Essential guidelines for computational method benchmarking

In computational biology and other sciences, researchers are frequently faced with a choice between several computational methods for performing data analyses. Benchmarking studies aim to rigorously compare the performance of different methods using well-characterized benchmark datasets, to determine the strengths of each method or to provide recommendations regarding suitable choices of methods for an analysis. However, benchmarking studies must be carefully designed and implemented to provide accurate, unbiased, and informative results. Here, we summarize key practical guidelines and recommendations for performing high-quality benchmarking analyses, based on our experiences in computational biology.Comment: Minor update

Essential guidelines for computational method benchmarking

In computational biology and other sciences, researchers are frequently faced with a choice between several computational methods for performing data analyses. Benchmarking studies aim to rigorously compare the performance of different methods using well-characterized benchmark datasets, to determine the strengths of each method or to provide recommendations regarding suitable choices of methods for an analysis. However, benchmarking studies must be carefully designed and implemented to provide accurate, unbiased, and informative results. Here, we summarize key practical guidelines and recommendations for performing high-quality benchmarking analyses, based on our experiences in computational biology

Provenance of Eocene river sediments from the central northern Sierra Nevada and implications for paleotopography

Geochronology of fluvial deposits can be used to characterize provenance, the paleotopography of sediment source regions, and the development of regional drainage systems. We present U-Pb and (U-Th)/He ages of detrital zircon grains from Eocene gravels preserved in several paleoriver systems along the western flank of the central and northern Sierra Nevada. These ages allow us to trace the sourcing of detritus in paleorivers and to constrain the evolution of the Sierra Nevada range front. U-Pb zircon age distributions are bimodal, with a dominant peak between 110 and 95 Ma and smaller but significant peaks in the Middle to Late Jurassic, matching the predominant ages of the Sierra Nevada batholith. A small fraction (<6%) of grains has pre-Mesozoic ages, which consistently match ages from prebatholithic assemblages within the northern part of the range. (U-Th)/He ages of a subset of double-dated zircons cluster between 114 and 74 Ma and are consistent with batholithic (U-Th)/He cooling ages in the northern Sierra. Our results indicate that the Eocene river systems in the central northern Sierra Nevada likely had proximal headwaters and had relatively steep axial gradients, draining smaller areas than was commonly thought. This also suggests that the northern Sierra Nevada would have had an established drainage divide and would have acted as a major topographic barrier during the early to mid-Cenozoic. The data presented here support a model of the Eocene northern Sierra Nevada characterized by a western slope with a gradient broadly similar to that of today

The effect of social devaluation, labelling and familiarity on children's attitudes and behavioural intentions towards a peer with symptoms of ADHD

The present study examined the attitudes and behavioural intentions of 336 children aged 7-11 towards a hypothetical peer with symptoms of ADHD to determine whether they were influenced by labelling, social devaluation or familiarity. Children read one of five vignettes describing the behaviour of a gender-neutral peer before completing self-report measures of attitudes and behavioural intentions. Results showed children held predominantly negative attitudes towards the hypothetical peer, which were more pronounced for inattentive than hyperactive/impulsive symptoms. These findings suggest that children were more likely to devalue internalising rather than externalising behaviours. Children also reported being more likely to engage in active/recreational and social activities rather than academic activities. In addition, the diagnostic label ‘ADHD’ led to more negative attitudes and behavioural intentions, while knowing someone with ADHD mediated the negative effect of hyperactive/impulsive symptoms on attitudes and behavioural intentions. Finally, significant positive relationships were found between attitudes and children’s willingness to engage in social, academic and physical activities. Policy and practice implications of these findings are discussed

Distribution and drivers of marine isoprene concentration across the Southern Ocean

© 2020 by the authors. Isoprene is a biogenic trace gas produced by terrestrial vegetation and marine phytoplankton. In the remote oceans, where secondary aerosols are mostly biogenic, marine isoprene emissions affect atmospheric chemistry and influence cloud formation and brightness. Here, we present the first compilation of new and published measurements of isoprene concentrations in the Southern Ocean and explore their distribution patterns. Surface ocean isoprene concentrations in November through April span 1 to 94 pM. A band of higher concentrations is observed around a latitude of ≈40° S and a surface sea temperature of 15 °C. High isoprene also occurs in high productivity waters near islands and continental coasts. We use concurrent measurements of physical, chemical, and biological variables to explore the main potential drivers of isoprene concentration by means of paired regressions and multivariate analysis. Isoprene is best explained by phytoplankton-related variables like the concentrations of chlorophyll-a, photoprotective pigments and particulate organic matter, photosynthetic efficiency (influenced by iron availability), and the chlorophyll-a shares of most phytoplankton groups, and not by macronutrients or bacterial abundance. A simple statistical model based on chlorophyll-a concentration and a sea surface temperature discontinuity accounts for half of the variance of isoprene concentrations in surface waters of the Southern Ocean

The characteristics of cognitive neuroscience tests in a schizophrenia cognition clinical trial: Psychometric properties and correlations with standard measures.

In comparison to batteries of standard neuropsychological tests, cognitive neuroscience tests may offer a more specific assessment of discrete neurobiological processes that may be aberrant in schizophrenia. However, more information regarding psychometric properties and correlations with standard neuropsychological tests and functional measures is warranted to establish their validity as treatment outcome measures. The N-back and AX-Continuous Performance Task (AX-CPT) are two promising cognitive neuroscience tests designed to measure specific components of working memory and contextual processing respectively. In the current study, we report the psychometric properties of multiple outcome measures from these two tests as well as their correlations with standard neuropsychological measures and functional capacity measures. The results suggest that while the AX-CPT and N-back display favorable psychometric properties, they do not exhibit greater sensitivity or specificity with functional measures than standard neurocognitive tests

Careless Responding in Online Studies is Associated With Alcohol Use: A Mega-Analysis

Objective: The prevalence of research conducted online in the addiction field has increased rapidly over the past decade. However, little focus has been given to careless responding in these online studies, despite the issues it may cause for statistical inference and generalizability. Our aim was to examine whether alcohol use is associated with careless responses. Method: Raw data were requested from online studies examining alcohol use and related problems which also addressed careless responding. We obtained 13 data sets of 12,237 participants (Mage = 42.16, SD = 15.65, 50.5% female). The sample had an average Alcohol Use Disorders Identification Test (AUDIT) score of 10.88 (SD = 7.77). Predictors included demographic information (age, gender) and AUDIT total scores. The primary outcome was whether an individual was classed as a careless responder, for example, by failing an explicit attention check question. Results: AUDIT total scores were associated with careless responding (OR = 1.07, 95% CI [1.06, 1.08], p < .001). Hazardous drinking or worse was associated with 2.21 greater odds (OR = 2.21, 95% CI [1.81, 2.71] of careless responding, whereas harmful drinking or worse was associated with 3.43 greater odds (OR = 3.43, 95% CI [2.83, 4.17]) and probable dependence was associated with 3.63 greater odds (OR = 3.63, 95% CI [2.95, 4.48]). Conclusions: Alcohol use and related problems are positively associated with careless responding in online research. Removal of individuals identified as careless responders may lead to issues of generalizability, and more care should be taken to identify and handle careless responder data

Statistical methodologies to pool across multiple intervention studies

Combining and analyzing data from heterogeneous randomized controlled trials of complex multiple-component intervention studies, or discussing them in a systematic review, is not straightforward. The present article describes certain issues to be considered when combining data across studies, based on discussions in an NIH-sponsored workshop on pooling issues across studies in consortia (see Belle et al. in Psychol Aging, 18(3):396-405, 2003). Several statistical methodologies are described and their advantages and limitations are explored. Whether weighting the different studies data differently, or via employing random effects, one must recognize that different pooling methodologies may yield different results. Pooling can be used for comprehensive exploratory analyses of data from RCTs and should not be viewed as replacing the standard analysis plan for each study. Pooling may help to identify intervention components that may be more effective especially for subsets of participants with certain behavioral characteristics. Pooling, when supported by statistical tests, can allow exploratory investigation of potential hypotheses and for the design of future interventions

Acute phenylalanine/tyrosine depletion of phasic dopamine in the rat brain

Dopamine plays a critical role in striatal and cortical function, and depletion of the dopamine precursors phenylalanine and tyrosine is used in humans to temporarily reduce dopamine and probe the role of dopamine in behavior. This method has been shown to alter addiction-related behaviors and cognitive functioning presumably by reducing dopamine transmission, but it is unclear what specific aspects of dopamine transmission are altered

Prescription of reninâ angiotensinâ aldosterone system inhibitors (RAASi) and its determinants in patients with advanced CKD under nephrologist care

Reninâ angiotensinâ aldosterone system inhibitors (RAASi) are recommended for chronic kidney disease (CKD) patients. In this study, we describe RAASi prescription patterns in the Chronic Kidney Disease Outcomes and Practice Patterns Study (CKDopps) in Brazil, Germany, France, and the United States (US). 5870 patients (mean age 66â 72 years; congestive heart failure [CHF] in 11%â 19%; diabetes in 43%â 54%; serum potassium â ¥5 in 20%â 35%) were included. RAASi prescription was more common in Germany (80%) and France (77%) than Brazil (66%) and the United States (52%), where the prevalence of prescription decreases particularly in patients with CKD stage 5. In the multivariable regression model, RAASi prescription was least common in the United States and more common in patients who were younger, had diabetes, hypertension, or less advanced CKD. In conclusion, RAASi prescription patterns vary by country, and by demographic and clinical characteristics. RAASi appear to be underused, even among patients with strong classâ specific recommendations. Although the reasons for this variation could not be fully identified in this crossâ sectional observation, our data indicate that the risk of hyperkalemia may contribute to the underuse of this class of agents in moderate to advanced CKD.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/150590/1/jch13563.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/150590/2/jch13563_am.pd