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Article ; Online: The Issues with Journal Issues

C. Sean Burns

Publications, Vol 11, Iss 7, p

Let Journals Be Digital Libraries

2023 Volume 7

Abstract: Science depends on a communication system, and today, that is largely provided by digital technologies such as the internet and web. Despite the fact that digital technologies provide the infrastructure for this communication system, peer-reviewed ... ...

Abstract	Science depends on a communication system, and today, that is largely provided by digital technologies such as the internet and web. Despite the fact that digital technologies provide the infrastructure for this communication system, peer-reviewed journals continue to mimic workflows and processes from the print era. This paper focuses on one artifact from the print era, the journal issue, and describes how this artifact has been detrimental to the communication of science, and therefore, to science itself. To replace the journal issue, this paper argues that scholarly publishing and journals could more fully embrace digital technologies by creating digital libraries to present and organize scholarly output.
Keywords	journals ; digital publishing ; scholarly publishing ; open science ; Communication. Mass media ; P87-96 ; Information resources (General) ; ZA3040-5185
Language	English
Publishing date	2023-02-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Book ; Online: The Issues with Journal Issues

Burns, C. Sean

Let Journals Be Digital Libraries

2023

Abstract: Science depends on a communication system, and today that is largely provided by digital technologies such as the internet and web. Despite that digital technologies provide the infrastructure for that communication system, peer-reviewed journals ... ...

Abstract	Science depends on a communication system, and today that is largely provided by digital technologies such as the internet and web. Despite that digital technologies provide the infrastructure for that communication system, peer-reviewed journals continue to mimic workflows and processes from the print era. This paper focuses on one artifact from the print era, the journal issue, and describes how this artifact has been detrimental to the communication of science and therefore to science itself. To replace the journal issue, this paper argues that scholarly publishing and journals could more fully embrace digital technologies by creating digital libraries to present and organize scholarly output. Comment: 17 pages, submitted to Publications
Keywords	Computer Science - Digital Libraries
Publishing date	2023-01-02
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Empowered Relief, cognitive behavioral therapy, and health education for people with chronic pain: a comparison of outcomes at 6-month Follow-up for a randomized controlled trial.

Darnall, Beth D / Burns, John W / Hong, Juliette / Roy, Anuradha / Slater, Kristin / Poupore-King, Heather / Ziadni, Maisa S / You, Dokyoung S / Jung, Corinne / Cook, Karon F / Lorig, Kate / Tian, Lu / Mackey, Sean C

Pain reports

2024 Volume 9, Issue 1, Page(s) e1116

Abstract: Introduction: We previously conducted a 3-arm randomized trial (263 adults with chronic low back pain) which compared group-based (1) single-session pain relief skills intervention (Empowered Relief; ER); (2) 8-session cognitive behavioral therapy (CBT) ...

Abstract	Introduction: We previously conducted a 3-arm randomized trial (263 adults with chronic low back pain) which compared group-based (1) single-session pain relief skills intervention (Empowered Relief; ER); (2) 8-session cognitive behavioral therapy (CBT) for chronic back pain; and (3) single-session health and back pain education class (HE). Results suggested non-inferiority of ER vs. CBT at 3 months post-treatment on an array of outcomes. Methods: Here, we tested the durability of treatment effects at 6 months post-treatment. We examined group differences in primary and secondary outcomes at 6 months and the degree to which outcomes eroded or improved from 3-month to 6-month within each treatment group. Results: Empowered Relief remained non-inferior to CBT on most outcomes, whereas both ER and CBT remained superior to HE on most outcomes. Outcome improvements within ER did not decrease significantly from 3-month to 6-month, and indeed ER showed additional 3- to 6-month improvements on pain catastrophizing, pain bothersomeness, and anxiety. Effects of ER at 6 months post-treatment (moderate term outcomes) kept pace with effects reported by participants who underwent 8-session CBT. Conclusions: The maintenance of these absolute levels implies strong stability of ER effects. Results extend to 6 months post-treatment previous findings documenting that ER and CBT exhibit similarly potent effects on outcomes.
Language	English
Publishing date	2024-01-25
Publishing country	United States
Document type	Journal Article
ISSN	2471-2531
ISSN (online)	2471-2531
DOI	10.1097/PR9.0000000000001116
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: MEDLINE search retrieval issues: A longitudinal query analysis of five vendor platforms.

Burns, C Sean / Nix, Tyler / Shapiro, Robert M / Huber, Jeffrey T

PloS one

2021 Volume 16, Issue 5, Page(s) e0234221

Abstract: This study compared the results of data collected from a longitudinal query analysis of the MEDLINE database hosted on multiple platforms that include PubMed, EBSCOHost, Ovid, ProQuest, and Web of Science. The goal was to identify variations among the ... ...

Abstract	This study compared the results of data collected from a longitudinal query analysis of the MEDLINE database hosted on multiple platforms that include PubMed, EBSCOHost, Ovid, ProQuest, and Web of Science. The goal was to identify variations among the search results on the platforms after controlling for search query syntax. We devised twenty-nine cases of search queries comprised of five semantically equivalent queries per case to search against the five MEDLINE database platforms. We ran our queries monthly for a year and collected search result count data to observe changes. We found that search results varied considerably depending on MEDLINE platform. Reasons for variations were due to trends in scholarly publication such as publishing individual papers online first versus complete issues. Some other reasons were metadata differences in bibliographic records; differences in the levels of specificity of search fields provided by the platforms and large fluctuations in monthly search results based on the same query. Database integrity and currency issues were observed as each platform updated its MEDLINE data throughout the year. Specific biomedical bibliographic databases are used to inform clinical decision-making, create systematic reviews, and construct knowledge bases for clinical decision support systems. They serve as essential information retrieval and discovery tools to help identify and collect research data and are used in a broad range of fields and as the basis of multiple research designs. This study should help clinicians, researchers, librarians, informationists, and others understand how these platforms differ and inform future work in their standardization.
MeSH term(s)	Biomedical Research ; Humans ; Information Storage and Retrieval/methods ; MEDLINE ; Search Engine/methods
Language	English
Publishing date	2021-05-06
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1932-6203
ISSN (online)	1932-6203
DOI	10.1371/journal.pone.0234221
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Sleep regularity is a stronger predictor of mortality risk than sleep duration: A prospective cohort study.

Windred, Daniel P / Burns, Angus C / Lane, Jacqueline M / Saxena, Richa / Rutter, Martin K / Cain, Sean W / Phillips, Andrew J K

Sleep

2023 Volume 47, Issue 1

Abstract: Abnormally short and long sleep are associated with premature mortality, and achieving optimal sleep duration has been the focus of sleep health guidelines. Emerging research demonstrates that sleep regularity, the day-to-day consistency of sleep-wake ... ...

Abstract	Abnormally short and long sleep are associated with premature mortality, and achieving optimal sleep duration has been the focus of sleep health guidelines. Emerging research demonstrates that sleep regularity, the day-to-day consistency of sleep-wake timing, can be a stronger predictor for some health outcomes than sleep duration. The role of sleep regularity in mortality, however, has not been investigated in a large cohort with objective data. We therefore aimed to compare how sleep regularity and duration predicted risk for all-cause and cause-specific mortality. We calculated Sleep Regularity Index (SRI) scores from > 10 million hours of accelerometer data in 60 977 UK Biobank participants (62.8 ± 7.8 years, 55.0% female, median[IQR] SRI: 81.0[73.8-86.3]). Mortality was reported up to 7.8 years after accelerometer recording in 1859 participants (4.84 deaths per 1000 person-years, mean (±SD) follow-up of 6.30 ± 0.83 years). Higher sleep regularity was associated with a 20%-48% lower risk of all-cause mortality (p < .001 to p = 0.004), a 16%-39% lower risk of cancer mortality (p < 0.001 to p = 0.017), and a 22%-57% lower risk of cardiometabolic mortality (p < 0.001 to p = 0.048), across the top four SRI quintiles compared to the least regular quintile. Results were adjusted for age, sex, ethnicity, and sociodemographic, lifestyle, and health factors. Sleep regularity was a stronger predictor of all-cause mortality than sleep duration, by comparing equivalent mortality models, and by comparing nested SRI-mortality models with and without sleep duration (p = 0.14-0.20). These findings indicate that sleep regularity is an important predictor of mortality risk and is a stronger predictor than sleep duration. Sleep regularity may be a simple, effective target for improving general health and survival.
MeSH term(s)	Humans ; Female ; Male ; Prospective Studies ; Sleep ; Life Style ; Actigraphy ; Time Factors
Language	English
Publishing date	2023-09-19
Publishing country	United States
Document type	Journal Article
ZDB-ID	424441-2
ISSN	1550-9109 ; 0161-8105
ISSN (online)	1550-9109
ISSN	0161-8105
DOI	10.1093/sleep/zsad253
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Article ; Online: The Impact of Biomass Heat Storage on the Canopy Energy Balance and Atmospheric Stability in the Community Land Model

Sean C. Swenson / Sean P. Burns / David M. Lawrence

Journal of Advances in Modeling Earth Systems, Vol 11, Iss 1, Pp 83-

2019 Volume 98

Abstract: ... in the mean nighttime canopy air temperature was reduced from −5.9 to 0.4 °C. Additional simulations ...

Abstract	Abstract Atmospheric models used for weather prediction and future climate projections rely on land models to calculate surface boundary conditions. Observations of near‐surface states and fluxes made at flux measurement sites provide valuable data with which to assess the quality of simulated lower boundary conditions. A previous assessment of the Community Land Model version 4.5 using data from the Niwot Ridge Subalpine Forest AmeriFlux tower showed that simulated latent heat fluxes could be improved by adjusting a parameter describing the maximum leaf wetted area, but biases in midday sensible heat flux and nighttime momentum flux were generally not reduced by model parameter perturbations. These biases are related to the model's lack of heat storage in vegetation biomass. A biomass heat capacity is parameterized in Community Land Model version 5 with measurable quantities such as canopy height, diameter at breast height, and tree number density. After implementing a parameterization describing the heat transfer between the forest biomass and the canopy air space, the biases in the mean midday sensible heat and mean nighttime momentum fluxes at Niwot Ridge are reduced from 47 to 13 W/m2 and from 0.12 to −0.03 m/s, respectively. The bias in the mean nighttime canopy air temperature was reduced from −5.9 to 0.4 °C. Additional simulations at other flux tower sites demonstrate a consistent reduction in midday sensible heat flux, a lower ratio of the sum of sensible and latent heat flux to net radiation, and an increase in nighttime canopy temperatures.
Keywords	biomass heat storage ; community land model ; atmospheric stability ; surface energy balance ; eddy covariance ; surface fluxes ; Physical geography ; GB3-5030 ; Oceanography ; GC1-1581
Subject code	551
Language	English
Publishing date	2019-01-01T00:00:00Z
Publisher	American Geophysical Union (AGU)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Loss of compensation afforded by accessory muscles of breathing leads to respiratory system compromise in the mdx mouse model of Duchenne muscular dystrophy.

O'Halloran, Ken D / Maxwell, Michael N / Marullo, Anthony L / Hamilton, Chantelle P / Ó Murchú, Seán C / Burns, David P / Mahony, Conor M / Slyne, Aoife D / Drummond, Sarah E

The Journal of physiology

2023 Volume 601, Issue 19, Page(s) 4441–4467

Abstract: Despite profound diaphragm weakness, peak inspiratory pressure-generating capacity is preserved in young mdx mice revealing adequate compensation by extra-diaphragmatic muscles of breathing in early dystrophic disease. We hypothesised that loss of ... ...

Abstract	Despite profound diaphragm weakness, peak inspiratory pressure-generating capacity is preserved in young mdx mice revealing adequate compensation by extra-diaphragmatic muscles of breathing in early dystrophic disease. We hypothesised that loss of compensation gives rise to respiratory system compromise in advanced dystrophic disease. Studies were performed in male wild-type (n = 196) and dystrophin-deficient mdx mice (n = 188) at 1, 4, 8, 12 and 16 months of age. In anaesthetised mice, inspiratory pressure and obligatory and accessory respiratory EMG activities were recorded during baseline and sustained tracheal occlusion for up to 30-40 s to evoke peak system activation to task failure. Obligatory inspiratory EMG activities were lower in mdx mice across the ventilatory range to peak activity, emerging in early dystrophic disease. Early compensation protecting peak inspiratory pressure-generating capacity in mdx mice, which appears to relate to transforming growth factor-β1-dependent fibrotic remodelling of the diaphragm and preserved accessory muscle function, was lost at 12 and 16 months of age. Denervation and surgical lesion of muscles of breathing in 4-month-old mice revealed a greater dependency on diaphragm for peak inspiratory performance in wild-type mice, whereas mdx mice were heavily dependent upon accessory muscles (including abdominal muscles) for peak performance. Accessory EMG activities were generally preserved or enhanced in young mdx mice, but peak EMG activities were lower than wild-type by 12 months of age. In general, ventilation was reasonably well protected in mdx mice until 16 months of age. Despite the early emergence of impairments in the principal obligatory muscles of breathing, peak inspiratory performance is compensated in early dystrophic disease due to diaphragm remodelling and facilitated contribution by accessory muscles of breathing. Loss of compensation afforded by accessory muscles underpins the emergence of respiratory system morbidity in advanced dystrophic disease. KEY POINTS: Despite diaphragm weakness, peak inspiratory performance is preserved in young dystrophin-deficient mdx mice revealing adequate compensation by extra-diaphragmatic muscles. Peak obligatory muscle (diaphragm, external intercostal, and parasternal intercostal) EMG activities are lower in mdx mice, emerging early in dystrophic disease, before the temporal decline in peak performance. Peak EMG activities of some accessory muscles are lower, whereas others are preserved. There is greater recruitment of the trapezius muscle in mdx mice during peak system activation. In phrenicotomised mice with confirmed diaphragm paralysis, there is a greater contribution made by extra-diaphragmatic muscles to peak inspiratory pressure in mdx compared with wild-type mice. Surgical lesion of accessory (including abdominal) muscles adversely affects peak pressure generation in mdx mice. Diaphragm remodelling leading to stiffening provides a mechanical advantage to peak pressure generation via the facilitated action of extra-diaphragmatic muscles in early dystrophic disease. Peak accessory EMG activities are lower in 12-month-old mdx compared to wild-type mice. Peak inspiratory pressure declines in mdx mice with advanced disease. We conclude that compensation afforded by accessory muscles of breathing declines in advanced dystrophic disease precipitating the emergence of respiratory system dysfunction.
MeSH term(s)	Male ; Mice ; Animals ; Mice, Inbred mdx ; Muscular Dystrophy, Duchenne ; Dystrophin ; Diaphragm ; Respiratory System ; Respiration Disorders ; Muscle Weakness ; Respiratory Muscles
Chemical Substances	Dystrophin
Language	English
Publishing date	2023-09-08
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	3115-x
ISSN	1469-7793 ; 0022-3751
ISSN (online)	1469-7793
ISSN	0022-3751
DOI	10.1113/JP285203
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Article ; Online: Characteristics of a Megajournal

Burns, C. Sean

Journal of Information Science Theory and Practice, Vol 3, Iss 2, Pp 16-

A Bibliometric Case Study

2015 Volume 30

Abstract: The term megajournal is used to describe publication platforms, like PLOS ONE, that claim to incorporate peer review processes and web technologies that allow fast review and publishing. These platforms also publish without the constraints of periodic ... ...

Abstract	The term megajournal is used to describe publication platforms, like PLOS ONE, that claim to incorporate peer review processes and web technologies that allow fast review and publishing. These platforms also publish without the constraints of periodic issues and instead publish daily. We conducted a yearlong bibliometric profile of a sample of articles published in the first several months after the launch of PeerJ, a peer reviewed, open access publishing platform in the medical and biological sciences. The profile included a study of author characteristics, peer review characteristics, usage and social metrics, and a citation analysis. We found that about 43% of the articles are collaborated on by authors from different nations. Publication delay averaged 68 days, based on the median. Almost 74% of the articles were coauthored by males and females, but less than a third were first authored by females. Usage and social metrics tended to be high after publication but declined sharply over the course of a year. Citations increased as social metrics declined. Google Scholar and Scopus citation counts were highly correlated after the first year of data collection (Spearman rho = 0.86). An analysis of reference lists indicated that articles tended to include unique journal titles. The purpose of the study is not to generalize to other journals but to chart the origin of PeerJ in order to compare to future analyses of other megajournals, which may play increasingly substantial roles in science communication.
Keywords	Megajournals ; Bibliometrics ; Gender Differences ; Peer Review ; Open Access ; Case Study ; Bibliography. Library science. Information resources ; Z
Subject code	001
Language	English
Publishing date	2015-06-01T00:00:00Z
Publisher	Korea Institute of Science and Technology Information
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Genome-wide gene by environment study of time spent in daylight and chronotype identifies emerging genetic architecture underlying light sensitivity.

Burns, Angus C / Phillips, Andrew J K / Rutter, Martin K / Saxena, Richa / Cain, Sean W / Lane, Jacqueline M

Sleep

2022 Volume 46, Issue 3

Abstract: Study objectives: Light is the primary stimulus for synchronizing the circadian clock in humans. There are very large interindividual differences in the sensitivity of the circadian clock to light. Little is currently known about the genetic basis for ... ...

Abstract	Study objectives: Light is the primary stimulus for synchronizing the circadian clock in humans. There are very large interindividual differences in the sensitivity of the circadian clock to light. Little is currently known about the genetic basis for these interindividual differences. Methods: We performed a genome-wide gene-by-environment interaction study (GWIS) in 280 897 individuals from the UK Biobank cohort to identify genetic variants that moderate the effect of daytime light exposure on chronotype (individual time of day preference), acting as "light sensitivity" variants for the impact of daylight on the circadian system. Results: We identified a genome-wide significant SNP mapped to the ARL14EP gene (rs3847634; p < 5 × 10-8), where additional minor alleles were found to enhance the morningness effect of daytime light exposure (βGxE = -.03, SE = 0.005) and were associated with increased gene ARL14EP expression in brain and retinal tissues. Gene-property analysis showed light sensitivity loci were enriched for genes in the G protein-coupled glutamate receptor signaling pathway and genes expressed in Per2+ hypothalamic neurons. Linkage disequilibrium score regression identified Bonferroni significant genetic correlations of greater light sensitivity GWIS with later chronotype and shorter sleep duration. Greater light sensitivity was nominally genetically correlated with insomnia symptoms and risk for post-traumatic stress disorder (PTSD). Conclusions: This study is the first to assess light as an important exposure in the genomics of chronotype and is a critical first step in uncovering the genetic architecture of human circadian light sensitivity and its links to sleep and mental health.
MeSH term(s)	Humans ; Chronotype ; Circadian Clocks/physiology ; Circadian Rhythm/genetics ; Sleep/genetics ; Sleep Initiation and Maintenance Disorders ; Sleep Wake Disorders ; Genome
Language	English
Publishing date	2022-12-12
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	424441-2
ISSN	1550-9109 ; 0161-8105
ISSN (online)	1550-9109
ISSN	0161-8105
DOI	10.1093/sleep/zsac287
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Article ; Online: Reply to Garen et al.: Within-canopy temperature data also do not support limited homeothermy.

Still, Christopher J / Page, Gerald F M / Rastogi, Bharat / Griffith, Daniel M / Aubrecht, Donald M / Kim, Youngil / Burns, Sean P / Hanson, Chad V / Kwon, Hyojung / Hawkins, Linnia / Meinzer, Frederick C / Sevanto, Sanna / Roberts, Dar A / Goulden, Mike / Pau, Stephanie / Detto, Matteo / Helliker, Brent R / Richardson, Andrew D

Proceedings of the National Academy of Sciences of the United States of America

2023 Volume 120, Issue 15, Page(s) e2302515120

MeSH term(s)	Temperature ; Body Temperature Regulation
Language	English
Publishing date	2023-04-03
Publishing country	United States
Document type	Journal Article ; Comment
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.2302515120
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