Publications by authors named "David J Harris"

99 Publications

A critical analysis of the functional parameters of the quiet eye using immersive virtual reality.

J Exp Psychol Hum Percept Perform 2021 Feb 14;47(2):308-321. Epub 2020 Dec 14.

School of Sport and Health Sciences, University of Exeter.

Directing ocular fixations toward a target assists the planning and control of visually guided actions. In far aiming tasks, the quiet eye, an instance of premovement gaze anchoring, has been extensively studied as a key performance variable. However, theories of quiet eye are yet to establish the exact functional role of the location and duration of the fixation. The present work used immersive virtual reality to manipulate key parameters of the quiet eye-location (Experiment 1) and duration (Experiment 2)-to test competing theoretical predictions about their importance. Across two preregistered experiments, novice participants (n = 127) completed a series of golf putts while their eye movements, putting accuracy, and putting kinematics were recorded. In Experiment 1, participants' premovement fixation was cued to locations on the ball, near the ball, and far from the ball. In Experiment 2, long and short quiet eye durations were induced using auditory tones as cues to movement phases. Linear mixed effects models indicated that manipulations of location and duration had little effect on performance or movement kinematics. The findings suggest that, for novices, the spatial and temporal parameters of the final fixation may not be critical for movement preprogramming and may instead reflect attentional control or movement inhibition functions. (PsycInfo Database Record (c) 2021 APA, all rights reserved).
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http://dx.doi.org/10.1037/xhp0000800DOI Listing
February 2021

Molecular screening indicates high prevalence and mixed infections of Hepatozoon parasites in wild felines from South Africa.

J S Afr Vet Assoc 2020 Nov 30;91(0):e1-e5. Epub 2020 Nov 30.

CIBIO Research Centre in Biodiversity and Genetic Resources, InBIO, Universidade do Porto, Vila do Conde.

Genetic diversity within partial 18S rRNA sequences from Hepatozoon protozoan parasites from wild felines in South Africa was assessed and compared with data from domestic cats to assess patterns of host specificity. Lions, leopards, servals, a caracal and an African wildcat were all positive for parasites of the Hepatozoon felis-complex. However, haplotypes were not species-specific, and potential mixed infections were widespread. Additional genetic markers are needed to untangle the extremely complex situation of these parasites in both domestic cats and wild felines in South Africa.
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http://dx.doi.org/10.4102/jsava.v91i0.2055DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7736645PMC
November 2020

De novo variants in MPP5 cause global developmental delay and behavioral changes.

Hum Mol Genet 2020 Dec;29(20):3388-3401

Division of Newborn Medicine, Department of Pediatrics, Boston Children's Hospital, Boston, MA 02115, USA.

Membrane Protein Palmitoylated 5 (MPP5) is a highly conserved apical complex protein essential for cell polarity, fate and survival. Defects in cell polarity are associated with neurologic disorders including autism and microcephaly. MPP5 is essential for neurogenesis in animal models, but human variants leading to neurologic impairment have not been described. We identified three patients with heterozygous MPP5 de novo variants (DNV) and global developmental delay (GDD) and compared their phenotypes and magnetic resonance imaging (MRI) to ascertain how MPP5 DNV leads to GDD. All three patients with MPP5 DNV experienced GDD with language delay/regression and behavioral changes. MRI ranged from normal to decreased gyral folding and microcephaly. The effects of MPP5 depletion on the developing brain were assessed by creating a heterozygous conditional knock out (het CKO) murine model with central nervous system (CNS)-specific Nestin-Cre drivers. In the het CKO model, Mpp5 depletion led to microcephaly, decreased cerebellar volume and cortical thickness. Het CKO mice had decreased ependymal cells and Mpp5 at the apical surface of cortical ventricular zone compared with wild type. Het CKO mice also failed to maintain progenitor pools essential for neurogenesis. The proportion of cortical cells undergoing apoptotic cell death increased, suggesting that cell death reduces progenitor population and neuron number. Het CKO mice also showed behavioral changes, similar to our patients. To our knowledge, this is the first report to show that variants in MPP5 are associated with GDD, behavioral abnormalities and language regression/delay. Murine modeling shows that neurogenesis is likely altered in these individuals, with cell death and skewed cellular composition playing significant roles.
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http://dx.doi.org/10.1093/hmg/ddaa224DOI Listing
December 2020

Tectonics, climate and the diversification of the tropical African terrestrial flora and fauna.

Biol Rev Camb Philos Soc 2021 Feb 13;96(1):16-51. Epub 2020 Sep 13.

Laboratoire des Sciences du Climat et de l'Environnement, LSCE/IPSL, CEA-CNRS-UVSQ, Université Paris-Saclay, Gif-sur-Yvette, F-91191, France.

Tropical Africa is home to an astonishing biodiversity occurring in a variety of ecosystems. Past climatic change and geological events have impacted the evolution and diversification of this biodiversity. During the last two decades, around 90 dated molecular phylogenies of different clades across animals and plants have been published leading to an increased understanding of the diversification and speciation processes generating tropical African biodiversity. In parallel, extended geological and palaeoclimatic records together with detailed numerical simulations have refined our understanding of past geological and climatic changes in Africa. To date, these important advances have not been reviewed within a common framework. Here, we critically review and synthesize African climate, tectonics and terrestrial biodiversity evolution throughout the Cenozoic to the mid-Pleistocene, drawing on recent advances in Earth and life sciences. We first review six major geo-climatic periods defining tropical African biodiversity diversification by synthesizing 89 dated molecular phylogeny studies. Two major geo-climatic factors impacting the diversification of the sub-Saharan biota are highlighted. First, Africa underwent numerous climatic fluctuations at ancient and more recent timescales, with tectonic, greenhouse gas, and orbital forcing stimulating diversification. Second, increased aridification since the Late Eocene led to important extinction events, but also provided unique diversification opportunities shaping the current tropical African biodiversity landscape. We then review diversification studies of tropical terrestrial animal and plant clades and discuss three major models of speciation: (i) geographic speciation via vicariance (allopatry); (ii) ecological speciation impacted by climate and geological changes, and (iii) genomic speciation via genome duplication. Geographic speciation has been the most widely documented to date and is a common speciation model across tropical Africa. We conclude with four important challenges faced by tropical African biodiversity research: (i) to increase knowledge by gathering basic and fundamental biodiversity information; (ii) to improve modelling of African geophysical evolution throughout the Cenozoic via better constraints and downscaling approaches; (iii) to increase the precision of phylogenetic reconstruction and molecular dating of tropical African clades by using next generation sequencing approaches together with better fossil calibrations; (iv) finally, as done here, to integrate data better from Earth and life sciences by focusing on the interdisciplinary study of the evolution of tropical African biodiversity in a wider geodiversity context.
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http://dx.doi.org/10.1111/brv.12644DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7821006PMC
February 2021

The re-occurrence of cardiomyopathy in propionic acidemia after liver transplantation.

JIMD Rep 2020 Jul 8;54(1):3-8. Epub 2020 Apr 8.

Department of Pediatrics University of California San Diego La Jolla California USA.

Cardiomyopathy is a frequent complication of propionic acidemia (PA). It is often fatal, and its occurrence is largely independent of classic metabolic treatment modalities. Liver transplantation (LT) is a treatment option for severe PA as the liver plays a vital role in metabolism of the precursors that accumulate in patients with PA. LT in PA is now considered to be a long-lasting and valid treatment to prevent cardiac disease. The subject of this report had severe cardiomyopathy that largely disappeared prior to undergoing a LT. Three years following the transplant, there was recurrence of cardiomyopathy following a surgery that was complicated with a postoperative aspiration pneumonia. On his last hospital admission, he was presented with pulmonary edema and heart failure. He continued with episodes of intractable hypotension, despite maximum inotropic and diuretic support. He died following redirection of care. We conclude that lethal cardiomyopathy may develop several years after successful LT in patients with PA.
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http://dx.doi.org/10.1002/jmd2.12119DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7358669PMC
July 2020

Long-term thermal sensitivity of Earth's tropical forests.

Authors:
Martin J P Sullivan Simon L Lewis Kofi Affum-Baffoe Carolina Castilho Flávia Costa Aida Cuni Sanchez Corneille E N Ewango Wannes Hubau Beatriz Marimon Abel Monteagudo-Mendoza Lan Qie Bonaventure Sonké Rodolfo Vasquez Martinez Timothy R Baker Roel J W Brienen Ted R Feldpausch David Galbraith Manuel Gloor Yadvinder Malhi Shin-Ichiro Aiba Miguel N Alexiades Everton C Almeida Edmar Almeida de Oliveira Esteban Álvarez Dávila Patricia Alvarez Loayza Ana Andrade Simone Aparecida Vieira Luiz E O C Aragão Alejandro Araujo-Murakami Eric J M M Arets Luzmila Arroyo Peter Ashton Gerardo Aymard C Fabrício B Baccaro Lindsay F Banin Christopher Baraloto Plínio Barbosa Camargo Jos Barlow Jorcely Barroso Jean-François Bastin Sarah A Batterman Hans Beeckman Serge K Begne Amy C Bennett Erika Berenguer Nicholas Berry Lilian Blanc Pascal Boeckx Jan Bogaert Damien Bonal Frans Bongers Matt Bradford Francis Q Brearley Terry Brncic Foster Brown Benoit Burban José Luís Camargo Wendeson Castro Carlos Céron Sabina Cerruto Ribeiro Victor Chama Moscoso Jerôme Chave Eric Chezeaux Connie J Clark Fernanda Coelho de Souza Murray Collins James A Comiskey Fernando Cornejo Valverde Massiel Corrales Medina Lola da Costa Martin Dančák Greta C Dargie Stuart Davies Nallaret Davila Cardozo Thales de Haulleville Marcelo Brilhante de Medeiros Jhon Del Aguila Pasquel Géraldine Derroire Anthony Di Fiore Jean-Louis Doucet Aurélie Dourdain Vincent Droissart Luisa Fernanda Duque Romeo Ekoungoulou Fernando Elias Terry Erwin Adriane Esquivel-Muelbert Sophie Fauset Joice Ferreira Gerardo Flores Llampazo Ernest Foli Andrew Ford Martin Gilpin Jefferson S Hall Keith C Hamer Alan C Hamilton David J Harris Terese B Hart Radim Hédl Bruno Herault Rafael Herrera Niro Higuchi Annette Hladik Eurídice Honorio Coronado Isau Huamantupa-Chuquimaco Walter Huaraca Huasco Kathryn J Jeffery Eliana Jimenez-Rojas Michelle Kalamandeen Marie Noël Kamdem Djuikouo Elizabeth Kearsley Ricardo Keichi Umetsu Lip Khoon Kho Timothy Killeen Kanehiro Kitayama Bente Klitgaard Alexander Koch Nicolas Labrière William Laurance Susan Laurance Miguel E Leal Aurora Levesley Adriano J N Lima Janvier Lisingo Aline P Lopes Gabriela Lopez-Gonzalez Tom Lovejoy Jon C Lovett Richard Lowe William E Magnusson Jagoba Malumbres-Olarte Ângelo Gilberto Manzatto Ben Hur Marimon Andrew R Marshall Toby Marthews Simone Matias de Almeida Reis Colin Maycock Karina Melgaço Casimiro Mendoza Faizah Metali Vianet Mihindou William Milliken Edward T A Mitchard Paulo S Morandi Hannah L Mossman Laszlo Nagy Henrique Nascimento David Neill Reuben Nilus Percy Núñez Vargas Walter Palacios Nadir Pallqui Camacho Julie Peacock Colin Pendry Maria Cristina Peñuela Mora Georgia C Pickavance John Pipoly Nigel Pitman Maureen Playfair Lourens Poorter John R Poulsen Axel Dalberg Poulsen Richard Preziosi Adriana Prieto Richard B Primack Hirma Ramírez-Angulo Jan Reitsma Maxime Réjou-Méchain Zorayda Restrepo Correa Thaiane Rodrigues de Sousa Lily Rodriguez Bayona Anand Roopsind Agustín Rudas Ervan Rutishauser Kamariah Abu Salim Rafael P Salomão Juliana Schietti Douglas Sheil Richarlly C Silva Javier Silva Espejo Camila Silva Valeria Marcos Silveira Murielle Simo-Droissart Marcelo Fragomeni Simon James Singh Yahn Carlos Soto Shareva Clement Stahl Juliana Stropp Rahayu Sukri Terry Sunderland Martin Svátek Michael D Swaine Varun Swamy Hermann Taedoumg Joey Talbot James Taplin David Taylor Hans Ter Steege John Terborgh Raquel Thomas Sean C Thomas Armando Torres-Lezama Peter Umunay Luis Valenzuela Gamarra Geertje van der Heijden Peter van der Hout Peter van der Meer Mark van Nieuwstadt Hans Verbeeck Ronald Vernimmen Alberto Vicentini Ima Célia Guimarães Vieira Emilio Vilanova Torre Jason Vleminckx Vincent Vos Ophelia Wang Lee J T White Simon Willcock John T Woods Verginia Wortel Kenneth Young Roderick Zagt Lise Zemagho Pieter A Zuidema Joeri A Zwerts Oliver L Phillips

Science 2020 05 21;368(6493):869-874. Epub 2020 May 21.

School of Geography, University of Leeds, Leeds, UK.

The sensitivity of tropical forest carbon to climate is a key uncertainty in predicting global climate change. Although short-term drying and warming are known to affect forests, it is unknown if such effects translate into long-term responses. Here, we analyze 590 permanent plots measured across the tropics to derive the equilibrium climate controls on forest carbon. Maximum temperature is the most important predictor of aboveground biomass (-9.1 megagrams of carbon per hectare per degree Celsius), primarily by reducing woody productivity, and has a greater impact per °C in the hottest forests (>32.2°C). Our results nevertheless reveal greater thermal resilience than observations of short-term variation imply. To realize the long-term climate adaptation potential of tropical forests requires both protecting them and stabilizing Earth's climate.
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http://dx.doi.org/10.1126/science.aaw7578DOI Listing
May 2020

In-task auditory performance-related feedback promotes cardiovascular markers of a challenge state during a pressurized task.

Anxiety Stress Coping 2020 09 18;33(5):497-510. Epub 2020 May 18.

School of Sport and Health Sciences, University of Exeter, Exeter, UK.

Individuals evaluate the demands and resources associated with a pressurized situation, which leads to distinct patterns of cardiovascular responses. While it is accepted that cognitive evaluations are updated throughout a pressurized situation, to date, cardiovascular markers have only been recorded immediately before, or averaged across, these situations. Thus, this study examined the influence of in-task performance-related feedback on cardiovascular markers of challenge and threat to explore fluctuations in these markers. Forty participants completed a pressurized visual search task while cardiovascular markers of challenge and threat were recorded. During the task, participants received either positive or negative feedback via distinct auditory tones to induce a challenge or threat state. Following task completion, cardiovascular markers were recorded during a recovery phase. Participants' cardiovascular responses changed across the experimental protocol. Specifically, while participants displayed a cardiovascular response more reflective of a challenge state following in-task performance-related feedback, participants exhibited a response more akin to a threat state later during the recovery phase. In-task auditory performance-related feedback promoted cardiovascular markers of a challenge state. These markers fluctuated over the experiment, suggesting that they, and presumably underlying demand and resource evaluations, are relatively dynamic in nature.
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http://dx.doi.org/10.1080/10615806.2020.1766681DOI Listing
September 2020

mutations in the X-linked gene cause intellectual disability with pigmentary mosaicism and storage disorder-like features.

J Med Genet 2020 12 14;57(12):808-819. Epub 2020 May 14.

Fédération Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (TRANSLAD), Centre Hospitalier Universitaire Dijon, Dijon, France.

Introduction: Pigmentary mosaicism (PM) manifests by pigmentation anomalies along Blaschko's lines and represents a clue toward the molecular diagnosis of syndromic intellectual disability (ID). Together with new insights on the role for lysosomal signalling in embryonic stem cell differentiation, mutations in the X-linked transcription factor 3 () have recently been reported in five patients. Functional analysis suggested these mutations to result in ectopic nuclear gain of functions.

Materials And Methods: Subsequent data sharing allowed the clustering of variants identified by exome sequencing on DNA extracted from leucocytes in patients referred for syndromic ID with or without PM.

Results: We describe the detailed clinical and molecular data of 17 individuals harbouring a variant, including the patients that initially allowed reporting as a new disease-causing gene. The 12 females and 5 males presented with pigmentation anomalies on Blaschko's lines, severe ID, epilepsy, storage disorder-like features, growth retardation and recognisable facial dysmorphism. The variant was at a mosaic state in at least two male patients. All variants were missense except one splice variant. Eleven of the 13 variants were localised in exon 4, 2 in exon 3, and 3 were recurrent variants.

Conclusion: This series further delineates the specific storage disorder-like phenotype with PM ascribed to mutation in exons 3 and 4. It confirms the identification of a novel X-linked human condition associated with mosaicism and dysregulation within the mechanistic target of rapamycin (mTOR) pathway, as well as a link between lysosomal signalling and human development.
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http://dx.doi.org/10.1136/jmedgenet-2019-106508DOI Listing
December 2020

A Framework for the Testing and Validation of Simulated Environments in Experimentation and Training.

Front Psychol 2020 31;11:605. Epub 2020 Mar 31.

School of Sport and Health Sciences, University of Exeter, Exeter, United Kingdom.

New computer technologies, like virtual reality (VR), have created opportunities to study human behavior and train skills in novel ways. VR holds significant promise for maximizing the efficiency and effectiveness of skill learning in a variety of settings (e.g., sport, medicine, safety-critical industries) through immersive learning and augmentation of existing training methods. In many cases the adoption of VR for training has, however, preceded rigorous testing and validation of the simulation tool. In order for VR to be implemented successfully for both training and psychological experimentation it is necessary to first establish whether the simulation captures fundamental features of the real task and environment, and elicits realistic behaviors. Unfortunately evaluation of VR environments too often confuses presentation and function, and relies on superficial visual features that are not the key determinants of successful training outcomes. Therefore evidence-based methods of establishing the fidelity and validity of VR environments are required. To this end, we outline a taxonomy of the subtypes of fidelity and validity, and propose a variety of practical methods for testing and validating VR training simulations. Ultimately, a successful VR environment is one that enables transfer of learning to the real-world. We propose that key elements of psychological, affective and ergonomic fidelity, are the real determinants of successful transfer. By adopting an evidence-based approach to VR simulation design and testing it is possible to develop valid environments that allow the potential of VR training to be maximized.
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http://dx.doi.org/10.3389/fpsyg.2020.00605DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7136518PMC
March 2020

Asynchronous carbon sink saturation in African and Amazonian tropical forests.

Authors:
Wannes Hubau Simon L Lewis Oliver L Phillips Kofi Affum-Baffoe Hans Beeckman Aida Cuní-Sanchez Armandu K Daniels Corneille E N Ewango Sophie Fauset Jacques M Mukinzi Douglas Sheil Bonaventure Sonké Martin J P Sullivan Terry C H Sunderland Hermann Taedoumg Sean C Thomas Lee J T White Katharine A Abernethy Stephen Adu-Bredu Christian A Amani Timothy R Baker Lindsay F Banin Fidèle Baya Serge K Begne Amy C Bennett Fabrice Benedet Robert Bitariho Yannick E Bocko Pascal Boeckx Patrick Boundja Roel J W Brienen Terry Brncic Eric Chezeaux George B Chuyong Connie J Clark Murray Collins James A Comiskey David A Coomes Greta C Dargie Thales de Haulleville Marie Noel Djuikouo Kamdem Jean-Louis Doucet Adriane Esquivel-Muelbert Ted R Feldpausch Alusine Fofanah Ernest G Foli Martin Gilpin Emanuel Gloor Christelle Gonmadje Sylvie Gourlet-Fleury Jefferson S Hall Alan C Hamilton David J Harris Terese B Hart Mireille B N Hockemba Annette Hladik Suspense A Ifo Kathryn J Jeffery Tommaso Jucker Emmanuel Kasongo Yakusu Elizabeth Kearsley David Kenfack Alexander Koch Miguel E Leal Aurora Levesley Jeremy A Lindsell Janvier Lisingo Gabriela Lopez-Gonzalez Jon C Lovett Jean-Remy Makana Yadvinder Malhi Andrew R Marshall Jim Martin Emanuel H Martin Faustin M Mbayu Vincent P Medjibe Vianet Mihindou Edward T A Mitchard Sam Moore Pantaleo K T Munishi Natacha Nssi Bengone Lucas Ojo Fidèle Evouna Ondo Kelvin S-H Peh Georgia C Pickavance Axel Dalberg Poulsen John R Poulsen Lan Qie Jan Reitsma Francesco Rovero Michael D Swaine Joey Talbot James Taplin David M Taylor Duncan W Thomas Benjamin Toirambe John Tshibamba Mukendi Darlington Tuagben Peter M Umunay Geertje M F van der Heijden Hans Verbeeck Jason Vleminckx Simon Willcock Hannsjörg Wöll John T Woods Lise Zemagho

Nature 2020 03 4;579(7797):80-87. Epub 2020 Mar 4.

Plant Systematic and Ecology Laboratory, Higher Teachers' Training College, University of Yaounde I, Yaounde, Cameroon.

Structurally intact tropical forests sequestered about half of the global terrestrial carbon uptake over the 1990s and early 2000s, removing about 15 per cent of anthropogenic carbon dioxide emissions. Climate-driven vegetation models typically predict that this tropical forest 'carbon sink' will continue for decades. Here we assess trends in the carbon sink using 244 structurally intact African tropical forests spanning 11 countries, compare them with 321 published plots from Amazonia and investigate the underlying drivers of the trends. The carbon sink in live aboveground biomass in intact African tropical forests has been stable for the three decades to 2015, at 0.66 tonnes of carbon per hectare per year (95 per cent confidence interval 0.53-0.79), in contrast to the long-term decline in Amazonian forests. Therefore the carbon sink responses of Earth's two largest expanses of tropical forest have diverged. The difference is largely driven by carbon losses from tree mortality, with no detectable multi-decadal trend in Africa and a long-term increase in Amazonia. Both continents show increasing tree growth, consistent with the expected net effect of rising atmospheric carbon dioxide and air temperature. Despite the past stability of the African carbon sink, our most intensively monitored plots suggest a post-2010 increase in carbon losses, delayed compared to Amazonia, indicating asynchronous carbon sink saturation on the two continents. A statistical model including carbon dioxide, temperature, drought and forest dynamics accounts for the observed trends and indicates a long-term future decline in the African sink, whereas the Amazonian sink continues to weaken rapidly. Overall, the uptake of carbon into Earth's intact tropical forests peaked in the 1990s. Given that the global terrestrial carbon sink is increasing in size, independent observations indicating greater recent carbon uptake into the Northern Hemisphere landmass reinforce our conclusion that the intact tropical forest carbon sink has already peaked. This saturation and ongoing decline of the tropical forest carbon sink has consequences for policies intended to stabilize Earth's climate.
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http://dx.doi.org/10.1038/s41586-020-2035-0DOI Listing
March 2020

Testing the Effects of 3D Multiple Object Tracking Training on Near, Mid and Far Transfer.

Front Psychol 2020 12;11:196. Epub 2020 Feb 12.

School of Sport and Health Sciences, University of Exeter, Exeter, United Kingdom.

Cognitive training (CT) aims to develop domain general mental abilities to support functions like decision making, multitasking, and performance under pressure. Research to date has indicated that CT likely aids performance on lab-based cognitive tests, but there has been little demonstration of transfer to tasks representative of real-world high performance environments. This study aimed to assess transfer from a CT intervention to near and mid-level transfer tasks, plus a far transfer test representative of real-world multitasking in a military environment. 84 participants were randomized to four independent training groups, using , a CT task based on 3D object tracking. There was no evidence for near transfer (to another object tracking task) or for far transfer to a route monitoring task designed to replicate real-world multitasking. There may, however, have been some improvement in working memory performance as a result of training. These findings raise further questions about whether domain general CT will transfer to real-world performance. Effective uses of CT may require more task specific training targeting mid-level transfer effects.
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http://dx.doi.org/10.3389/fpsyg.2020.00196DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7028766PMC
February 2020

Examining the roles of working memory and visual attention in multiple object tracking expertise.

Cogn Process 2020 May 3;21(2):209-222. Epub 2020 Feb 3.

School of Sport and Health Sciences, University of Exeter, St Luke's Campus, Exeter, EX1 2LU, UK.

When tracking multiple moving targets among visually similar distractors, human observers are capable of distributing attention over several spatial locations. It is unclear, however, whether capacity limitations or perceptual-cognitive abilities are responsible for the development of expertise in multiple object tracking. Across two experiments, we examined the role of working memory and visual attention in tracking expertise. In Experiment 1, individuals who regularly engaged in object tracking sports (soccer and rugby) displayed improved tracking performance, relative to non-tracking sports (swimming, rowing, running) (p = 0.02, η = 0.163), but no differences in gaze strategy (ps > 0.31). In Experiment 2, participants trained on an adaptive object tracking task showed improved tracking performance (p = 0.005, d = 0.817), but no changes in gaze strategy (ps > 0.07). They did, however, show significant improvement in a working memory transfer task (p < 0.001, d = 0.970). These findings indicate that the development of tracking expertise is more closely linked to processing capacity limits than perceptual-cognitive strategies.
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http://dx.doi.org/10.1007/s10339-020-00954-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7203592PMC
May 2020

A non-canonical role for p27Kip1 in restricting proliferation of corneal endothelial cells during development.

PLoS One 2020 13;15(1):e0226725. Epub 2020 Jan 13.

Department of Biomedical Sciences, Quillen College of Medicine, East Tennessee State University, Johnson City, TN, United States of America.

The cell cycle regulator p27Kip1 is a critical factor controlling cell number in many lineages. While its anti-proliferative effects are well-established, the extent to which this is a result of its function as a cyclin-dependent kinase (CDK) inhibitor or through other known molecular interactions is not clear. To genetically dissect its role in the developing corneal endothelium, we examined mice harboring two loss-of-function alleles, a null allele (p27-) that abrogates all protein function and a knockin allele (p27CK-) that targets only its interaction with cyclins and CDKs. Whole-animal mutants, in which all cells are either homozygous knockout or knockin, exhibit identical proliferative increases (~0.6-fold) compared with wild-type tissues. On the other hand, use of mosaic analysis with double markers (MADM) to produce infrequently-occurring clones of wild-type and mutant cells within the same tissue environment uncovers a roughly three- and six-fold expansion of individual p27CK-/CK- and p27-/- cells, respectively. Mosaicism also reveals distinct migration phenotypes, with p27-/- cells being highly restricted to their site of production and p27CK-/CK- cells more widely scattered within the endothelium. Using a density-based clustering algorithm to quantify dispersal of MADM-generated clones, a four-fold difference in aggregation is seen between the two types of mutant cells. Overall, our analysis reveals that, in developing mouse corneal endothelium, p27 regulates cell number by acting cell autonomously, both through its interactions with cyclins and CDKs and through a cyclin-CDK-independent mechanism(s). Combined with its parallel influence on cell motility, it constitutes a potent multi-functional effector mechanism with major impact on tissue organization.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0226725PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6957298PMC
April 2020

Cradles and museums of generic plant diversity across tropical Africa.

New Phytol 2020 03 2;225(5):2196-2213. Epub 2019 Dec 2.

DIADE, IRD, University of Montpellier, 911 Avenue Agropolis, 34394, Montpellier, France.

Determining where species diversify (cradles) and persist (museums) over evolutionary time is fundamental to understanding the distribution of biodiversity and for conservation prioritization. Here, we identify cradles and museums of angiosperm generic diversity across tropical Africa, one of the most biodiverse regions on Earth. Regions containing nonrandom concentrations of young (neo-) and old (paleo-) endemic taxa were identified using distribution data of 1719 genera combined with a newly generated time-calibrated mega-phylogenetic tree. We then compared the identified regions with the current network of African protected areas (PAs). At the generic level, phylogenetic diversity and endemism are mainly concentrated in the biogeographically complex region of Eastern Africa. We show that mountainous areas are centres of both neo- and paleo-endemism. By contrast, the Guineo-Congolian lowland rain forest region is characterized by widespread and old lineages. We found that the overlap between centres of phylogenetic endemism and PAs is high (> 85%). We show the vital role played by mountains acting simultaneously as cradles and museums of tropical African plant biodiversity. By contrast, lowland rainforests act mainly as museums for generic diversity. Our study shows that incorporating large-scale taxonomically verified distribution datasets and mega-phylogenies lead to an improved understanding of tropical plant biodiversity evolution.
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http://dx.doi.org/10.1111/nph.16293DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7027791PMC
March 2020

Virtually the same? How impaired sensory information in virtual reality may disrupt vision for action.

Exp Brain Res 2019 Nov 4;237(11):2761-2766. Epub 2019 Sep 4.

School of Sport and Health Sciences, University of Exeter, St Luke's Campus, Exeter, EX1 2LU, UK.

Virtual reality (VR) is a promising tool for expanding the possibilities of psychological experimentation and implementing immersive training applications. Despite a recent surge in interest, there remains an inadequate understanding of how VR impacts basic cognitive processes. Due to the artificial presentation of egocentric distance cues in virtual environments, a number of cues to depth in the optic array are impaired or placed in conflict with each other. Moreover, realistic haptic information is all but absent from current VR systems. The resulting conflicts could impact not only the execution of motor skills in VR but also raise deeper concerns about basic visual processing, and the extent to which virtual objects elicit neural and behavioural responses representative of real objects. In this brief review, we outline how the novel perceptual environment of VR may affect vision for action, by shifting users away from a dorsal mode of control. Fewer binocular cues to depth, conflicting depth information and limited haptic feedback may all impair the specialised, efficient, online control of action characteristic of the dorsal stream. A shift from dorsal to ventral control of action may create a fundamental disparity between virtual and real-world skills that has important consequences for how we understand perception and action in the virtual world.
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http://dx.doi.org/10.1007/s00221-019-05642-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6794235PMC
November 2019

Deep Brain Stimulation at End of Life: Clinical and Ethical Considerations.

J Palliat Med 2020 04 12;23(4):582-585. Epub 2019 Aug 12.

Department of Palliative Medicine, Cleveland Clinic, Cleveland, Ohio.

Deep brain stimulation (DBS) is an implanted neurological device effective in treating motor symptoms of Parkinson disease (PD), such as tremor, rigidity, and bradykinesia. More than 150,000 patients worldwide have been implanted with DBS devices. Questions arise at the end of life concerning how to provide best care for patients with DBS, including its continued benefit or potential complications, yet, no published articles provide guidance for hospice providers regarding the management of DBS devices in end-of-life care. With contributions from hospice physicians, a neurosurgeon, and ethicists, this article provides recommendations to address clinical and ethical challenges in optimizing DBS for patients with PD nearing the end of life.
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http://dx.doi.org/10.1089/jpm.2019.0129DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7104899PMC
April 2020

To err again is human: exploring a bidirectional relationship between pressure and performance failure feedback.

Anxiety Stress Coping 2019 11 18;32(6):670-678. Epub 2019 Jul 18.

College of Life and Environmental Sciences, University of Exeter , Exeter , UK.

While the potentially negative effects of pressure on skilled performance have been well studied in laboratory-based research, theoretically driven questions based on real-world performance data are lacking. We aimed to test the predictions of the newly developed Attentional Control Theory: Sport (ACTS), using archived play-by-play data from the past seven seasons of the National Football League (American Football). An additive scoring system was developed to characterize the degree of pressure on 212,356 individual offensive plays and a Bayesian regression model was used to test the relationship between performance, pressure and preceding negative outcomes, as outlined in ACTS. There was found to be a clear increase in the incidence of failures on high pressure plays (odds ratio = 1.20), and on plays immediately following a previous play failure (odds ratio = 1.09). Additionally, a combined interactive effect of previous failure pressure indicated that the feedback effect of negative outcomes was greater when pressure was already high (odds ratio = 1.10), in line with the predictions of ACTS. These findings reveal the importance of exploring momentary changes in pressure in real-world sport settings, and the role of failure feedback in influencing the pressure-performance relationship.
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http://dx.doi.org/10.1080/10615806.2019.1643459DOI Listing
November 2019

Genetic diversity of Hepatozoon (Apicomplexa) from domestic cats in South Africa, with a global reassessment of Hepatozoon felis diversity.

J S Afr Vet Assoc 2019 Jun 20;90(0):e1-e6. Epub 2019 Jun 20.

CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Vairão, Portugal; and Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto.

Genetic diversity within partial 18S rRNA sequences from Hepatozoon protozoan parasites from domestic cats in South Africa was assessed and compared against published data to assess global biogeographic patterns. Multiple distinct haplotypes of Hepatozoon felis were identified, as well as an unrelated Hepatozoon lineage. Hepatozoon felis genetic diversity globally is very high, indicating a likely complex of species. The recently described Hepatozoon apri from wild boars is closely related to some lineages of H. felis. Sarcocystis and Babesia parasites were also detected. Since Hepatozoon felis is apparently a species complex, potential differences between genetically distinct forms need to be assessed. The finding of an unrelated Hepatozoon indicates that felids can be infected by more species of Hepatozoonthan currently known, and that trophic interactions may increase the number of Hepatozoon species found in carnivores. Genetic screening again is demonstrated to identify previously unrecognised parasites from vertebrate hosts.
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http://dx.doi.org/10.4102/jsava.v90i0.1747DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6620482PMC
June 2019

Hidden Markov Models Reveal Tactical Adjustment of Temporally Clustered Courtship Displays in Response to the Behaviors of a Robotic Female.

Am Nat 2019 07 31;194(1):1-16. Epub 2019 May 31.

We present a statistical approach-a custom-built hidden Markov model (HMM)-that is broadly applicable to the analysis of temporally clustered display events, as found in many animals, including birds, orthopterans, and anurans. This HMM can simultaneously estimate both the expected lengths of each animal's display bouts and their within-bout display rates. We highlight the HMM's ability to estimate changes in animals' display effort over time and across different social contexts, using data from male greater sage grouse (). Male display effort was modeled across three sites in two experimental treatments (robotic female simulating interested or uninterested behavior) and in the presence or absence of live females. Across contexts, we show that sage grouse males primarily adjust their bout lengths rather than their within-bout display rates. Males' responses to female behavior were correlated with male mating success: males with more matings showed high display persistence regardless of female behavior, while males with fewer matings tended to invest selectively in females that were already showing interest in mating. Additionally, males with higher mating success responded more to the presence of a female than males with fewer matings did. We conclude with suggestions for adapting our HMM approach for use in other animal systems.
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http://dx.doi.org/10.1086/703518DOI Listing
July 2019

Phenotypic variability in deficiency of the α subunit of succinate-CoA ligase.

JIMD Rep 2019 Mar 14;46(1):63-69. Epub 2019 Mar 14.

Division of Genetics and Genomics, Manton Center for Orphan Disease Research Boston Children's Hospital, Harvard Medical School Boston Massachusetts.

Succinyl-CoA synthetase or succinate-CoA ligase deficiency can result from biallelic mutations in gene that encodes for the alpha subunit of the succinyl-CoA synthetase. Mutations in this gene were initially associated with fatal infantile lactic acidosis. We describe an individual with a novel biallelic pathogenic mutation in with a less severe phenotype dominated by behavioral problems. The mutation was identified to be c.512A>G corresponding to a p.Asn171Ser change in the protein. The liquid chromatography tandem mass spectrometry-based enzyme activity assay on cultured fibroblasts revealed a markedly reduced activity of succinyl-CoA synthetase enzyme when both ATP and GTP were substrates, affecting both ADP-forming and GDP-forming functions of the enzyme.
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http://dx.doi.org/10.1002/jmd2.12018DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6498818PMC
March 2019

Perceptual-cognitive expertise when refereeing the scrum in rugby union.

J Sports Sci 2019 Aug 25;37(15):1778-1786. Epub 2019 Mar 25.

b College of Life and Environmental Sciences , University of Exeter , Exeter , UK.

Compared to sports performers, relatively little is known about how sports officials make decisions at a perceptual-cognitive level. Thus, this study examined the decision-making accuracy and gaze behaviour of rugby union referees of varying skill levels while reviewing scrum scenarios. Elite ( = 9) and trainee ( = 9) referees, as well as experienced players ( = 9), made decisions while watching ten projected scrum clips and wearing a mobile eye-tracker. Decision-making accuracy and gaze behaviour were recorded for each scrum. The elite and trainee referees made more accurate decisions than the players, and differences in gaze behavior were observed. The elite and trainee referees displayed lower search rates, spent more time fixating central-pack (i.e., front rows, binds, and contact point) and less time fixating outer-pack (e.g., second rows) and non-pack (e.g., other) locations, and exhibited lower entropy than the players. While search rate failed to predict decision-making accuracy, the time spent fixating central-, outer-, and non-pack locations, as well as entropy, were significant predictors. The findings have implications for training perceptual-cognitive skill among sports officials.
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http://dx.doi.org/10.1080/02640414.2019.1594568DOI Listing
August 2019

The persistence of carbon in the African forest understory.

Nat Plants 2019 02 21;5(2):133-140. Epub 2019 Jan 21.

Service of Wood Biology, Royal Museum for Central Africa, Tervuren, Belgium.

Quantifying carbon dynamics in forests is critical for understanding their role in long-term climate regulation. Yet little is known about tree longevity in tropical forests, a factor that is vital for estimating carbon persistence. Here we calculate mean carbon age (the period that carbon is fixed in trees) in different strata of African tropical forests using (1) growth-ring records with a unique timestamp accurately demarcating 66 years of growth in one site and (2) measurements of diameter increments from the African Tropical Rainforest Observation Network (23 sites). We find that in spite of their much smaller size, in understory trees mean carbon age (74 years) is greater than in sub-canopy (54 years) and canopy (57 years) trees and similar to carbon age in emergent trees (66 years). The remarkable carbon longevity in the understory results from slow and aperiodic growth as an adaptation to limited resource availability. Our analysis also reveals that while the understory represents a small share (11%) of the carbon stock, it contributes disproportionally to the forest carbon sink (20%). We conclude that accounting for the diversity of carbon age and carbon sequestration among different forest strata is critical for effective conservation management and for accurate modelling of carbon cycling.
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http://dx.doi.org/10.1038/s41477-018-0316-5DOI Listing
February 2019

An external focus of attention promotes flow experience during simulated driving.

Eur J Sport Sci 2019 Jul 27;19(6):824-833. Epub 2018 Dec 27.

a School of Sport and Health Sciences , University of Exeter , Exeter , UK.

Achieving a state of flow is associated with positive experiences and improved sporting performance (Jackson & Csikszentmihalyi, 1999). Focused attention is a fundamental component of the flow experience, but to date there has been little investigation of whether attention plays a causal role in creating flow, or is a product of it. Consequently, this study aimed to test the effect of an attentional focus manipulation on flow and performance in a simulated driving task. It was predicted that an external focus would lead to improved visuomotor control, greater flow experience and improved performance. Thirty-three participants from a student population completed the driving task under both internal and external focus instructions. Eye movements and steering wheel movements were recorded during each race. Participants reported greater flow experience ( < .001, = 1.78) and enhanced outcome expectancies (= .02, = 0.41) under external, compared to internal focus conditions, however, there was no effect on visuomotor control (gaze-steering coordination and steering entropy) or racing performance (s > 0.28). These findings suggest that adopting an external focus of attention may contribute to positive performance states such as flow.
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http://dx.doi.org/10.1080/17461391.2018.1560508DOI Listing
July 2019

Interspace between Popliteal Artery and posterior Capsule of the Knee (IPACK) Injectate Spread: A Cadaver Study.

J Ultrasound Med 2019 Mar 19;38(3):741-745. Epub 2018 Sep 19.

Departments of Anesthesiology and Perioperative Medicine, Mayo Clinic, Rochester, Minnesota, USA.

Objectives: Local anesthetic injection into the interspace between the popliteal artery and the posterior capsule of the knee (IPACK) has the potential to provide motor-sparing analgesia to the posterior knee after total knee arthroplasty. The primary objective of this cadaveric study was to evaluate injectate spread to relevant anatomic structures with IPACK injection.

Methods: After receipt of Institutional Review Board Biospecimen Subcommittee approval, IPACK injection was performed on fresh-frozen cadavers. The popliteal fossa in each specimen was dissected and examined for injectate spread.

Results: Ten fresh-frozen cadaver knees were included in the study. Injectate was observed to spread in the popliteal fossa at a mean ± SD of 6.1 ± 0.7 cm in the medial-lateral dimension and 10.1 ± 3.2 cm in the proximal-distal dimension. No injectate was noted to be in contact with the proximal segment of the sciatic nerve, but 3 specimens showed injectate spread to the tibial nerve. In 3 specimens, the injectate showed possible contact with the common peroneal nerve. The middle genicular artery was consistently surrounded by injectate.

Conclusions: This cadaver study of IPACK injection demonstrated spread throughout the popliteal fossa without proximal sciatic involvement. However, the potential for injectate to spread to the tibial or common peroneal nerve was demonstrated. Consistent surrounding of the middle genicular artery with injectate suggests a potential mechanism of analgesia for the IPACK block, due to the predictable relationship between articular sensory nerves and this artery. Further study is needed to determine the ideal site of IPACK injection.
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http://dx.doi.org/10.1002/jum.14761DOI Listing
March 2019

A Systematic Review of Commercial Cognitive Training Devices: Implications for Use in Sport.

Front Psychol 2018 11;9:709. Epub 2018 May 11.

Sport and Health Sciences, University of Exeter, Exeter, United Kingdom.

Cognitive training (CT) aims to develop a range of skills, like attention and decision-making, through targeted training of core cognitive functions. While CT can target context specific skills, like movement anticipation, much CT is domain general, focusing on core abilities (e.g., selective attention) for transfer to a range of real-world tasks, such as spotting opponents. Commercial CT (CCT) devices are highly appealing for athletes and coaches due to their ease of use and eye-catching marketing claims. The extent to which this training transfers to performance in the sporting arena is, however, unclear. Therefore, this paper sought to provide a systematic review of evidence for beneficial training effects of CCT devices and evaluate their application to sport. An extensive search of electronic databases (PubMed, PsychInfo, GoogleScholar, and SportDiscus) was conducted to identify peer-reviewed evidence of training interventions with commercially available CT devices. Forty-three studies met the inclusion criteria and were retained for quality assessment and synthesis of results. Seventeen studies assessed transfer effects beyond laboratory cognitive tests, but only 1 directly assessed transfer to a sporting task. The review of evidence showed limited support for far transfer benefits from CCT devices to sporting tasks, mainly because studies did not target the sporting environment. Additionally, a number of methodological issues with the CCT literature were identified, including small sample sizes, lack of retention tests, and limited replication of findings by researchers independent of the commercial product. Therefore, evidence for sporting benefits is currently limited by the paucity of representative transfer tests and a focus on populations with health conditions. Currently there is little direct evidence that the use of CCT devices can transfer to benefits for sporting performance. This conclusion, however, stems more from a lack of experimental studies in the sporting field and a lack of experimental rigor, rather than convincing null effects. Subsequently, there is an opportunity for researchers to develop more reliable findings in this area through systematic assessment in athletic populations and major methodological improvements.
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http://dx.doi.org/10.3389/fpsyg.2018.00709DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5958310PMC
May 2018

A randomised trial of observational learning from 2D and 3D models in robotically assisted surgery.

Surg Endosc 2018 11 14;32(11):4527-4532. Epub 2018 May 14.

Sport and Health Sciences, University of Exeter, Exeter, UK.

Background: Advances in 3D technology mean that both robotic surgical devices and surgical simulators can now incorporate stereoscopic viewing capabilities. While depth information may benefit robotic surgical performance, it is unclear whether 3D viewing also aids skill acquisition when learning from observing others. As observational learning plays a major role in surgical skills training, this study aimed to evaluate whether 3D viewing provides learning benefits in a robotically assisted surgical task.

Methods: 90 medical students were assigned to either (1) 2D or (2) 3D observation of a consultant surgeon performing a training task on the daVinci S robotic system, or (3) a no observation control, in a randomised parallel design. Subsequent performance and instrument movement metrics were assessed immediately following observation and at one-week retention.

Results: Both 2D and 3D groups outperformed no observation controls following the observation intervention (ps < 0.05), but there was no difference between 2D and 3D groups at any of the timepoints. There was also no difference in movement parameters between groups.

Conclusions: While 3D viewing systems may have beneficial effects for surgical performance, these results suggest that depth information has limited utility during observational learning of surgical skills in novices. The task constraints and end goals may provide more important information for learning than the relative motion of surgical instruments in 3D space.
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http://dx.doi.org/10.1007/s00464-018-6203-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6182323PMC
November 2018

Long-term community change through multiple rapid transitions in a desert rodent community.

Ecology 2018 07 7;99(7):1523-1529. Epub 2018 Jun 7.

Department of Wildlife Ecology and Conservation, University of Florida, 110 Newins-Ziegler Hall, Gainesville, Florida, 32611, USA.

While studies increasingly document long-term change in community composition, whether long-term change occurs gradually or via rapid reorganization events remains unclear. We used Latent Dirichlet Allocation (LDA) and a change-point model to examine the long-term dynamics of a desert rodent community undergoing compositional change over a 38-yr span. Our approach detected three rapid reorganization events, where changes in the relative abundances of dominant and rare species occurred, and a separate period of increased variance in the structure of the community. These events coincided with time periods, possibly related to climate events, where the total abundance of rodents was extremely low. There are a variety of processes that could link low abundance events with a higher probability of rapid ecological transitions, including higher importance of stochastic processes (i.e., competitive interactions or priority effects) and the removal of structuring effects of competitive dominants or incumbent species. Continued study of the dynamics of community change will provide important information not only on the processes structuring communities, but will also provide guidance for forecasting how communities will undergo change in the future.
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http://dx.doi.org/10.1002/ecy.2373DOI Listing
July 2018

Opportunities and obstacles for deep learning in biology and medicine.

J R Soc Interface 2018 04;15(141)

Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA

Deep learning describes a class of machine learning algorithms that are capable of combining raw inputs into layers of intermediate features. These algorithms have recently shown impressive results across a variety of domains. Biology and medicine are data-rich disciplines, but the data are complex and often ill-understood. Hence, deep learning techniques may be particularly well suited to solve problems of these fields. We examine applications of deep learning to a variety of biomedical problems-patient classification, fundamental biological processes and treatment of patients-and discuss whether deep learning will be able to transform these tasks or if the biomedical sphere poses unique challenges. Following from an extensive literature review, we find that deep learning has yet to revolutionize biomedicine or definitively resolve any of the most pressing challenges in the field, but promising advances have been made on the prior state of the art. Even though improvements over previous baselines have been modest in general, the recent progress indicates that deep learning methods will provide valuable means for speeding up or aiding human investigation. Though progress has been made linking a specific neural network's prediction to input features, understanding how users should interpret these models to make testable hypotheses about the system under study remains an open challenge. Furthermore, the limited amount of labelled data for training presents problems in some domains, as do legal and privacy constraints on work with sensitive health records. Nonetheless, we foresee deep learning enabling changes at both bench and bedside with the potential to transform several areas of biology and medicine.
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http://dx.doi.org/10.1098/rsif.2017.0387DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5938574PMC
April 2018

Forecasting biodiversity in breeding birds using best practices.

PeerJ 2018 8;6:e4278. Epub 2018 Feb 8.

Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, FL, United States of America.

Biodiversity forecasts are important for conservation, management, and evaluating how well current models characterize natural systems. While the number of forecasts for biodiversity is increasing, there is little information available on how well these forecasts work. Most biodiversity forecasts are not evaluated to determine how well they predict future diversity, fail to account for uncertainty, and do not use time-series data that captures the actual dynamics being studied. We addressed these limitations by using best practices to explore our ability to forecast the species richness of breeding birds in North America. We used hindcasting to evaluate six different modeling approaches for predicting richness. Hindcasts for each method were evaluated annually for a decade at 1,237 sites distributed throughout the continental United States. All models explained more than 50% of the variance in richness, but none of them consistently outperformed a baseline model that predicted constant richness at each site. The best practices implemented in this study directly influenced the forecasts and evaluations. Stacked species distribution models and "naive" forecasts produced poor estimates of uncertainty and accounting for this resulted in these models dropping in the relative performance compared to other models. Accounting for observer effects improved model performance overall, but also changed the rank ordering of models because it did not improve the accuracy of the "naive" model. Considering the forecast horizon revealed that the prediction accuracy decreased across all models as the time horizon of the forecast increased. To facilitate the rapid improvement of biodiversity forecasts, we emphasize the value of specific best practices in making forecasts and evaluating forecasting methods.
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http://dx.doi.org/10.7717/peerj.4278DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5808145PMC
February 2018

Phylogenetic classification of the world's tropical forests.

Authors:
J W Ferry Slik Janet Franklin Víctor Arroyo-Rodríguez Richard Field Salomon Aguilar Nikolay Aguirre Jorge Ahumada Shin-Ichiro Aiba Luciana F Alves Anitha K Andres Avella Francisco Mora Gerardo A Aymard C Selene Báez Patricia Balvanera Meredith L Bastian Jean-François Bastin Peter J Bellingham Eduardo van den Berg Polyanna da Conceição Bispo Pascal Boeckx Katrin Boehning-Gaese Frans Bongers Brad Boyle Fabian Brambach Francis Q Brearley Sandra Brown Shauna-Lee Chai Robin L Chazdon Shengbin Chen Phourin Chhang George Chuyong Corneille Ewango Indiana M Coronado Jurgi Cristóbal-Azkarate Heike Culmsee Kipiro Damas H S Dattaraja Priya Davidar Saara J DeWalt Hazimah Din Donald R Drake Alvaro Duque Giselda Durigan Karl Eichhorn Eduardo Schmidt Eler Tsutomu Enoki Andreas Ensslin Adandé Belarmain Fandohan Nina Farwig Kenneth J Feeley Markus Fischer Olle Forshed Queila Souza Garcia Satish Chandra Garkoti Thomas W Gillespie Jean-Francois Gillet Christelle Gonmadje Iñigo Granzow-de la Cerda Daniel M Griffith James Grogan Khalid Rehman Hakeem David J Harris Rhett D Harrison Andy Hector Andreas Hemp Jürgen Homeier M Shah Hussain Guillermo Ibarra-Manríquez I Faridah Hanum Nobuo Imai Patrick A Jansen Carlos Alfredo Joly Shijo Joseph Kuswata Kartawinata Elizabeth Kearsley Daniel L Kelly Michael Kessler Timothy J Killeen Robert M Kooyman Yves Laumonier Susan G Laurance William F Laurance Michael J Lawes Susan G Letcher Jeremy Lindsell Jon Lovett Jose Lozada Xinghui Lu Anne Mette Lykke Khairil Bin Mahmud Ni Putu Diana Mahayani Asyraf Mansor Andrew R Marshall Emanuel H Martin Darley Calderado Leal Matos Jorge A Meave Felipe P L Melo Zhofre Huberto Aguirre Mendoza Faizah Metali Vincent P Medjibe Jean Paul Metzger Thiago Metzker D Mohandass Miguel A Munguía-Rosas Rodrigo Muñoz Eddy Nurtjahy Eddie Lenza de Oliveira Onrizal Pia Parolin Marc Parren N Parthasarathy Ekananda Paudel Rolando Perez Eduardo A Pérez-García Ulf Pommer Lourens Poorter Lan Qie Maria Teresa F Piedade José Roberto Rodrigues Pinto Axel Dalberg Poulsen John R Poulsen Jennifer S Powers Rama Chandra Prasad Jean-Philippe Puyravaud Orlando Rangel Jan Reitsma Diogo S B Rocha Samir Rolim Francesco Rovero Andes Rozak Kalle Ruokolainen Ervan Rutishauser Gemma Rutten Mohd Nizam Mohd Said Felipe Z Saiter Philippe Saner Braulio Santos João Roberto Dos Santos Swapan Kumar Sarker Christine B Schmitt Jochen Schoengart Mark Schulze Douglas Sheil Plinio Sist Alexandre F Souza Wilson Roberto Spironello Tereza Sposito Robert Steinmetz Tariq Stevart Marcio Seiji Suganuma Rahayu Sukri Aisha Sultana Raman Sukumar Terry Sunderland Supriyadi H S Suresh Eizi Suzuki Marcelo Tabarelli Jianwei Tang Ed V J Tanner Natalia Targhetta Ida Theilade Duncan Thomas Jonathan Timberlake Márcio de Morisson Valeriano Johan van Valkenburg Tran Van Do Hoang Van Sam John H Vandermeer Hans Verbeeck Ole Reidar Vetaas Victor Adekunle Simone A Vieira Campbell O Webb Edward L Webb Timothy Whitfeld Serge Wich John Williams Susan Wiser Florian Wittmann Xiaobo Yang C Yves Adou Yao Sandra L Yap Rakan A Zahawi Rahmad Zakaria Runguo Zang

Proc Natl Acad Sci U S A 2018 02 5;115(8):1837-1842. Epub 2018 Feb 5.

Key Laboratory of Forest Ecology and Environment of State Forestry Administration, Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing 100091, China.

Knowledge about the biogeographic affinities of the world's tropical forests helps to better understand regional differences in forest structure, diversity, composition, and dynamics. Such understanding will enable anticipation of region-specific responses to global environmental change. Modern phylogenies, in combination with broad coverage of species inventory data, now allow for global biogeographic analyses that take species evolutionary distance into account. Here we present a classification of the world's tropical forests based on their phylogenetic similarity. We identify five principal floristic regions and their floristic relationships: () Indo-Pacific, () Subtropical, () African, () American, and () Dry forests. Our results do not support the traditional neo- versus paleotropical forest division but instead separate the combined American and African forests from their Indo-Pacific counterparts. We also find indications for the existence of a global dry forest region, with representatives in America, Africa, Madagascar, and India. Additionally, a northern-hemisphere Subtropical forest region was identified with representatives in Asia and America, providing support for a link between Asian and American northern-hemisphere forests.
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http://dx.doi.org/10.1073/pnas.1714977115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5828595PMC
February 2018