scholarly journals Genetic and Transcriptomic Biomarkers in Neurodegenerative Diseases: Current Situation and the Road Ahead

Cells ◽  
2021 ◽  
Vol 10 (5) ◽  
pp. 1030
Author(s):  
Julie Lake ◽  
Catherine S. Storm ◽  
Mary B. Makarious ◽  
Sara Bandres-Ciga
Keyword(s):  
Neurodegenerative Diseases ◽  
Large Scale ◽  
Disease Diagnosis ◽  
Open Science ◽  
Future Directions ◽  
The Road ◽  
Current State ◽  
Molecular Complexity ◽  
Science Framework ◽  
Lateral Sclerosis

Neurodegenerative diseases are etiologically and clinically heterogeneous conditions, often reflecting a spectrum of disease rather than well-defined disorders. The underlying molecular complexity of these diseases has made the discovery and validation of useful biomarkers challenging. The search of characteristic genetic and transcriptomic indicators for preclinical disease diagnosis, prognosis, or subtyping is an area of ongoing effort and interest. The next generation of biomarker studies holds promise by implementing meaningful longitudinal and multi-modal approaches in large scale biobank and healthcare system scale datasets. This work will only be possible in an open science framework. This review summarizes the current state of genetic and transcriptomic biomarkers in Parkinson’s disease, Alzheimer’s disease, and amyotrophic lateral sclerosis, providing a comprehensive landscape of recent literature and future directions.

scholarly journals ManyBirds: A multi-site collaborative Open Science approach to avian cognition and behaviour research

2021 ◽  
Author(s):  
Megan Lambert ◽  
Benjamin George Farrar ◽  
Elias Garcia-Pelegrin ◽  
Stephan A. Reber ◽  
Rachael Miller
Keyword(s):  
Comparative Studies ◽  
Convergent Evolution ◽  
Large Scale ◽  
Open Science ◽  
Future Directions ◽  
Avian Cognition ◽  
Current State ◽  
Science Approach ◽  
Insight Into ◽  
Representative Samples

Comparative cognitive and behaviour research aims to investigate cognitive evolution by comparing performance in different species to understand how these abilities have evolved. Ideally, this requires large and diverse samples, however, these can be difficult to obtain by single labs or institutions, leading to potential reproducibility and generalisation issues with small, less representative samples. To help mitigate these issues, we are establishing a multi-site collaborative Open Science approach called ManyBirds, with the aim of providing new insight into the evolution of avian cognition and behaviour through large-scale comparative studies, following the lead of exemplary ManyPrimates, ManyBabies and ManyDogs projects. Here, we outline a) why we should study birds, including the origin of modern birds, avian brains, convergent evolution of cognition, and the replicability crisis; b) the current state of the avian cognition field, including a ‘snapshot’ review; c) the ManyBirds project, with plans, infrastructure, limitations, implications and future directions. In sharing this process, we hope that this may be useful for other researchers in devising similar projects in other taxa, like non-avian reptiles or mammals, and to encourage further collaborations with ManyBirds and related ManyX projects. Ultimately, we hope to promote collaboration between ManyX projects to allow for wider investigation of the evolution of cognition across all animals, including potentially humans.

ATP-binding cassette transporters and neurodegenerative diseases

2021 ◽  
Author(s):  
Jared S. Katzeff ◽  
Woojin Scott Kim
Keyword(s):  
Neurodegenerative Diseases ◽  
Abc Transporters ◽  
Brain Diseases ◽  
Atp Binding ◽  
Future Directions ◽  
Diverse Range ◽  
The Brain ◽  
Lateral Sclerosis ◽  
Atp Binding Cassette

Abstract ATP-binding cassette (ABC) transporters are one of the largest groups of transporter families in humans. ABC transporters mediate the translocation of a diverse range of substrates across cellular membranes, including amino acids, nucleosides, lipids, sugars and xenobiotics. Neurodegenerative diseases are a group of brain diseases that detrimentally affect neurons and other brain cells and are usually associated with deposits of pathogenic proteins in the brain. Major neurodegenerative diseases include Alzheimer’s disease, Parkinson’s disease and amyotrophic lateral sclerosis. ABC transporters are highly expressed in the brain and have been implicated in a number of pathological processes underlying neurodegenerative diseases. This review outlines the current understanding of the role of ABC transporters in neurodegenerative diseases, focusing on some of the most important pathways, and also suggests future directions for research in this field.

scholarly journals The Role of Trust in the Social Heuristics Hypothesis

2018 ◽  
Author(s):  
Andres Montealegre ◽  
William Jimenez-Leal
Keyword(s):  
Statistical Power ◽  
Open Science ◽  
Equivalence Testing ◽  
Future Directions ◽  
Online Study ◽  
The United Kingdom ◽  
Null Result ◽  
The Social ◽  
Science Framework

According to the social heuristics hypothesis, people intuitively cooperate or defect depending on which behavior is beneficial in their interactions. If cooperation is beneficial, people intuitively cooperate, but if defection is beneficial, they intuitively defect. However, deliberation promotes defection. Here, we tested two novel predictions regarding the role of trust in the social heuristics hypothesis. First, whether trust promotes intuitive cooperation. Second, whether preferring to think intuitively or deliberatively moderates the effect of trust on cooperation. In addition, we examined whether deciding intuitively promotes cooperation, compared to deciding deliberatively. To evaluate these predictions, we conducted a lab study in Colombia and an online study in the United Kingdom (N = 1,066; one study was pre-registered). Unexpectedly, higher trust failed to promote intuitive cooperation, though higher trust promoted cooperation. In addition, preferring to think intuitively or deliberatively failed to moderate the effect of trust on cooperation, although preferring to think intuitively increased cooperation. Moreover, deciding intuitively failed to promote cooperation, and equivalence testing confirmed that this null result was explained by the absence of an effect, rather than a lack of statistical power (equivalence bounds: d = -0.26 and 0.26). An intuitive cooperation effect emerged when non-compliant participants were excluded, but this effect could be due to selection biases. Taken together, most results failed to support the social heuristics hypothesis. We conclude by discussing implications, future directions, and limitations. The materials, data, and code are available on the Open Science Framework (https://osf.io/939jv/).

scholarly journals Peripheral Glycolysis in Neurodegenerative Diseases

2020 ◽  
Vol 21 (23) ◽  
pp. 8924 ◽  
Author(s):  
Simon M. Bell ◽  
Toby Burgess ◽  
James Lee ◽  
Daniel J. Blackburn ◽  
Scott P. Allen ◽  
...  
Keyword(s):  
Nervous System ◽  
Neurodegenerative Diseases ◽  
Neurodegenerative Disease ◽  
Blood Cells ◽  
Large Scale ◽  
White Blood Cells ◽  
Peripheral Cells ◽  
Multiple Patients ◽  
Brain And Spinal Cord ◽  
Lateral Sclerosis

Neurodegenerative diseases are a group of nervous system conditions characterised pathologically by the abnormal deposition of protein throughout the brain and spinal cord. One common pathophysiological change seen in all neurodegenerative disease is a change to the metabolic function of nervous system and peripheral cells. Glycolysis is the conversion of glucose to pyruvate or lactate which results in the generation of ATP and has been shown to be abnormal in peripheral cells in Alzheimer’s disease, Parkinson’s disease, and Amyotrophic Lateral Sclerosis. Changes to the glycolytic pathway are seen early in neurodegenerative disease and highlight how in multiple neurodegenerative conditions pathology is not always confined to the nervous system. In this paper, we review the abnormalities described in glycolysis in the three most common neurodegenerative diseases. We show that in all three diseases glycolytic changes are seen in fibroblasts, and red blood cells, and that liver, kidney, muscle and white blood cells have abnormal glycolysis in certain diseases. We highlight there is potential for peripheral glycolysis to be developed into multiple types of disease biomarker, but large-scale bio sampling and deciphering how glycolysis is inherently altered in neurodegenerative disease in multiple patients’ needs to be accomplished first to meet this aim.

scholarly journals Ritual, Identity Fusion, and the Inauguration of President Trump: A pseudo-experiment of Ritual Modes theory

2018 ◽  
Author(s):  
Rohan Kapitány ◽  
Christopher Michael Kavanagh ◽  
Michael Buhrmester ◽  
Martha Newson ◽  
Harvey Whitehouse
Keyword(s):  
Large Scale ◽  
Emotional Responses ◽  
Open Science ◽  
Social Identities ◽  
Self Reflection ◽  
The Us ◽  
Identity Fusion ◽  
Science Framework ◽  
Fusion Theory ◽  
Diverse Groups

The US Presidential Inauguration is a symbolic event which arouses significant emotional responses among diverse groups, and is of considerable significance to Americans’ personal and social identities. We argue that the inauguration qualifies as an Imagistic Ritual (Whitehouse, 2004). Such ritual experiences are thought to produce identity fusion: a visceral sense of oneness with the group. The 2017 Inauguration of President Trump was a unique opportunity to examine how a large-scale naturalistic imagistic ritual influences the social identities of Americans who supported and opposed President Trump. We conducted a pre-registered 7-week longitudinal investigation among an online sample of Americans in order to examine how President Trump’s Inauguration influenced identity fusion. One core prediction was that the affective responses to the inauguration would predict positive changes in fusion, mediated by self-reflection. We did not find support for this. However, the inauguration was associated with flashbulb-like memories, and positive emotional response at the time of the event predicted changes in fusion to both ingroup and outgroup targets. Finally, both positive and negative emotional responses inspired self-reflection, but did not mediate the relationship with fusion. We discuss the implications of our findings for models linking group psychology, fusion theory, and ritual modes. All material available at the Open Science Framework: https://bit.ly/2Qu0G37.

scholarly journals Proteotoxicity and Neurodegenerative Diseases

2020 ◽  
Vol 21 (16) ◽  
pp. 5646 ◽  
Author(s):  
Clara Ruz ◽  
Jose Luis Alcantud ◽  
Francisco Vives Montero ◽  
Raquel Duran ◽  
Sara Bandres-Ciga
Keyword(s):  
Neurodegenerative Diseases ◽  
Recent Literature ◽  
Driving Forces ◽  
Biological Complexity ◽  
Disease Etiology ◽  
Current State ◽  
Daunting Challenge ◽  
Cell Proteome ◽  
Essential Insight ◽  
Lateral Sclerosis

Neurodegenerative diseases are a major burden for our society, affecting millions of people worldwide. A main goal of past and current research is to enhance our understanding of the mechanisms underlying proteotoxicity, a common theme among these incurable and debilitating conditions. Cell proteome alteration is considered to be one of the main driving forces that triggers neurodegeneration, and unraveling the biological complexity behind the affected molecular pathways constitutes a daunting challenge. This review summarizes the current state on key processes that lead to cellular proteotoxicity in Alzheimer’s disease, Parkinson’s disease, Huntington’s disease, and amyotrophic lateral sclerosis, providing a comprehensive landscape of recent literature. A foundational understanding of how proteotoxicity affects disease etiology and progression may provide essential insight towards potential targets amenable of therapeutic intervention.

scholarly journals Presence-only and Presence-absence Data for Comparing Species Distribution Modeling Methods

2020 ◽  
Vol 15 (2) ◽  
pp. 69-80
Author(s):  
Jane Elith ◽  
Catherine Graham ◽  
Roozbeh Valavi ◽  
Meinrad Abegg ◽  
Caroline Bruce ◽  
...  
Keyword(s):  
Species Distribution ◽  
Large Scale ◽  
R Package ◽  
Open Science ◽  
Species Occurrence ◽  
Distribution Models ◽  
Algorithm Performance ◽  
Modeling Methods ◽  
Science Framework ◽  
Occurrence Records

Species distribution models (SDMs) are widely used to predict and study distributions of species. Many different modeling methods and associated algorithms are used and continue to emerge. It is important to understand how different approaches perform, particularly when applied to species occurrence records that were not gathered in struc­tured surveys (e.g. opportunistic records). This need motivated a large-scale, collaborative effort, published in 2006, that aimed to create objective comparisons of algorithm performance. As a benchmark, and to facilitate future comparisons of approaches, here we publish that dataset: point location records for 226 anonymized species from six regions of the world, with accompanying predictor variables in raster (grid) and point formats. A particularly interesting characteristic of this dataset is that independent presence-absence survey data are available for evaluation alongside the presence-only species occurrence data intended for modeling. The dataset is available on Open Science Framework and as an R package and can be used as a benchmark for modeling approaches and for testing new ways to evaluate the accuracy of SDMs.

scholarly journals Comprehensive Literature Review of Hyperpolarized Carbon-13 MRI: The Road to Clinical Application

Metabolites ◽  
2021 ◽  
Vol 11 (4) ◽  
pp. 219
Author(s):  
Michael Vaeggemose ◽  
Rolf F. Schulte ◽  
Christoffer Laustsen
Keyword(s):  
Literature Review ◽  
Clinical Application ◽  
Clinical Applications ◽  
Metabolic Imaging ◽  
Limiting Factor ◽  
Future Directions ◽  
The Road ◽  
Current State ◽  
Comprehensive Literature Review ◽  
The Status

This review provides a comprehensive assessment of the development of hyperpolarized (HP) carbon-13 metabolic MRI from the early days to the present with a focus on clinical applications. The status and upcoming challenges of translating HP carbon-13 into clinical application are reviewed, along with the complexity, technical advancements, and future directions. The road to clinical application is discussed regarding clinical needs and technological advancements, highlighting the most recent successes of metabolic imaging with hyperpolarized carbon-13 MRI. Given the current state of hyperpolarized carbon-13 MRI, the conclusion of this review is that the workflow for hyperpolarized carbon-13 MRI is the limiting factor.

scholarly journals OpenWorm: overview and recent advances in integrative biological simulation of Caenorhabditis elegans

2018 ◽  
Vol 373 (1758) ◽  
pp. 20170382 ◽  
Author(s):  
Gopal P. Sarma ◽  
Chee Wai Lee ◽  
Tom Portegys ◽  
Vahid Ghayoomie ◽  
Travis Jacobs ◽  
...  
Keyword(s):  
Caenorhabditis Elegans ◽  
Large Scale ◽  
Management Practices ◽  
Open Science ◽  
Independent Research ◽  
Future Directions ◽  
C Elegans ◽  
Science Management ◽  
Fundamental Biology ◽  
Biological Simulation

The adoption of powerful software tools and computational methods from the software industry by the scientific research community has resulted in a renewed interest in integrative, large-scale biological simulations. These typically involve the development of computational platforms to combine diverse, process-specific models into a coherent whole. The OpenWorm Foundation is an independent research organization working towards an integrative simulation of the nematode Caenorhabditis elegans , with the aim of providing a powerful new tool to understand how the organism's behaviour arises from its fundamental biology. In this perspective, we give an overview of the history and philosophy of OpenWorm, descriptions of the constituent sub-projects and corresponding open-science management practices, and discuss current achievements of the project and future directions. This article is part of a discussion meeting issue ‘Connectome to behaviour: modelling C. elegans at cellular resolution’.

scholarly journals Attention control: The missing link between sensory discrimination and intelligence

2020 ◽  
Author(s):  
Jason S. Tsukahara ◽  
Tyler L. Harrison ◽  
Christopher Draheim ◽  
Jessie Martin ◽  
Randall W Engle
Keyword(s):  
Cognitive Abilities ◽  
Structural Equation ◽  
Large Scale ◽  
Intelligence Testing ◽  
Working Memory Capacity ◽  
Open Science ◽  
Attention Control ◽  
Sensory Discrimination ◽  
Modelling Studies ◽  
Science Framework

Intelligence is correlated with the ability to make fine sensory discriminations. Although this relationship has been known since the beginning of intelligence testing, the mechanisms underlying this relationship are still unknown. In two large-scale structural equation modelling studies, we investigated whether individual differences in attention control abilities can explain the relationship between sensory discrimination and intelligence. Across the two studies, we replicated the finding that attention control fully mediated the relationships of intelligence/working memory capacity to sensory discrimination. Our findings show that attention control plays a prominent role in relating sensory discrimination to higher-order cognitive abilities. [Data, analysis scripts, and results output are available via the Open Science Framework: https://osf.io/hsqru/]

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