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  1. Article ; Online: Publication bias impacts on effect size, statistical power, and magnitude (Type M) and sign (Type S) errors in ecology and evolutionary biology.

    Yang, Yefeng / Sánchez-Tójar, Alfredo / O'Dea, Rose E / Noble, Daniel W A / Koricheva, Julia / Jennions, Michael D / Parker, Timothy H / Lagisz, Malgorzata / Nakagawa, Shinichi

    BMC biology

    2023  Volume 21, Issue 1, Page(s) 71

    Abstract: ... statistical power, and errors in magnitude (Type M or exaggeration ratio) and sign (Type S). We show strong ... statistical power (15%) with a 4-fold exaggeration of effects on average (Type M error rates = 4.4). Notably ... publication bias reduced power from 23% to 15% and increased type M error rates from 2.7 to 4.4 because it creates ...

    Abstract Collaborative efforts to directly replicate empirical studies in the medical and social sciences have revealed alarmingly low rates of replicability, a phenomenon dubbed the 'replication crisis'. Poor replicability has spurred cultural changes targeted at improving reliability in these disciplines. Given the absence of equivalent replication projects in ecology and evolutionary biology, two inter-related indicators offer the opportunity to retrospectively assess replicability: publication bias and statistical power. This registered report assesses the prevalence and severity of small-study (i.e., smaller studies reporting larger effect sizes) and decline effects (i.e., effect sizes decreasing over time) across ecology and evolutionary biology using 87 meta-analyses comprising 4,250 primary studies and 17,638 effect sizes. Further, we estimate how publication bias might distort the estimation of effect sizes, statistical power, and errors in magnitude (Type M or exaggeration ratio) and sign (Type S). We show strong evidence for the pervasiveness of both small-study and decline effects in ecology and evolution. There was widespread prevalence of publication bias that resulted in meta-analytic means being over-estimated by (at least) 0.12 standard deviations. The prevalence of publication bias distorted confidence in meta-analytic results, with 66% of initially statistically significant meta-analytic means becoming non-significant after correcting for publication bias. Ecological and evolutionary studies consistently had low statistical power (15%) with a 4-fold exaggeration of effects on average (Type M error rates = 4.4). Notably, publication bias reduced power from 23% to 15% and increased type M error rates from 2.7 to 4.4 because it creates a non-random sample of effect size evidence. The sign errors of effect sizes (Type S error) increased from 5% to 8% because of publication bias. Our research provides clear evidence that many published ecological and evolutionary findings are inflated. Our results highlight the importance of designing high-power empirical studies (e.g., via collaborative team science), promoting and encouraging replication studies, testing and correcting for publication bias in meta-analyses, and adopting open and transparent research practices, such as (pre)registration, data- and code-sharing, and transparent reporting.
    MeSH term(s) Bias ; Biology ; Publication Bias ; Reproducibility of Results ; Retrospective Studies ; Meta-Analysis as Topic
    Language English
    Publishing date 2023-04-03
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2133020-7
    ISSN 1741-7007 ; 1741-7007
    ISSN (online) 1741-7007
    ISSN 1741-7007
    DOI 10.1186/s12915-022-01485-y
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Review of historic article: Butler, J.A.V., Johns, E.W. and Philips, D. M. P. 1968. Recent investigations on histones and their functions. Progress in Biophysics and molecular biology, 18, 209-244.

    Noble, Denis

    Progress in biophysics and molecular biology

    2022  Volume 171, Page(s) 26–28

    Abstract: This Historic Article was based on pioneering work by the laboratory of the Founding Editor of the journal to characterise the different forms of histones in the nucleus and their relationship with DNA. The classification determined in 1968 bears strong ... ...

    Abstract This Historic Article was based on pioneering work by the laboratory of the Founding Editor of the journal to characterise the different forms of histones in the nucleus and their relationship with DNA. The classification determined in 1968 bears strong relationship to that known today. Most importantly, the work clarified that the inhibitory effect of histones on DNA is a general one and would not explain the subsequent differentiation of cells during development in multicellular organisms. Extensive work on the amino acids in histones leads to the understanding that negatively charged DNA naturally attaches itself to positively charged histones.
    MeSH term(s) Biophysics ; DNA ; Histones ; Molecular Biology
    Chemical Substances Histones ; DNA (9007-49-2)
    Language English
    Publishing date 2022-04-07
    Publishing country England
    Document type Letter
    ZDB-ID 209302-9
    ISSN 1873-1732 ; 0079-6107
    ISSN (online) 1873-1732
    ISSN 0079-6107
    DOI 10.1016/j.pbiomolbio.2022.04.001
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Review of historic article: Ebashi, S & Endo, M. 1968 Calcium Ion and Muscle Contraction. Progress in Biophysics and Molecular Biology, 18, 123-183.

    Noble, Denis

    Progress in biophysics and molecular biology

    2022  Volume 171, Page(s) 24–25

    Abstract: The 1968 review article on Calcium ion and muscle contraction by Setsuro Ebashi and Makoto Endo is one of the highest cited in the journal since it was required reading in the early days of understanding what triggers contraction of the myofilaments. It ... ...

    Abstract The 1968 review article on Calcium ion and muscle contraction by Setsuro Ebashi and Makoto Endo is one of the highest cited in the journal since it was required reading in the early days of understanding what triggers contraction of the myofilaments. It correctly identified the major steps in excitation-contraction coupling and still inspires mathematical models of muscle activity today. It also successfully identified the role of troponin.
    MeSH term(s) Biophysics ; Calcium/metabolism ; Calcium Signaling/physiology ; Ions ; Molecular Biology ; Muscle Contraction/physiology
    Chemical Substances Ions ; Calcium (SY7Q814VUP)
    Language English
    Publishing date 2022-04-04
    Publishing country England
    Document type Letter ; Review
    ZDB-ID 209302-9
    ISSN 1873-1732 ; 0079-6107
    ISSN (online) 1873-1732
    ISSN 0079-6107
    DOI 10.1016/j.pbiomolbio.2022.03.009
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Publication bias impacts on effect size, statistical power, and magnitude (Type M) and sign (Type S) errors in ecology and evolutionary biology

    Yefeng Yang / Alfredo Sánchez-Tójar / Rose E. O’Dea / Daniel W. A. Noble / Julia Koricheva / Michael D. Jennions / Timothy H. Parker / Malgorzata Lagisz / Shinichi Nakagawa

    BMC Biology, Vol 21, Iss 1, Pp 1-

    2023  Volume 20

    Abstract: ... statistical power, and errors in magnitude (Type M or exaggeration ratio) and sign (Type S). We show strong ... statistical power (15%) with a 4-fold exaggeration of effects on average (Type M error rates = 4.4). Notably ... publication bias reduced power from 23% to 15% and increased type M error rates from 2.7 to 4.4 because it creates ...

    Abstract Abstract Collaborative efforts to directly replicate empirical studies in the medical and social sciences have revealed alarmingly low rates of replicability, a phenomenon dubbed the ‘replication crisis’. Poor replicability has spurred cultural changes targeted at improving reliability in these disciplines. Given the absence of equivalent replication projects in ecology and evolutionary biology, two inter-related indicators offer the opportunity to retrospectively assess replicability: publication bias and statistical power. This registered report assesses the prevalence and severity of small-study (i.e., smaller studies reporting larger effect sizes) and decline effects (i.e., effect sizes decreasing over time) across ecology and evolutionary biology using 87 meta-analyses comprising 4,250 primary studies and 17,638 effect sizes. Further, we estimate how publication bias might distort the estimation of effect sizes, statistical power, and errors in magnitude (Type M or exaggeration ratio) and sign (Type S). We show strong evidence for the pervasiveness of both small-study and decline effects in ecology and evolution. There was widespread prevalence of publication bias that resulted in meta-analytic means being over-estimated by (at least) 0.12 standard deviations. The prevalence of publication bias distorted confidence in meta-analytic results, with 66% of initially statistically significant meta-analytic means becoming non-significant after correcting for publication bias. Ecological and evolutionary studies consistently had low statistical power (15%) with a 4-fold exaggeration of effects on average (Type M error rates = 4.4). Notably, publication bias reduced power from 23% to 15% and increased type M error rates from 2.7 to 4.4 because it creates a non-random sample of effect size evidence. The sign errors of effect sizes (Type S error) increased from 5% to 8% because of publication bias. Our research provides clear evidence that many published ecological and evolutionary findings are inflated. Our results ...
    Keywords Open science ; Replicability ; Reproducibility ; Transparency ; Selective reporting ; Questionable research practices ; Biology (General) ; QH301-705.5
    Subject code 501
    Language English
    Publishing date 2023-04-01T00:00:00Z
    Publisher BMC
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Article ; Online: An Observational Cerebral Magnetic Resonance Imaging Study Following 7 Days at 4554 m.

    Kühn, Sven / Gerlach, Darius / Noblé, Hans-Jürgen / Weber, Frank / Rittweger, Jörn / Jordan, Jens / Limper, Ulrich

    High altitude medicine & biology

    2019  Volume 20, Issue 4, Page(s) 407–416

    Abstract: Background: ...

    Abstract Background:
    MeSH term(s) Acclimatization ; Adult ; Altitude ; Altitude Sickness/complications ; Altitude Sickness/diagnostic imaging ; Altitude Sickness/pathology ; Brain/diagnostic imaging ; Brain/pathology ; Brain Edema/diagnostic imaging ; Brain Edema/etiology ; Brain Edema/pathology ; Female ; Humans ; Italy ; Magnetic Resonance Imaging ; Male ; Middle Aged
    Language English
    Publishing date 2019-11-14
    Publishing country United States
    Document type Journal Article ; Observational Study ; Research Support, Non-U.S. Gov't
    ZDB-ID 2076262-8
    ISSN 1557-8682 ; 1527-0297
    ISSN (online) 1557-8682
    ISSN 1527-0297
    DOI 10.1089/ham.2019.0056
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: The M-Maze task: An automated method for studying fear memory in rats exposed to protracted aversive conditioning.

    Souza, Rimenez R / Robertson, Nicole M / Pruitt, David T / Noble, Lindsey / Meyers, Eric C / Gonzales, Phillip A / Bleker, Nathaniel P / Carey, Holle L / Hays, Seth A / Kilgard, Michael P / McIntyre, Christa K / Rennaker, Robert L

    Journal of neuroscience methods

    2018  Volume 298, Page(s) 54–65

    Abstract: ... the M-Maze task, a system that measures extinction of conditioned fear using suppression of operant ... behavior. The apparatus consists of an M-shaped maze where rats are trained to alternate nose poking at two ... impairments in M-Maze tests, as well as enhanced anxiety, and social withdrawal.: Comparison ...

    Abstract Background: Fear conditioning (FC) in rodents is the most used animal model to investigate the neurobiology of posttraumatic stress disorder (PTSD). Although research using FC has generated a better understanding of fear memories, studies often rely on mild or moderate FC training and behavioral analysis generally focuses on measuring freezing responses within few test sessions.
    New method: We introduce the M-Maze task, a system that measures extinction of conditioned fear using suppression of operant behavior. The apparatus consists of an M-shaped maze where rats are trained to alternate nose poking at two pellet dispensers. Proximity sensors measure the animal's locomotion, as well as the latencies and number of operant behaviors. Here we also describe the protracted aversive conditioning (PAC), a rat model of severe fear that induces resistant extinction following a 4-day conditioning protocol that combines delay, unpredictable, and short- and long-trace conditioning.
    Results: An intense one-day auditory FC protocol induced a sharp elevation in transit time and suppression of nose pokes by conditioned cues, but in contrast to what is found in PTSD patients, fear extinction was rapidly observed. On the other hand, PAC alone or in combination with exposure to single prolonged stress induced persistent extinction impairments in M-Maze tests, as well as enhanced anxiety, and social withdrawal.
    Comparison with other existing methods: The M-Maze task is fully automated and allows multiple animals to be tested simultaneously in long-term experiments. Moreover, PAC training can be an alternative approach to study extinction-resistant fear.
    Conclusions: The M-Maze task allows rapid and unbiased measurements of fear-induced suppression. We suggest that long-term assessment of extinction impairments would lead to a better understanding of the neurobiology of persistent fear and the screening for new therapies.
    MeSH term(s) Animals ; Auditory Perception ; Automation, Laboratory/instrumentation ; Automation, Laboratory/methods ; Avoidance Learning ; Conditioning (Psychology) ; Disease Models, Animal ; Electroshock ; Equipment Design ; Extinction, Psychological ; Fear ; Male ; Maze Learning ; Memory ; Motor Activity ; Psychological Tests ; Rats, Sprague-Dawley ; Reflex, Startle ; Social Behavior ; Stress Disorders, Post-Traumatic
    Language English
    Publishing date 2018-02-13
    Publishing country Netherlands
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 282721-9
    ISSN 1872-678X ; 0165-0270
    ISSN (online) 1872-678X
    ISSN 0165-0270
    DOI 10.1016/j.jneumeth.2018.02.004
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Resolving the M-cell debate: why and how.

    Nattel, Stanley / Antzelevitch, Charles / Noble, Denis

    Heart rhythm

    2011  Volume 8, Issue 8, Page(s) 1293–1295

    MeSH term(s) Action Potentials/physiology ; Anesthetics, General/pharmacology ; Electrophysiologic Techniques, Cardiac ; Heart/drug effects ; Heart/physiology ; Heart Conduction System/physiology ; Heart Ventricles/cytology ; Humans ; Ion Channels/drug effects ; Ion Channels/physiology ; Myocardium/cytology ; Sodium Channels/drug effects ; Sodium Channels/physiology
    Chemical Substances Anesthetics, General ; Ion Channels ; Sodium Channels
    Language English
    Publishing date 2011-07-14
    Publishing country United States
    Document type Editorial ; Research Support, Non-U.S. Gov't
    ZDB-ID 2229357-7
    ISSN 1556-3871 ; 1547-5271
    ISSN (online) 1556-3871
    ISSN 1547-5271
    DOI 10.1016/j.hrthm.2011.06.002
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article: The Multiscale TROPIcal CatchmentS critical zone observatory M‐TROPICS dataset II: Land use, hydrology and sediment production monitoring in Houay Pano, northern Lao PDR

    Boithias, Laurie / Auda, Yves / Audry, Stéphane / Bricquet, Jean‐Pierre / Chanhphengxay, Alounsavath / Chaplot, Vincent / de Rouw, Anneke / Henry des Tureaux, Thierry / Huon, Sylvain / Janeau, Jean‐Louis / Latsachack, Keooudone / Le Troquer, Yann / Lestrelin, Guillaume / Maeght, Jean‐Luc / Marchand, Pierre / Moreau, Pierre / Noble, Andrew / Pando‐Bahuon, Anne / Phachomphon, Kongkeo /
    Phanthavong, Khambai / Pierret, Alain / Ribolzi, Olivier / Riotte, Jean / Robain, Henri / Rochelle‐Newall, Emma / Sayavong, Saysongkham / Sengtaheuanghoung, Oloth / Silvera, Norbert / Sipaseuth, Nivong / Soulileuth, Bounsamay / Souliyavongsa, Xaysatith / Sounyaphong, Phapvilay / Tasaketh, Sengkeo / Thammahacksa, Chanthamousone / Thiebaux, Jean‐Pierre / Valentin, Christian / Vigiak, Olga / Viguier, Marion / Xayyathip, Khampaseuth

    Hydrological processes. 2021 May, v. 35, no. 5

    2021  

    Abstract: ... of critical zone observatories named Multiscale TROPIcal CatchmentS (M‐TROPICS). The data shared by M‐TROPICS ... at both microplot (1 ) and small catchment (0.6 km²) scales. The monitored catchment is part of the network ...

    Abstract Mountain regions of the humid tropics are characterized by steep slopes and heavy rains. These regions are thus prone to both high surface runoff and soil erosion. In Southeast Asia, uplands are also subject to rapid land‐use change, predominantly as a result of increased population pressure and market forces. Since 1998, the Houay Pano site, located in northern Lao PDR (19.85°N 102.17°E) within the Mekong basin, aims at assessing the long‐term impact of the conversion of traditional slash‐and‐burn cultivation systems to commercial perennial monocultures such as teak tree plantations, on the catchment hydrological response and sediment yield. The instrumented site monitors hydro‐meteorological and soil loss parameters at both microplot (1 ) and small catchment (0.6 km²) scales. The monitored catchment is part of the network of critical zone observatories named Multiscale TROPIcal CatchmentS (M‐TROPICS). The data shared by M‐TROPICS in Houay Pano are (1) rainfall, (2) air temperature, air relative humidity, wind speed, and global radiation, (3) catchment land use, (4) stream water level, suspended particulate matter, bed particulate matter and stones, (5) soil surface features, and (6) soil surface runoff and soil detachment. The dataset has already been used to interpret suspended particulate matter and bed particulate matter sources and dynamics, to assess the impact of land‐use change on catchment hydrology, soil erosion, and sediment yields, to understand bacteria fate and weed seed transport across the catchment, and to build catchment‐scale models focused on hydrology and water quality issues. The dataset may be further used to, for example, assess the role of headwater catchments in large tropical river basin hydrology, support the interpretation of new variables measured in the catchment (e.g., contaminants other than faecal bacteria), and assess the relative impacts of both climate and land‐use change on the catchment.
    Keywords Tectona grandis ; air ; air temperature ; basins ; data collection ; hydrometeorology ; land use change ; long term effects ; markets ; particulates ; population growth ; population pressure ; rain ; relative humidity ; runoff ; sediment yield ; sediments ; seed dispersal ; soil ; soil erosion ; streams ; trees ; water quality ; watershed hydrology ; watersheds ; weeds ; wind speed ; Laos
    Language English
    Dates of publication 2021-05
    Publishing place John Wiley & Sons, Inc.
    Document type Article
    Note NAL-AP-2-clean ; JOURNAL ARTICLE
    ZDB-ID 1479953-4
    ISSN 1099-1085 ; 0885-6087
    ISSN (online) 1099-1085
    ISSN 0885-6087
    DOI 10.1002/hyp.14126
    Database NAL-Catalogue (AGRICOLA)

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  9. Article: The role of stimulus meaning (m) in serial verbal learning.

    NOBLE, C E

    Journal of experimental psychology

    2004  Volume 43, Issue 6, Page(s) 437–446

    MeSH term(s) Humans ; Learning ; Serial Learning ; Verbal Learning
    Language English
    Publishing date 2004-02-03
    Publishing country United States
    Document type Journal Article
    ISSN 0022-1015
    ISSN 0022-1015
    DOI 10.1037/h0056619
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Book ; Online ; E-Book: Navigating life with dementia

    Noble, James M.

    (Brain & life books)

    2022  

    Abstract: Navigating Life with Dementia' is designed as a handbook including tools to manage both day-to-day issues and to anticipate the long-term impact of the disease for dementia patients as well as their friends and families. This volume will help families ... ...

    Institution American Academy of Neurology,
    Author's details James M. Noble, MD, MS, CPH, FAAN
    Series title Brain & life books
    Abstract 'Navigating Life with Dementia' is designed as a handbook including tools to manage both day-to-day issues and to anticipate the long-term impact of the disease for dementia patients as well as their friends and families. This volume will help families in all stages of dementia care, beginning with the earliest hints of cognitive problems through advanced stages. In easily understood language, the book thoroughly covers the complexities of the dementias, the establishment of a diagnosis, what to expect throughout the stages of disease, and how to best anticipate and manage common problems.
    Keywords Dementia/Patients ; Dementia/Patients/Rehabilitation ; Health and Wellbeing ; Clinical & internal medicine
    Subject code 616.83
    Language English
    Dates of publication 2022-2022
    Size 1 online resource (305 pages)
    Publisher Oxford University Press
    Publishing place New York, NY
    Document type Book ; Online ; E-Book
    Note At foot of cover title: American Academy of Neurology. ; Also issued in print: 2022.
    Remark Zugriff für angemeldete ZB MED-Nutzerinnen und -Nutzer
    ISBN 0-19-762868-0 ; 0-19-049570-7 ; 0-19-049569-3 ; 9780190495688 ; 978-0-19-762868-3 ; 978-0-19-049570-1 ; 978-0-19-049569-5 ; 0190495685
    Database ZB MED Catalogue: Medicine, Health, Nutrition, Environment, Agriculture

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