Publications by authors named "Matt Jones"

70 Publications

Relationships between community composition, productivity and invasion resistance in semi-natural bacterial microcosms.

Elife 2021 Oct 18;10. Epub 2021 Oct 18.

Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, United Kingdom.

Common garden experiments that inoculate a standardised growth medium with synthetic microbial communities (i.e. constructed from individual isolates or using dilution cultures) suggest that the ability of the community to resist invasions by additional microbial taxa can be predicted by the overall community productivity (broadly defined as cumulative cell density and/or growth rate). However, to the best of our knowledge, no common garden study has yet investigated the relationship between microbial community composition and invasion resistance in microcosms whose compositional differences reflect natural, rather than laboratory-designed, variation. We conducted experimental invasions of two bacterial strains ( and ) into laboratory microcosms inoculated with 680 different mixtures of bacteria derived from naturally occurring microbial communities collected in the field. Using 16S rRNA gene amplicon sequencing to characterise microcosm starting composition, and high-throughput assays of community phenotypes including productivity and invader survival, we determined that productivity is a key predictor of invasion resistance in natural microbial communities, substantially mediating the effect of composition on invasion resistance. The results suggest that similar general principles govern invasion in artificial and natural communities, and that factors affecting resident community productivity should be a focal point for future microbial invasion experiments.
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http://dx.doi.org/10.7554/eLife.71811DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8523168PMC
October 2021

Learning offline: memory replay in biological and artificial reinforcement learning.

Trends Neurosci 2021 10 1;44(10):808-821. Epub 2021 Sep 1.

Department of Engineering Mathematics and Bristol Robotics Laboratory, University of Bristol, Bristol, UK.

Learning to act in an environment to maximise rewards is among the brain's key functions. This process has often been conceptualised within the framework of reinforcement learning, which has also gained prominence in machine learning and artificial intelligence (AI) as a way to optimise decision making. A common aspect of both biological and machine reinforcement learning is the reactivation of previously experienced episodes, referred to as replay. Replay is important for memory consolidation in biological neural networks and is key to stabilising learning in deep neural networks. Here, we review recent developments concerning the functional roles of replay in the fields of neuroscience and AI. Complementary progress suggests how replay might support learning processes, including generalisation and continual learning, affording opportunities to transfer knowledge across the two fields to advance the understanding of biological and artificial learning and memory.
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http://dx.doi.org/10.1016/j.tins.2021.07.007DOI Listing
October 2021

Single-objective selective-volume illumination microscopy enables high-contrast light-field imaging.

Opt Lett 2021 Jun;46(12):2860-2863

The performance of light-field microscopy is improved by selectively illuminating the relevant subvolume of the specimen with a second objective lens. Here we advance this approach to a single-objective geometry, using an oblique one-photon illumination path or two-photon illumination to accomplish selective-volume excitation. The elimination of the second orthogonally oriented objective to selectively excite the volume of interest simplifies specimen mounting; yet, this single-objective approach still reduces the out-of-volume background, resulting in improvements in image contrast, effective resolution, and volume reconstruction quality. We validate our new, to the best of our knowledge, approach through imaging live developing zebrafish, demonstrating the technology's ability to capture imaging data from large volumes synchronously with high contrast while remaining compatible with standard microscope sample mounting.
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http://dx.doi.org/10.1364/OL.413849DOI Listing
June 2021

Anti-bias training for (sc)RNA-seq: experimental and computational approaches to improve precision.

Brief Bioinform 2021 May 6. Epub 2021 May 6.

University of Warwick, CV4 7AL Coventry, UK.

RNA-seq, including single cell RNA-seq (scRNA-seq), is plagued by insufficient sensitivity and lack of precision. As a result, the full potential of (sc)RNA-seq is limited. Major factors in this respect are the presence of global bias in most datasets, which affects detection and quantitation of RNA in a length-dependent fashion. In particular, scRNA-seq is affected by technical noise and a high rate of dropouts, where the vast majority of original transcripts is not converted into sequencing reads. We discuss these biases origins and implications, bioinformatics approaches to correct for them, and how biases can be exploited to infer characteristics of the sample preparation process, which in turn can be used to improve library preparation.
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http://dx.doi.org/10.1093/bib/bbab148DOI Listing
May 2021

3 -5 crosstalk contributes to transcriptional bursting.

Genome Biol 2021 02 4;22(1):56. Epub 2021 Feb 4.

School of Life Sciences, University of Warwick, Coventry, UK.

Background: Transcription in mammalian cells is a complex stochastic process involving shuttling of polymerase between genes and phase-separated liquid condensates. It occurs in bursts, which results in vastly different numbers of an mRNA species in isogenic cell populations. Several factors contributing to transcriptional bursting have been identified, usually classified as intrinsic, in other words local to single genes, or extrinsic, relating to the macroscopic state of the cell. However, some possible contributors have not been explored yet. Here, we focus on processes at the 3 and 5 ends of a gene that enable reinitiation of transcription upon termination.

Results: Using Bayesian methodology, we measure the transcriptional bursting in inducible transgenes, showing that perturbation of polymerase shuttling typically reduces burst size, increases burst frequency, and thus limits transcriptional noise. Analysis based on paired-end tag sequencing (PolII ChIA-PET) suggests that this effect is genome wide. The observed noise patterns are also reproduced by a generative model that captures major characteristics of the polymerase flux between the ends of a gene and a phase-separated compartment.

Conclusions: Interactions between the 3 and 5 ends of a gene, which facilitate polymerase recycling, are major contributors to transcriptional noise.
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http://dx.doi.org/10.1186/s13059-020-02227-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7860045PMC
February 2021

Computational Modeling of Attentional Impairments in Disruptive Mood Dysregulation and Attention-Deficit/Hyperactivity Disorder.

J Am Acad Child Adolesc Psychiatry 2021 05 24;60(5):637-645. Epub 2020 Nov 24.

National Institute of Mental Health, Bethesda, Maryland.

Objective: Computational models provide information about cognitive components underlying behavior. When applied to psychopathology-relevant processes, they offer additional insight to observed differences in behavioral performance. Drift diffusion models have been successfully applied to investigate processing efficiency during binary choice tasks. Using these models, we examine the association between psychopathology (irritability and inattention/hyperactivity) and processing efficiency under different attentional demands.

Method: A total of 187 youths with attention-deficit/hyperactivity disorder (ADHD), disruptive mood dysregulation disorder (DMDD), both disorders, or no major psychopathology (age, mean ± SD, 13.09 ± 2.55 y, 34% female) completed an Eriksen Flanker task. Of these, 87 youths provided complete data on dimensional measures of the core symptom of DMDD (irritability) and those of ADHD (inattention and hyperactivity).

Results: In a categorical diagnosis-based analysis (n = 187), we found significant interactive effects among ADHD, DMDD, and task condition on processing efficiency, whereby changes in processing efficiency between conflict and nonconflict conditions were larger in youths without psychopathology compared with patients. Analysis of symptom severity (n = 87) across diagnoses similarly revealed an interaction between symptom dimensions and task condition on processing efficiency. Irritability moderated the magnitude of association between inattention symptoms and difference in processing efficiency between conflict and nonconflict conditions.

Conclusion: Adapting processing efficiency to cognitive demands may represent a shared cognitive endophenotype for both ADHD and DMDD. Highly irritable and/or inattentive youth may have difficulty adjusting processing efficiency to changing task demands, possibly reflecting impairments in cognitive flexibility.
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http://dx.doi.org/10.1016/j.jaac.2020.08.468DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8096646PMC
May 2021

The Evolution of Ultrasound in Medicine: A Case Report of Point-of-care Ultrasound in the Self-diagnosis of Acute Appendicitis.

Clin Pract Cases Emerg Med 2020 Nov;4(4):527-529

Eastern Virginia Medical School, Department of Emergency Medicine, Norfolk, Virginia.

Introduction: Point-of-care ultrasound (POCUS) education during medical school develops physicians who are properly prepared for the next generation of medicine. The authors present the case of a first-year medical student who self-diagnosed appendicitis using POCUS.

Case Report: A 25-year-old, first-year medical student presented to the emergency department with lower abdominal pain. What seemed like a straightforward appendicitis presentation came with a twist; the student brought self-performed ultrasound imaging of his appendix.

Conclusion: The student's ultrasound skill set reflects favorably on the rapid evolution of ultrasound teaching in medical education.
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http://dx.doi.org/10.5811/cpcem.2020.7.48158DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7676787PMC
November 2020

The congruency sequence effect in a modified prime-probe task indexes response-general control.

J Exp Psychol Hum Percept Perform 2020 Nov 3;46(11):1387-1396. Epub 2020 Sep 3.

Department of Psychology and Neuroscience.

Adapting flexibly to recent events is essential in everyday life. A robust measure of such adaptive behavior is the congruency sequence effect (CSE) in the prime-probe task, which refers to a smaller congruency effect after incongruent trials than after congruent trials. Prior findings indicate that the CSE in the prime-probe task reflects control processes that modulate response activation after the prime onsets but before the probe appears. They also suggest that similar control processes operate even in a modified prime-probe task wherein the initial prime is a relevant target, rather than merely a distractor. Because adaptive behavior frequently occurs in the absence of irrelevant stimuli, the present study investigates the nature of the control processes that operate in this modified prime-probe task. Specifically, it investigates whether these control processes modulate only the response cued by the prime (response-specific control) or also other responses (response-general control). To make this distinction, we employed a novel variant of the modified prime-probe task wherein primes and probes are mapped to different responses (i.e., effectors), such that only response-general control processes can engender a CSE. Critically, we observed a robust CSE in each of 2 experiments. This outcome supports the response-general control hypothesis. More broadly, it suggests that the control processes underlying the CSE overlap with general mechanisms for adapting to sequential dependencies in the environment. (PsycInfo Database Record (c) 2020 APA, all rights reserved).
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http://dx.doi.org/10.1037/xhp0000790DOI Listing
November 2020

A Neurologist's Guide to REM Sleep Behavior Disorder.

Front Neurol 2020 8;11:610. Epub 2020 Jul 8.

Department of Neurology, Southmead Hospital, Bristol, United Kingdom.

REM Sleep Behavior Disorder (RBD) is a chronic sleep condition characterized by dream enactment and loss of REM atonia. Individuals often present to clinic with complaints of injury to themselves or their bed-partner due to violent movements during sleep. RBD patients have a high risk of developing one of the neurodegenerative α-synucleinopathy diseases: over 70% will develop parkinsonism or dementia within 12 years of their diagnosis. RBD patients also exhibit accelerated disease progression and a more severe phenotype than α-synucleinopathy sufferers without RBD. The disease's low prevalence and the relatively limited awareness of the condition amongst medical professionals makes the diagnosis and treatment of RBD challenging. Uncertainty in patient management is further exacerbated by a lack of clinical guidelines for RBD patient care. There are no binary prognostic markers for RBD disease course and there are no clinical guidelines for neurodegeneration scaling or tracking in these patients. Both clinicians and patients are therefore forced to deal with uncertain outcomes. In this review, we summarize RBD pathology and differential diagnoses, diagnostic, and treatment guidelines as well as prognostic recommendations with a look to current research in the scientific field. We aim to raise awareness and develop a framework for best practice for RBD patient management.
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http://dx.doi.org/10.3389/fneur.2020.00610DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7360679PMC
July 2020

GAVeCeLT-WoCoVA Consensus on subcutaneously anchored securement devices for the securement of venous catheters: Current evidence and recommendations for future research.

J Vasc Access 2021 Sep 2;22(5):716-725. Epub 2020 Jul 2.

University Hospital Agostino Gemelli, Rome, Italy.

Background: Subcutaneously anchored securement devices (or subcutaneous engineered securement devices) have been introduced recently into the clinical practice, but the number of published studies is still scarce. The Italian Group of Long-Term Central Venous Access Devices (GAVeCeLT)-in collaboration with WoCoVA (World Congress on Vascular Access)-has developed a Consensus about the effectiveness, safety, and cost-effectiveness of such devices.

Methods: After the definition of a panel of experts, a systematic collection and review of the literature on subcutaneously anchored securement devices was performed. The panel has been divided in two working groups, one focusing on adult patients and the other on children and neonates.

Results: Although the quality of evidence is generally poor, since it is based mainly on non-controlled prospective studies, the panel has concluded that subcutaneously anchored securement devices are overall effective in reducing the risk of dislodgment and they appear to be safe in all categories of patients, being associated only with rare and negligible local adverse effects; cost-effectiveness is demonstrated-or highly likely-in specific populations of patients with long-term venous access and/or at high risk of dislodgment.

Conclusion: Subcutaneously anchored securement is a very promising strategy for avoiding dislodgment. Further studies are warranted, in particular for the purpose of defining (a) the best management of the anchoring device so to avoid local problems, (b) the patient populations in which it may be considered highly cost-effective and even mandatory, (c) the possible benefit in terms of reduction of other catheter-related complications such as venous thrombosis and/or infection, and-last but not least-(d) their impact on the workload and stress level of nurses taking care of the devices.
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http://dx.doi.org/10.1177/1129729820924568DOI Listing
September 2021

Behavioural and neural evidence for self-reinforcing expectancy effects on pain.

Nat Hum Behav 2018 11 29;2(11):838-855. Epub 2018 Oct 29.

Department of Psychology and Neuroscience and Institute of Cognitive Science, University of Colorado Boulder, Boulder, CO, USA.

Beliefs and expectations often persist despite evidence to the contrary. Here we examine two potential mechanisms underlying such 'self-reinforcing' expectancy effects in the pain domain: modulation of perception and biased learning. In two experiments, cues previously associated with symbolic representations of high or low temperatures preceded painful heat. We examined trial-to-trial dynamics in participants' expected pain, reported pain and brain activity. Subjective and neural pain responses assimilated towards cue-based expectations, and pain responses in turn predicted subsequent expectations, creating a positive dynamic feedback loop. Furthermore, we found evidence for a confirmation bias in learning: higher- and lower-than-expected pain triggered greater expectation updating for high- and low-pain cues, respectively. Individual differences in this bias were reflected in the updating of pain-anticipatory brain activity. Computational modelling provided converging evidence that expectations influence both perception and learning. Together, perceptual assimilation and biased learning promote self-reinforcing expectations, helping to explain why beliefs can be resistant to change.
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http://dx.doi.org/10.1038/s41562-018-0455-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6768437PMC
November 2018

Relating causal and probabilistic approaches to contextuality.

Authors:
Matt Jones

Philos Trans A Math Phys Eng Sci 2019 Nov 16;377(2157):20190133. Epub 2019 Sep 16.

Department of Psychology and Neuroscience, University of Colorado Boulder, Boulder, CO, USA.

A primary goal in recent research on contextuality has been to extend this concept to cases of inconsistent connectedness, where observables have different distributions in different contexts. This article proposes a solution within the framework of probabi- listic causal models, which extend hidden-variables theories, and then demonstrates an equivalence to the contextuality-by-default (CbD) framework. CbD distinguishes contextuality from direct influences of context on observables, defining the latter purely in terms of probability distributions. Here, we take a causal view of direct influences, defining direct influence within any causal model as the probability of all latent states of the system in which a change of context changes the outcome of a measurement. Model-based contextuality (M-contextuality) is then defined as the necessity of stronger direct influences to model a full system than when considered individually. For consistently connected systems, M-contextuality agrees with standard contextuality. For general systems, it is proved that M-contextuality is equivalent to the property that any model of a system must contain 'hidden influences', meaning direct influences that go in opposite directions for different latent states, or equivalently signalling between observers that carries no information. This criterion can be taken as formalizing the 'no-conspiracy' principle that has been proposed in connection with CbD. M-contextuality is then proved to be equivalent to CbD-contextuality, thus providing a new interpretation of CbD-contextuality as the non-existence of a model for a system without hidden direct influences. This article is part of the theme issue 'Contextuality and probability in quantum mechanics and beyond'.
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http://dx.doi.org/10.1098/rsta.2019.0133DOI Listing
November 2019

Stepwise versus globally optimal search in children and adults.

Cognition 2019 10 12;191:103965. Epub 2019 Aug 12.

MPRG iSearch, Max Planck Institute for Human Development, Berlin, Germany; Technical University of Munich, Germany.

How do children and adults search for information when stepwise-optimal strategies fail to identify the most efficient query? The value of questions is often measured in terms of stepwise information gain (expected reduction of entropy on the next time step) or other stepwise-optimal methods. However, such myopic models are not guaranteed to identify the most efficient sequence of questions, that is, the shortest path to the solution. In two experiments we contrast stepwise methods with globally optimal strategies and study how younger children (around age 8, N = 52), older children (around age 10, N = 99), and adults (N = 101) search in a 20-questions game where planning ahead is required to identify the most efficient first question. Children searched as efficiently as adults, but also as myopically. Both children and adults tended to rely on heuristic stepwise-optimal strategies, focusing primarily on questions' implications for the next time step, rather than planning ahead.
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http://dx.doi.org/10.1016/j.cognition.2019.05.002DOI Listing
October 2019

Uncovering the rules of microbial community invasions.

Nat Ecol Evol 2019 08 29;3(8):1162-1171. Epub 2019 Jul 29.

Silwood Park Campus, Department of Life Sciences, Imperial College London, Ascot, UK.

Understanding the ecological and evolutionary processes determining the outcome of biological invasions has been the subject of decades of research with most work focusing on macro-organisms. In the context of microbes, invasions remain poorly understood despite being increasingly recognized as important. To shed light on the factors affecting the success of microbial community invasions, we perform simulations using an individual-based nearly neutral model that combines ecological and evolutionary processes. Our simulations qualitatively recreate many empirical patterns and lead to a description of five general rules of invasion: (1) larger communities evolve better invaders and better defenders; (2) where invader and resident fitness difference is large, invasion success is essentially deterministic; (3) propagule pressure contributes to invasion success, if and only if, invaders and residents are competitively similar; (4) increasing the diversity of invaders has a similar effect to increasing the number of invaders; and (5) more diverse communities more successfully resist invasion.
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http://dx.doi.org/10.1038/s41559-019-0952-9DOI Listing
August 2019

Computational Modeling in Pediatric Mental Health.

J Am Acad Child Adolesc Psychiatry 2019 05;58(5):471-473

University of Colorado, Boulder.

Computational modeling has recently become of great interest to mental health clinicians as a tool for discovering the nature of pathophysiology and for clinical assessment, prediction, and treatment. Computational psychiatry is a term used to describe the application of computational modeling to behavioral and mental health problems. The National Institute of Mental Health (NIMH) has taken an interest in computational modeling, suggesting applications of interest, such as understanding the neural basis of mental illness, discovering new treatments, and predicting treatment response. In this brief overview, our goal is to touch on major themes that have emerged in computational psychiatry.
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http://dx.doi.org/10.1016/j.jaac.2018.12.009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6615469PMC
May 2019

Verbal and spatial acquisition as a function of distributed practice and code-specific interference.

Mem Cognit 2019 05;47(4):779-791

University of Colorado Boulder, Boulder, CO, USA.

Theories of memory must account for memory performance during both the acquisition (i.e., ongoing learning) and retention (i.e., following disuse) stages of training. One factor affecting both stages is whether repeated encounters with a set of material occur with no delay between blocks (massed) or alternating with another intervening task (spaced). Whereas the retention advantage for spaced over massed practice is well accounted for by some current theories of memory, theories of decay or general interference predict massed, rather than spaced, advantages during acquisition. In a series of 3 experiments, we show that the effects of spacing on acquisition depend on the relationship between primary and delay tasks. Specifically, massed acquisition advantages occur only in the presence of code-specific interference (the engagement in two alternating tasks both emphasizing the same processing code, such as verbal or spatial processing codes; e.g., learning letter-number pairs and reading text), whereas spaced acquisition advantages are observed only when code-specific interference is absent. These results present a challenge for major theories of memory. Furthermore, we argue that code-specific interference is important for researchers of the spacing and interleaving effects to take into consideration, as the relationship between the alternating tasks used has a substantial impact on acquisition performance.
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http://dx.doi.org/10.3758/s13421-019-00892-xDOI Listing
May 2019

Escherichia coli can survive stress by noisy growth modulation.

Nat Commun 2018 12 17;9(1):5333. Epub 2018 Dec 17.

Sainsbury Laboratory, University of Cambridge, Cambridge, CB2 1LR, UK.

Gene expression can be noisy, as can the growth of single cells. Such cell-to-cell variation has been implicated in survival strategies for bacterial populations. However, it remains unclear how single cells couple gene expression with growth to implement these strategies. Here, we show how noisy expression of a key stress-response regulator, RpoS, allows E. coli to modulate its growth dynamics to survive future adverse environments. We reveal a dynamic positive feedback loop between RpoS and growth rate that produces multi-generation RpoS pulses. We do so experimentally using single-cell, time-lapse microscopy and microfluidics and theoretically with a stochastic model. Next, we demonstrate that E. coli prepares for sudden stress by entering prolonged periods of slow growth mediated by RpoS. This dynamic phenotype is captured by the RpoS-growth feedback model. Our synthesis of noisy gene expression, growth, and survival paves the way for further exploration of functional phenotypic variability.
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http://dx.doi.org/10.1038/s41467-018-07702-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6297224PMC
December 2018

Learning relational concepts from within- versus between-category comparisons.

J Exp Psychol Gen 2018 Nov;147(11):1571-1596

Department of Psychology and Neuroscience.

This article examines relational category learning in light of 2 influential theories of concept acquisition: the structure-mapping theory of analogy and theories of feature-based category learning. According to current theories of analogy, comparing 2 instances of a relational concept enables alignment of their elements and reveals their shared relational structure. Therefore, learning relationally defined categories should be faster when comparing items of the same category than when comparing items of different categories. By contrast, feature-based theories predict a benefit of between-category comparisons, because such comparisons direct attention to the features that discriminate the categories. The present experiments tested these predictions using a 2-category classification-learning task in which 2 items are presented on every trial: either in the same category (match condition) or in different categories (contrast condition). Subjects in the contrast condition outperformed those in the match condition for feature-based categories (Experiment 1) and across 4 different types of relational categories (Experiments 1-4). Although theorists have posited that structure-mapping theory is directly applicable to relational category learning, the present findings pose a distinct challenge to this assertion. We propose that many relational categories are learnable based solely on which relations are present in the stimulus rather than requiring explicitly compositional representations based on role-filler binding. This process would be akin to feature processing and would not require structural alignment. This theoretical proposal, together with the empirical results, may lead to a better understanding of when people do and do not engage in the cognitively demanding process of structural alignment. (PsycINFO Database Record (c) 2018 APA, all rights reserved).
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http://dx.doi.org/10.1037/xge0000517DOI Listing
November 2018

Dissolved Mn(III) in water treatment works: Prevalence and significance.

Water Res 2018 09 17;140:181-190. Epub 2018 Apr 17.

Environment & Sustainability Institute and Camborne School of Mines, University of Exeter, Penryn, Cornwall, TR10 9DF, United Kingdom.

Dissolved Mn(III) has been identified at all stages throughout a Water Treatment Works (WTW) receiving inflow from a peaty upland catchment in NE England. Ninety percent of the influent total manganese into the WTW is particulate Mn, in the form of Mn oxide (>0.2 μm). Approximately 9% (mean value, n = 22, range of 0-100%) of the dissolved (<0.2 μm) influent Mn is present as dissolved Mn(III). Mn(III) concentrations are highest (mean of 49% of total dissolved Mn; n = 26, range of 17-89%) within the WTW where water comes into contact with the organic-rich sludges which are produced as waste products in the WTW. These Mn(III)-containing wastewaters are recirculated to the head of the works and constitute a large input of Mn(III) into the WTW. This is the first report of Mn(III) being identified in a WTW. The ability of Mn(III) to act as both an oxidant and a reductant is of interest to the water industry. Understanding the formation and removal of Mn(III) within may help reduce Mn oxide deposits in pipe networks. Further understanding how the ratio of Mn(III) to Mn(II) can be used to optimise dissolved Mn removal would save the water industry significant money in reducing discoloration 'events' at the customers' tap.
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http://dx.doi.org/10.1016/j.watres.2018.04.038DOI Listing
September 2018

Narrow-sense heritability estimation of complex traits using identity-by-descent information.

Heredity (Edinb) 2018 12 28;121(6):616-630. Epub 2018 Mar 28.

Institute for Behavioral Genetics, University of Colorado, Boulder, CO, 80309, USA.

Heritability is a fundamental parameter in genetics. Traditional estimates based on family or twin studies can be biased due to shared environmental or non-additive genetic variance. Alternatively, those based on genotyped or imputed variants typically underestimate narrow-sense heritability contributed by rare or otherwise poorly tagged causal variants. Identical-by-descent (IBD) segments of the genome share all variants between pairs of chromosomes except new mutations that have arisen since the last common ancestor. Therefore, relating phenotypic similarity to degree of IBD sharing among classically unrelated individuals is an appealing approach to estimating the near full additive genetic variance while possibly avoiding biases that can occur when modeling close relatives. We applied an IBD-based approach (GREML-IBD) to estimate heritability in unrelated individuals using phenotypic simulation with thousands of whole-genome sequences across a range of stratification, polygenicity levels, and the minor allele frequencies of causal variants (CVs). In simulations, the IBD-based approach produced unbiased heritability estimates, even when CVs were extremely rare, although precision was low. However, population stratification and non-genetic familial environmental effects shared across generations led to strong biases in IBD-based heritability. We used data on two traits in ~120,000 people from the UK Biobank to demonstrate that, depending on the trait and possible confounding environmental effects, GREML-IBD can be applied to very large genetic datasets to infer the contribution of very rare variants lost using other methods. However, we observed apparent biases in these real data, suggesting that more work may be required to understand and mitigate factors that influence IBD-based heritability estimates.
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http://dx.doi.org/10.1038/s41437-018-0067-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6221881PMC
December 2018

Global screening for Critical Habitat in the terrestrial realm.

PLoS One 2018 22;13(3):e0193102. Epub 2018 Mar 22.

UN Environment World Conservation Monitoring Centre (UNEP-WCMC), Cambridge, United Kingdom.

Critical Habitat has become an increasingly important concept used by the finance sector and businesses to identify areas of high biodiversity value. The International Finance Corporation (IFC) defines Critical Habitat in their highly influential Performance Standard 6 (PS6), requiring projects in Critical Habitat to achieve a net gain of biodiversity. Here we present a global screening layer of Critical Habitat in the terrestrial realm, derived from global spatial datasets covering the distributions of 12 biodiversity features aligned with guidance provided by the IFC. Each biodiversity feature is categorised as 'likely' or 'potential' Critical Habitat based on: 1. Alignment between the biodiversity feature and the IFC Critical Habitat definition; and 2. Suitability of the spatial resolution for indicating a feature's presence on the ground. Following the initial screening process, Critical Habitat must then be assessed in-situ by a qualified assessor. This analysis indicates that a total of 10% and 5% of the global terrestrial environment can be considered as likely and potential Critical Habitat, respectively, while the remaining 85% did not overlap with any of the biodiversity features assessed and was classified as 'unknown'. Likely Critical Habitat was determined principally by the occurrence of Key Biodiversity Areas and Protected Areas. Potential Critical Habitat was predominantly characterised by data representing highly threatened and unique ecosystems such as ever-wet tropical forests and tropical dry forests. The areas we identified as likely or potential Critical Habitat are based on the best available global-scale data for the terrestrial realm that is aligned with IFC's Critical Habitat definition. Our results can help businesses screen potential development sites at the early project stage based on a range of biodiversity features. However, the study also demonstrates several important data gaps and highlights the need to incorporate new and improved global spatial datasets as they become available.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0193102PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5863962PMC
June 2018

Heuristics as Bayesian inference under extreme priors.

Cogn Psychol 2018 05 6;102:127-144. Epub 2018 Mar 6.

University College London, United Kingdom; The Alan Turing Institute, United Kingdom. Electronic address:

Simple heuristics are often regarded as tractable decision strategies because they ignore a great deal of information in the input data. One puzzle is why heuristics can outperform full-information models, such as linear regression, which make full use of the available information. These "less-is-more" effects, in which a relatively simpler model outperforms a more complex model, are prevalent throughout cognitive science, and are frequently argued to demonstrate an inherent advantage of simplifying computation or ignoring information. In contrast, we show at the computational level (where algorithmic restrictions are set aside) that it is never optimal to discard information. Through a formal Bayesian analysis, we prove that popular heuristics, such as tallying and take-the-best, are formally equivalent to Bayesian inference under the limit of infinitely strong priors. Varying the strength of the prior yields a continuum of Bayesian models with the heuristics at one end and ordinary regression at the other. Critically, intermediate models perform better across all our simulations, suggesting that down-weighting information with the appropriate prior is preferable to entirely ignoring it. Rather than because of their simplicity, our analyses suggest heuristics perform well because they implement strong priors that approximate the actual structure of the environment. We end by considering how new heuristics could be derived by infinitely strengthening the priors of other Bayesian models. These formal results have implications for work in psychology, machine learning and economics.
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http://dx.doi.org/10.1016/j.cogpsych.2017.11.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5886040PMC
May 2018

Elevated success of multispecies bacterial invasions impacts community composition during ecological succession.

Ecol Lett 2018 04 14;21(4):516-524. Epub 2018 Feb 14.

Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, UK.

Successful microbial invasions are determined by a species' ability to occupy a niche in the new habitat whilst resisting competitive exclusion by the resident community. Despite the recognised importance of biotic factors in determining the invasiveness of microbial communities, the success and impact of multiple concurrent invaders on the resident community has not been examined. Simultaneous invasions might have synergistic effects, for example if resident species need to exhibit divergent phenotypes to compete with the invasive populations. We used three phylogenetically diverse bacterial species to invade two compositionally distinct communities in a controlled, naturalised in vitro system. By initiating the invader introductions at different stages of succession, we could disentangle the relative importance of resident community structure, invader diversity and time pre-invasion. Our results indicate that multiple invaders increase overall invasion success, but do not alter the successional trajectory of the whole community.
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http://dx.doi.org/10.1111/ele.12916DOI Listing
April 2018

Temporal heterogeneity increases with spatial heterogeneity in ecological communities.

Ecology 2018 04 15;99(4):858-865. Epub 2018 Feb 15.

National Center for Ecological Analysis and Synthesis, 735 State Street, Suite 300, Santa Barbara, California, 93101, USA.

Heterogeneity is increasingly recognized as a foundational characteristic of ecological systems. Under global change, understanding temporal community heterogeneity is necessary for predicting the stability of ecosystem functions and services. Indeed, spatial heterogeneity is commonly used in alternative stable state theory as a predictor of temporal heterogeneity and therefore an early indicator of regime shifts. To evaluate whether spatial heterogeneity in species composition is predictive of temporal heterogeneity in ecological communities, we analyzed 68 community data sets spanning freshwater and terrestrial systems where measures of species abundance were replicated over space and time. Of the 68 data sets, 55 (81%) had a weak to strongly positive relationship between spatial and temporal heterogeneity, while in the remaining communities the relationship was weak to strongly negative (19%). Based on a mixed model analysis, we found a significant but weak overall positive relationship between spatial and temporal heterogeneity across all data sets combined, and within aquatic and terrestrial data sets separately. In addition, lifespan and successional stage were negatively and positively related to temporal heterogeneity, respectively. We conclude that spatial heterogeneity may be a predictor of temporal heterogeneity in ecological communities, and that this relationship may be a general property of many terrestrial and aquatic communities.
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http://dx.doi.org/10.1002/ecy.2154DOI Listing
April 2018

Evaluating Youtube as A Source of Patient Information on Dupuytren's Disease.

World J Plast Surg 2017 Sep;6(3):396-398

Botnar Research Centre, NDORMS, University of Oxford, Nuffield Orthopaedic Centre, Oxford, UK.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5714992PMC
September 2017

Emergency Physician-performed Transesophageal Echocardiography in Simulated Cardiac Arrest.

West J Emerg Med 2017 Aug 19;18(5):830-834. Epub 2017 Jul 19.

Virginia Commonwealth University, Department of Emergency Medicine, Richmond, Virginia.

Introduction: Transesophageal echocardiography (TEE) is a well-established method of evaluating cardiac pathology. It has many advantages over transthoracic echocardiography (TTE), including the ability to image the heart during active cardiopulmonary resuscitation. This prospective simulation study aims to evaluate the ability of emergency medicine (EM) residents to learn TEE image acquisition techniques and demonstrate those techniques to identify common pathologic causes of cardiac arrest.

Methods: This was a prospective educational cohort study with 40 EM residents from two participating academic medical centers who underwent an educational model and testing protocol. All participants were tested across six cases, including two normals, pericardial tamponade, acute myocardial infarction (MI), ventricular fibrillation (VF), and asystole presented in random order. Primary endpoints were correct identification of the cardiac pathology, if any, and time to sonographic diagnosis. Calculated endpoints included sensitivity, specificity, and positive and negative predictive values for emergency physician (EP)-performed TEE. We calculated a kappa statistic to determine the degree of inter-rater reliability.

Results: Forty EM residents completed both the educational module and testing protocol. This resulted in a total of 80 normal TEE studies and 160 pathologic TEE studies. Our calculations for the ability to diagnose life-threatening cardiac pathology by EPs in a high-fidelity TEE simulation resulted in a sensitivity of 98%, specificity of 99%, positive likelihood ratio of 78.0, and negative likelihood ratio of 0.025. The average time to diagnose each objective structured clinical examination case was as follows: normal A in 35 seconds, normal B in 31 seconds, asystole in 13 seconds, tamponade in 14 seconds, acute MI in 22 seconds, and VF in 12 seconds. Inter-rater reliability between participants was extremely high, resulting in a kappa coefficient across all cases of 0.95.

Conclusion: EM residents can rapidly perform TEE studies in a simulated cardiac arrest environment with a high degree of precision and accuracy. Performance of TEE studies on human patients in cardiac arrest is the next logical step to determine if our simulation data hold true in clinical practice.
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http://dx.doi.org/10.5811/westjem.2017.5.33543DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5576618PMC
August 2017

Biotic resistance shapes the influence of propagule pressure on invasion success in bacterial communities.

Ecology 2017 Jul 26;98(7):1743-1749. Epub 2017 May 26.

Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, United Kingdom.

The number of invaders and the timing of invasion are recognized as key determinants of successful invasions. Despite the recognized importance of "propagule pressure," invasion ecology has largely focused on how characteristics of the native community confer invasion resistance. We simultaneously manipulated community composition and invader propagule pressure in microcosm communities of freshwater bacteria. We show that high propagule pressures can be necessary to establish an invader population, but that the influence of propagule pressure depends on the composition of the resident species. In particular, the number of individuals invading was most important to invasion success when one of the species in a resident community is a strong competitor against other species. By contrast, the timing of invasion was most important when communities had lower growth rates. The results suggest that the importance of propagule pressure varies both between communities and within the same community over time, and therefore have implications for the way we understand the relationship between biotic resistance and invasion success.
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http://dx.doi.org/10.1002/ecy.1852DOI Listing
July 2017

Timing of quizzes during learning: Effects on motivation and retention.

J Exp Psychol Appl 2017 06 9;23(2):128-137. Epub 2017 Mar 9.

Department of Psychology and Neuroscience, University of Colorado Boulder.

This article investigates how the timing of quizzes given during learning impacts retention of studied material. We investigated the hypothesis that interspersing quizzes among study blocks increases student engagement, thus improving learning. Participants learned 8 artificial facts about each of 8 plant categories, with the categories blocked during learning. Quizzes about 4 of the 8 facts from each category occurred either immediately after studying the facts for that category (standard) or after studying the facts from all 8 categories (postponed). In Experiment 1, participants were given tests shortly after learning and several days later, including both the initially quizzed and unquizzed facts. Test performance was better in the standard than in the postponed condition, especially for categories learned later in the sequence. This result held even for the facts not quizzed during learning, suggesting that the advantage cannot be due to any direct testing effects. Instead the results support the hypothesis that interrupting learning with quiz questions is beneficial because it can enhance learner engagement. Experiment 2 provided further support for this hypothesis, based on participants' retrospective ratings of their task engagement during the learning phase. These findings have practical implications for when to introduce quizzes in the classroom. (PsycINFO Database Record
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http://dx.doi.org/10.1037/xap0000123DOI Listing
June 2017

A fast and accurate method for detection of IBD shared haplotypes in genome-wide SNP data.

Eur J Hum Genet 2017 05 8;25(5):617-624. Epub 2017 Feb 8.

Institute for Behavioral Genetics, University of Colorado at Boulder, Boulder, CO, USA.

Identical by descent (IBD) segments are used to understand a number of fundamental issues in genetics. IBD segments are typically detected using long stretches of identical alleles between haplotypes in phased, whole-genome SNP data. Phase or SNP call errors in genomic data can degrade accuracy of IBD detection and lead to false-positive/negative calls and to under/overextension of true IBD segments. Furthermore, the number of comparisons increases quadratically with sample size, requiring high computational efficiency. We developed a new IBD segment detection program, FISHR (Find IBD Shared Haplotypes Rapidly), in an attempt to accurately detect IBD segments and to better estimate their endpoints using an algorithm that is fast enough to be deployed on very large whole-genome SNP data sets. We compared the performance of FISHR to three leading IBD segment detection programs: GERMLINE, refined IBD, and HaploScore. Using simulated and real genomic sequence data, we show that FISHR is slightly more accurate than all programs at detecting long (>3 cm) IBD segments but slightly less accurate than refined IBD at detecting short (~1 cm) IBD segments. More centrally, FISHR outperforms all programs in determining the true endpoints of IBD segments, which is crucial for several applications of IBD information. FISHR takes two to three times longer than GERMLINE to run, whereas both GERMLINE and FISHR were orders of magnitude faster than refined IBD and HaploScore. Overall, FISHR provides accurate IBD detection in unrelated individuals and is computationally efficient enough to be utilized on large SNP data sets >60 000 individuals.
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http://dx.doi.org/10.1038/ejhg.2017.6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5437913PMC
May 2017

ECG-based PICC tip verification system: an evaluation 5 years on.

Br J Nurs 2016 Oct;25(19):S4-S10

Consultant Anaesthetist, East Kent Hospitals University NHS Foundation Trust, Kent.

In 2011, the vascular access team at East Kent Hospitals University NHS Foundation Trust safely and successfully incorporated the use of electrocardiogram (ECG) guidance technology for verification of peripherally inserted central catheters (PICC) tip placement into their practice. This study, 5 years on, compared the strengths and limitations of using this ECG method with the previous gold-standard of post-procedural chest X-ray. The study was undertaken using an embedded case study approach, and the cost, accuracy and efficiency of both systems were evaluated and compared. Using ECG to confirm PICC tip position was found to be cheaper, quicker and more accurate than post-procedural chest X-ray.
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http://dx.doi.org/10.12968/bjon.2016.25.19.S4DOI Listing
October 2016
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