR'. In Recommendation 2 the subcommittee stated '- detector improvements proceed at a rate that allows a timely determination of the flavor dependence of the quark-antiquark sea polarization through W-asymmetry measurements' as we are proposing here. On September 13, 2004 DOE requested from BNL a report articulating a research plan for the RHIC spin physics program. The document was submitted to DOE on January 31, 2005. It pointed out that one of three top priorities for the program lies in the clean and elegant measurement of the quark and anti-quark polarizations sorted by quark flavor through the parity-violating production of W bosons

Novel Loci for Adiponectin Levels and Their Influence on Type 2 Diabetes and Metabolic Traits : A Multi-Ethnic Meta-Analysis of 45,891 Individuals

J. Kaprio, S. Ripatti ja M.-L. Lokki työryhmien jäseniä.Peer reviewe

A Review of Breast Calcifications on Mammography in a Tertiary Health Institution in Nigeria

Background Breast calcifications seen on mammograms may be associated with benign or malignant conditions which require accurate characterization for treatment and screening purposes. This study was undertaken to review mammographic calcifications. Materials and Methods A descriptive study of all mammograms taken in the radiology department of a tertiary institution within an 11 month period in 2009 was done, using a Villa Systemi stereotactic mammography machine and Concept MC Utrasound Scan machine. Biopsies were performed where indicated and histology results were compared with radiological findings. Data was analyzed using the Epi-info statistical software. Results Out of the 248 patients assessed, the predominant presenting symptoms were breast pain (30.2%) and breast lump (27.4%). While assessing the mammograms, various types of calcifications described as skin (17.0%); worm-like (4.3%); coarse (16.0%); popcorn (6.4%); rod like (8.5%); milk (5.3%); rim (4.3%); vascular (20.2%); micro- 12(12.8%); and widespread pleomorphic calcifications (5.3%) were seen. Calcifications were commoner in the lower quadrant and were evenly distributed in the inner and outer quadrants. Histology revealed that all the widespread pleomorphic calcifications and 75% of the micro-calcifications seen were malignant. Conclusion This study confirms that calcifications are commonly seen on mammograms with microand pleomorphic calcifications as common features in malignant breast lesions. Key words: Mammography, breast, calcification

Hepatitis C virus co infection in HIV positive patients

Background: Hepatitis C virus (HCV) co infection is reported common in HIV positive individuals and also responsible for increasing morbidity and mortality among them.Objective: This study was undertaken to determine the prevalence of antibodies to HCV (anti- HCV) among HIV positive patients.Methods: This cross sectional study was carried out among HIV positive patients and HIV negative blood donors.HIV infection was diagnosed in patients using Determine HIV- 1/2 rapid kits and Elisa based immunocombfirm, while Dialab Elisa kits were used for screening blood donors for HIV and also assaying anti HCV in all subjects.Results: Anti-HCV was detected in 14.7% of patients and 1.1% of HIV negative blood donors. .HIV/ HCV co-infection rate was highest in the 30-39years age group (P&gt; 0.05)Conclusion: Findings demonstrate a high prevalence with 13 fold higher risk of   HCV co infection among HIV-positive patientsKeywords: Hepatitis C, HIV, co-infectio