scholarly journals Collaboration and Open Science Initiatives in Primate Research

2021 ◽  
Author(s):  
ManyPrimates ◽  
Alba Motes Rodrigo ◽  
Charlotte Canteloup ◽  
Sonja J. Ebel ◽  
Christopher I Petkov ◽  
...  
Keyword(s):  
Cognitive Abilities ◽  
Large Scale ◽  
Open Science ◽  
Small Sample ◽  
Primate Research ◽  
Research Model ◽  
Primate Cognition ◽  
History Of ◽  
Small Sample Sizes ◽  
Successful Collaboration

Traditionally, primate cognition research has been conducted by independent teams on small populations of a few species. Such limited variation and small sample sizes pose problems that prevent us from reconstructing the evolutionary history of primate cognition. In this chapter, we discuss how large-scale collaboration, a research model successfully implemented in other fields, makes it possible to obtain the large and diverse datasets needed to conduct robust comparative analysis of primate cognitive abilities. We discuss the advantages and challenges of large-scale collaborations and argue for the need for more open science practices in the field. We describe these collaborative projects in psychology and primatology and introduce ManyPrimates as the first, successful collaboration that has established an infrastructure for large-scale, inclusive research in primate cognition. Considering examples of large-scale collaborations both in primatology and psychology, we conclude that this type of research model is feasible and has the potential to address otherwise unattainable questions in primate cognition.

scholarly journals Collaborative open science as a way to reproducibility and new insights in primate cognition research

2019 ◽  
Author(s):  
Many Primates ◽  
Drew Altschul ◽  
Michael J. Beran ◽  
Manuel Bohn ◽  
Kai Caspar ◽  
...  
Keyword(s):  
Large Scale ◽  
Open Science ◽  
Small Sample ◽  
Primate Species ◽  
Primate Cognition ◽  
Research Attention ◽  
Questionable Research Practices ◽  
Wide Range ◽  
Research Questions ◽  
Small Sample Sizes

The field of primate cognition studies how primates, including humans, perceive, process, store, retrieve, and use information to guide decision making and other behavior. Much of this research is motivated by a desire to understand how these abilities evolved. Large and diverse samples from a wide range of species are vital to achieving this goal. In reality, however, primate cognition research suffers from small sample sizes and is often limited to a handful of species, which constrains the evolutionary inferences we can draw. We conducted a systematic review of primate cognition research published between 2014 and 2019 to quantify the extent of this problem. Across 574 studies, the median sample size was 7 individuals. Less than 15% of primate species were studied at all, and only 19% of studies included more than one species. Further, the species that were studied varied widely in how much research attention they received, partly because a small number of test sites contributed most of the studies. These results suggest that the generalizability of primate cognition studies may be severely limited. Publication bias, questionable research practices, and a lack of replication attempts may exacerbate these problems. We describe the ManyPrimates project as one approach to overcoming some of these issues by establishing an infrastructure for large-scale collaboration in primate cognition research. Building on similar initiatives in other areas of psychology, this approach has already yielded one of the largest and most diverse primate samples to date and enables us to ask many research questions that can only be addressed through collaboration.

scholarly journals Use of Antiplatelet Agents Decreases the Positive Predictive Value of Fecal Immunochemical Tests for Colorectal Cancer but Does Not Affect Their Sensitivity

2021 ◽  
Vol 11 (6) ◽  
pp. 497
Author(s):  
Yoonsuk Jung ◽  
Eui Im ◽  
Jinhee Lee ◽  
Hyeah Lee ◽  
Changmo Moon
Keyword(s):  
Colorectal Cancer ◽  
Large Scale ◽  
Screening Program ◽  
Antiplatelet Agents ◽  
Population Based ◽  
Small Sample ◽  
Antithrombotic Agents ◽  
Predictive Values ◽  
Prescription Rates ◽  
Small Sample Sizes

Previous studies have evaluated the effects of antithrombotic agents on the performance of fecal immunochemical tests (FITs) for the detection of colorectal cancer (CRC), but the results were inconsistent and based on small sample sizes. We studied this topic using a large-scale population-based database. Using the Korean National Cancer Screening Program Database, we compared the performance of FITs for CRC detection between users and non-users of antiplatelet agents and warfarin. Non-users were matched according to age and sex. Among 5,426,469 eligible participants, 768,733 used antiplatelet agents (mono/dual/triple therapy, n = 701,683/63,211/3839), and 19,569 used warfarin, while 4,638,167 were non-users. Among antiplatelet agents, aspirin, clopidogrel, and cilostazol ranked first, second, and third, respectively, in terms of prescription rates. Users of antiplatelet agents (3.62% vs. 4.45%; relative risk (RR): 0.83; 95% confidence interval (CI): 0.78–0.88), aspirin (3.66% vs. 4.13%; RR: 0.90; 95% CI: 0.83–0.97), and clopidogrel (3.48% vs. 4.88%; RR: 0.72; 95% CI: 0.61–0.86) had lower positive predictive values (PPVs) for CRC detection than non-users. However, there were no significant differences in PPV between cilostazol vs. non-users and warfarin users vs. non-users. For PPV, the RR (users vs. non-users) for antiplatelet monotherapy was 0.86, while the RRs for dual and triple antiplatelet therapies (excluding cilostazol) were 0.67 and 0.22, respectively. For all antithrombotic agents, the sensitivity for CRC detection was not different between users and non-users. Use of antiplatelet agents, except cilostazol, may increase the false positives without improving the sensitivity of FITs for CRC detection.

scholarly journals Age and sex dependent variability of type 2 dopamine receptors in the human brain: A large-scale PET cohort

2021 ◽  
Author(s):  
Tuulia Malén ◽  
Tomi Karjalainen ◽  
Janne Isojärvi ◽  
Aki Vehtari ◽  
Paul-Christian Bürkner ◽  
...  
Keyword(s):  
Human Brain ◽  
Large Scale ◽  
Movement Control ◽  
Heterogeneous Data ◽  
Small Sample ◽  
Cross Sectional ◽  
Psychiatric Conditions ◽  
Small Sample Sizes ◽  
Age And Sex

BACKGROUND: The dopamine system contributes to a multitude of functions ranging from reward and motivation to learning and movement control, making it a key component in goal-directed behavior. Altered dopaminergic function is observed in neurological and psychiatric conditions. Numerous factors have been proposed to influence dopamine function, but due to small sample sizes and heterogeneous data analysis methods in previous studies their specific and joint contributions remain unresolved. METHODS: In this cross-sectional register-based study we investigated how age, sex, body mass index (BMI), as well as cerebral hemisphere and regional volume influence striatal type 2 dopamine receptor (D2R) availability in the human brain. We analyzed a large historical dataset (n=156, 120 males and 36 females) of [11C]raclopride PET scans performed between 2004 and 2018. RESULTS: Striatal D2R availability decreased through age for both sexes and was higher in females versus males throughout age. BMI and striatal D2R availability were weakly associated. There was no consistent lateralization of striatal D2R. The observed effects were independent of regional volumes. These results were validated using two different spatial normalization methods, and the age and sex effects also replicated in an independent sample (n=135). CONCLUSIONS: D2R density is dependent on age and sex, which may contribute to the vulnerability of neurological and psychiatric conditions involving altering D2R expression.

How Strong Is the Evidence for the Effectiveness of Working Memory Training?

2019 ◽  
pp. 58-76
Author(s):  
Claudia C. von Bastian ◽  
Sabrina Guye ◽  
Carla De Simoni
Keyword(s):  
Working Memory ◽  
Cognitive Abilities ◽  
Small Sample ◽  
Sound Studies ◽  
Working Memory Training ◽  
Memory Training ◽  
Sample Sizes ◽  
Small Sample Sizes ◽  
Transfer Tasks ◽  
Larger Sample

This chapter argues that the question of whether working memory training can induce cognitive plasticity in terms of transfer effects cannot be conclusively answered yet due to persisting methodological issues across the literature. The shortcomings discussed include the lack of theoretically motivated selection of training and transfer tasks, the lack of active control groups, and small sample sizes. These problems call into question the strength of the existing evidence. Indeed, reevaluating published findings with Bayesian inference indicated that only a subset of published studies contributed interpretable evidence. The chapter concludes that the current body of literature cannot conclusively support claims that WM training does or does not improve cognitive abilities and stresses the need for theory-driven, methodologically sound studies with larger sample sizes.

scholarly journals Epigenome-wide meta-analysis of blood DNA methylation and its association with subcortical volumes: findings from the ENIGMA Epigenetics Working Group

2019 ◽  
Author(s):  
Tianye Jia ◽  
Congying Chu ◽  
Yun Liu ◽  
Jenny van Dongen ◽  
Evangelos Papastergios ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Nucleus Accumbens ◽  
Large Scale ◽  
Biomarker Discovery ◽  
Association Studies ◽  
Meta Analysis ◽  
Hippocampal Volume ◽  
Small Sample ◽  
Small Sample Sizes ◽  
Meta Analyses

AbstractDNA methylation, which is modulated by both genetic factors and environmental exposures, may offer a unique opportunity to discover novel biomarkers of disease-related brain phenotypes, even when measured in other tissues than brain, such as blood. A few studies of small sample sizes have revealed associations between blood DNA methylation and neuropsychopathology, however, large-scale epigenome-wide association studies (EWAS) are needed to investigate the utility of DNA methylation profiling as a peripheral marker for the brain. Here, in an analysis of eleven international cohorts, totalling 3337 individuals, we report epigenome-wide meta-analyses of blood DNA methylation with volumes of the hippocampus, thalamus and nucleus accumbens (NAcc)—three subcortical regions selected for their associations with disease and heritability and volumetric variability. Analyses of individual CpGs revealed genome-wide significant associations with hippocampal volume at two loci. No significant associations were found for analyses of thalamus and nucleus accumbens volumes. Cluster-based analyses revealed additional differentially methylated regions (DMRs) associated with hippocampal volume. DNA methylation at these loci affected expression of proximal genes involved in learning and memory, stem cell maintenance and differentiation, fatty acid metabolism and type-2 diabetes. These DNA methylation marks, their interaction with genetic variants and their impact on gene expression offer new insights into the relationship between epigenetic variation and brain structure and may provide the basis for biomarker discovery in neurodegeneration and neuropsychiatric conditions.

A review of the Usambara forest snake Geodipsas vauerocegae and the Uluguru forest snake G. procterae

1995 ◽  
Vol 16 (2) ◽  
pp. 123-136 ◽  
Author(s):  
Mogens Andersen ◽  
Kim M. Howell ◽  
Jens B. Rasmussen
Keyword(s):  
Natural History ◽  
Small Sample ◽  
Sample Sizes ◽  
Geographical Differences ◽  
Udzungwa Mountains ◽  
Uluguru Mountains ◽  
History Of ◽  
Small Sample Sizes

AbstractVariation in external and internal characters of the endemic Tanzanian species Geodipsas vauerocegae and G. procterae have been examined. On the basis of the small sample sizes, no significant geographical differences can be demonstrated. Three recently collected specimens from the Udzungwa Mountains, however, seem to have slightly lower numbers of ventrals than those from the Uluguru Mountains. All available knowledge on the natural history of the species has been summarized.

scholarly journals Defining the biological bases of individual differences in musicality

2015 ◽  
Vol 370 (1664) ◽  
pp. 20140092 ◽  
Author(s):  
Bruno Gingras ◽  
Henkjan Honing ◽  
Isabelle Peretz ◽  
Laurel J. Trainor ◽  
Simon E. Fisher
Keyword(s):  
Large Scale ◽  
Twin Studies ◽  
Small Sample ◽  
Aptitude Tests ◽  
Large Scale Assessment ◽  
Genome Wide ◽  
Entry Points ◽  
High Heritability ◽  
Small Sample Sizes ◽  
Complex Human Traits

Advances in molecular technologies make it possible to pinpoint genomic factors associated with complex human traits. For cognition and behaviour, identification of underlying genes provides new entry points for deciphering the key neurobiological pathways. In the past decade, the search for genetic correlates of musicality has gained traction. Reports have documented familial clustering for different extremes of ability, including amusia and absolute pitch (AP), with twin studies demonstrating high heritability for some music-related skills, such as pitch perception. Certain chromosomal regions have been linked to AP and musical aptitude, while individual candidate genes have been investigated in relation to aptitude and creativity. Most recently, researchers in this field started performing genome-wide association scans. Thus far, studies have been hampered by relatively small sample sizes and limitations in defining components of musicality, including an emphasis on skills that can only be assessed in trained musicians. With opportunities to administer standardized aptitude tests online, systematic large-scale assessment of musical abilities is now feasible, an important step towards high-powered genome-wide screens. Here, we offer a synthesis of existing literatures and outline concrete suggestions for the development of comprehensive operational tools for the analysis of musical phenotypes.

scholarly journals Massive Factorial Design Untangles Coding Sequences Determinants of Translation Efficacy

2017 ◽  
Author(s):  
Guillaume Cambray ◽  
Joao C. Guimaraes ◽  
Adam Paul Arkin
Keyword(s):  
Large Scale ◽  
Small Sample ◽  
Translation Efficiency ◽  
E Coli ◽  
Synthetic Dna ◽  
Critical Design ◽  
Codon Composition ◽  
Expression Activity ◽  
Small Sample Sizes ◽  
Epigenetic Disruption

AbstractComparative analyses of natural sequences or variant libraries are often used to infer mechanisms of expression, activity and evolution. Contingent selective histories and small sample sizes can profoundly bias such approaches. Both limitations can be lifted using precise design of large-scale DNA synthesis. Here, we precisely design 5E. coligenomes worth of synthetic DNA to untangle the relative contributions of 8 interlaced sequence properties described independently as major determinants of translation inEscherichia coli. To expose hierarchical effects, we engineer an inducible translational coupling device enabling epigenetic disruption of mRNA secondary structures. We find that properties commonly believed to modulate translation generally explain less than a third of the variation in protein production. We describe dominant effects of mRNA structures over codon composition on both initiation and elongation, and previously uncharacterized relationships among factors controlling translation. These results advance our understanding of translation efficiency and expose critical design challenges.

Replication Initiatives in Psychology

2018 ◽  
Author(s):  
Jennifer Bastart ◽  
Richard Anthony Klein ◽  
Hans IJzerman
Keyword(s):  
Large Scale ◽  
Behavioral Science ◽  
Scientific Misconduct ◽  
Open Science ◽  
Research Practices ◽  
Critical Function ◽  
Online Tools ◽  
History Of ◽  
Cumulative Knowledge ◽  
The Stability

Replication is one key component towards a robust cumulative knowledge base. It plays a critical function in assessing the stability of the scientific literature. Replication involves closely repeating the procedure of a study and determining if the results are similar to the original. For decades, behavioral scientists were reluctant to publish replications. Reasons were epistemic and pragmatic. First of all, original studies were viewed as conclusive in most cases, and failures to replicate were often attributed to mistakes by the replicating researcher. In addition, failures to replicate may be caused by numerous factors. This inherent ambiguity made replications less desirable to journals. On the other hand, replication successes were expected and considered to contribute little beyond what was already known. Finally, editorial policies did not encourage the publication of replications, leaving the robustness of scientific findings largely unreported. A series of events ultimately led the research community to reconsider replication and research practices at large: the discovery of several cases of large-scale scientific misconduct (i.e., fraud), the invention and/or application of new statistical tools to assess strength of evidence, high-profile publications suggesting that some common practices may be less robust than previously assumed, failure to replicate some major findings of the field, and the creation of new, online tools aimed to promote transparency in the field. To deal with what is often regarded as the crisis of confidence, initiatives have been developed to increase the transparency of research practices, including (but not limited to) pre-registration of studies, effect size predictions and sample size/power estimation, and, of course, replications. Replication projects themselves evolved in quality: From replications that were originally as small in sample as problematically small original studies to large-scale “Many Labs” collaborative projects. Ultimately, the development of higher quality replication projects and open science tools has led (and will continue to lead) to a clearer understanding of human behavior and cognition and have contributed to a clearer distinction between exploratory and confirmatory behavioral science. The current bibliography gives an overview of the history of replications, of the development of tools and guidelines, and of review papers discussing theoretical implications of replications.

Bariatric Surgery in Patients With Inflammatory Bowel Disease: A Case-Control Study from the GETAID

2021 ◽  
Author(s):  
Catherine Reenaers ◽  
Arnaud de Roover ◽  
Laurent Kohnen ◽  
Maria Nachury ◽  
Marion Simon ◽  
...  
Keyword(s):  
Bariatric Surgery ◽  
Inflammatory Bowel Disease ◽  
Weight Loss ◽  
Bowel Disease ◽  
Small Sample ◽  
Control Group ◽  
Prevalence Of Obesity ◽  
History Of ◽  
Inflammatory Bowel ◽  
Small Sample Sizes

Abstract Background The prevalence of obesity and the number of bariatric surgeries in both the general population and in patients with inflammatory bowel disease (IBD) have increased significantly in recent years. Due to small sample sizes and the lack of adequate controls, no definite conclusions can be drawn from the available studies on the safety and efficacy of bariatric surgery (BS) in patients with IBD. Our aim was to assess safety, weight loss, and deficiencies in patients with IBD and obesity who underwent BS and compare findings to a control group. Methods Patients with IBD and a history of BS were retrospectively recruited to centers belonging to the Groupe d’Etude Thérapeutique des Affections Inflammatoires du Tube Digestif (GETAID). Patients were matched 1:2 for age, sex, body mass index (BMI), hospital of surgery, and type of BS with non-IBD patients who underwent BS. Complications, rehospitalizations, weight, and deficiencies after BS were collected in cases and controls. Results We included 88 procedures in 85 patients (64 Crohn’s disease, 20 ulcerative colitis, 1 unclassified IBD) with a mean BMI of 41.6 ± 5.9 kg/m2. Bariatric surgery included Roux-en-Y gastric bypass (n = 3), sleeve gastrectomy (n = 73), and gastric banding (n = 12). Eight (9%) complications were reported, including 4 (5%) requiring surgery. At a mean follow-up of 34 months, mean weight was 88.6 ± 22.4 kg. No difference was observed between cases and controls for postoperative complications (P = .31), proportion of weight loss (P = .27), or postoperative deficiencies (P = .99). Conclusions Bariatric surgery is a safe and effective procedure in patients with IBD and obesity; outcomes in this patient group were similar to those observed in a control population.

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