bluuebunny/crossref_metadata_2025_split huggingface dataset:
RepeatFS: a file system providing reproducibility through provenance and automation
Authors: Westbrook Anthony , Varki Elizabeth , Thomas W Kelley 
Published: October 2020

Abstract

Motivation
Reproducibility is of central importance to the scientific process. The difficulty of consistently replicating and verifying experimental results is magnified in the era of big data, in which bioinformatics analysis often involves complex multi-application pipelines operating on terabytes of data. These processes result in thousands of possible permutations of data preparation steps, software versions and command-line arguments. Existing reproducibility frameworks are cumbersome and involve redesigning computational methods. To address these issues, we developed RepeatFS, a file system that records, replicates and verifies informatics workflows with no alteration to the original methods. RepeatFS also provides several other features to help promote analytical transparency and reproducibility, including provenance visualization and task automation.

Results
We used RepeatFS to successfully visualize and replicate a variety of bioinformatics tasks consisting of over a million operations with no alteration to the original methods. RepeatFS correctly identified all software inconsistencies that resulted in replication differences.

Availabilityand implementation
RepeatFS is implemented in Python 3. Its source code and documentation are available at https://github.com/ToniWestbrook/repeatfs.

Supplementary information
Supplementary data are available at Bioinformatics online.
Estimates of Inactivated Influenza Vaccine Effectiveness Among Children in Senegal: Results From 2 Consecutive Cluster-Randomized Controlled Trials in 2010 and 2011
Authors: Niang Mbayame Nd , Sugimoto Jonathan D , Diallo Aldiouma , Diarra Bou , Ortiz Justin R , Lewis Kristen D C , Lafond Kathryn E , Halloran M Elizabeth , Widdowson Marc-Alain , Neuzil Kathleen M , Victor John C 
Published: October 2020

AbstractBackgroundWe report results of years 2 and 3 of consecutive cluster-randomized controlled trials of trivalent inactivated influenza vaccine (IIV3) in Senegal.MethodsWe cluster-randomized (1:1) 20 villages to annual vaccination with IIV3 or inactivated poliovirus vaccine (IPV) of age-eligible residents (6 months–10 years). The primary outcome was total vaccine effectiveness against laboratory-confirmed influenza illness (LCI) among age-eligible children (modified intention-to-treat population [mITT]). Secondary outcomes were indirect (herd protection) and population (overall community) vaccine effectiveness.ResultsWe vaccinated 74% of 12 408 age-eligible children in year 2 (June 2010–April 11) and 74% of 11 988 age-eligible children in year 3 (April 2011–December 2011) with study vaccines. Annual cumulative incidence of LCI was 4.7 (year 2) and 4.2 (year 3) per 100 mITT child vaccinees of IPV villages. In year 2, IIV3 matched circulating influenza strains. The total effectiveness was 52.8% (95% confidence interval [CI], 32.3–67.0), and the population effectiveness was 36.0% (95% CI, 10.2–54.4) against LCI caused by any influenza strain. The indirect effectiveness against LCI by A/H3N2 was 56.4% (95% CI, 39.0–68.9). In year 3, 74% of influenza detections were vaccine-mismatched to circulating B/Yamagata and 24% were vaccine-matched to circulating A/H3N2. The year 3 total effectiveness against LCI was −14.5% (95% CI, −81.2–27.6). Vaccine effectiveness varied by type/subtype of influenza in both years.ConclusionsIIV3 was variably effective against influenza illness in Senegalese children, with total and indirect vaccine effectiveness present during the year when all circulating strains matched the IIV3 formulation.Clinical Trials RegistrationNCT00893906.
Anthropocene-related disease
Authors: Gluckman Peter D , Low Felicia M , Hanson Mark A 
Published: October 2020

Abstract
While the Anthropocene is often discussed in terms of the health of the planet, there has been less attention paid to its impact on the health of humans. We argue that there is now sufficient evidence of broad and growing adverse effects on human health to consider Anthropocene-related diseases and their impact on public health as a category of conditions needing specific recognition and preventative action. Using the examples of climate change-related health challenges, non-communicable disease, antimicrobial resistance and the unique challenges of the digital environment, we discuss how the profound and pervasive environmental changes of the Anthropocene can affect our health, with broad effects on societal health. We frame this concept in terms of human evolutionary history and cultural evolution’s runaway characteristics, reflecting our drive for continual and cumulative innovation for reasons beyond simply survival and Darwinian fitness. As the causative agents are often remote from those populations most adversely affected, prevention and mitigation require collective societal and policy actions.
Lay summary: There is increasing evidence that our uniquely evolved ability to modify our environments rapidly and at an accelerating pace is having impacts on our health, particularly non-communicable diseases and poor mental wellbeing. Reframing these public health challenges as Anthropocene-related diseases emphasizes the need for collective responsibility and systems approaches to prevention.
Validity of the Global Activity Limitation Indicator (GALI) to evaluate severity of disability
Authors: Tarazona Belisa , González-Enríquez Jesús , Almazán-Isla Javier , Alcalde-Cabero Enrique , de Pedro-Cuesta Jesús , Galán Iñaki 
Published: October 2020

Abstract
Our aim was to estimate the validity of the Global Activity Limitation Indicator (GALI) when measuring the severity level of disability. Data came from 153 residents of Spain, who requested an evaluation of their degree of disability. We compared disability classifications (severe vs. non-severe) from GALI against those from the 36-item questionnaire WHODAS 2.0, the current gold standard measure of disability. The sensitivity of GALI to detect severe disability was 58.3% [95% confidence interval (CI):43.2–72.4], and the specificity was 84.8% (95% CI: 76.4–91.0). Thus, the validity of GALI to accurately categorize the degree of severity of an individual’s disability is not high, this in great part due to its limited sensitivity.
Culture Volume Influences the Dynamics of Adaptation under Long-Term Stationary Phase
Authors: Gross Jonathan , Avrani Sarit , Katz Sophia , Hilau Sabrin , Hershberg Ruth 
Published: October 2020

AbstractEscherichia coli and many other bacterial species, which are incapable of sporulation, can nevertheless survive within resource exhausted media by entering a state termed long-term stationary phase (LTSP). We have previously shown that E. coli populations adapt genetically under LTSP in an extremely convergent manner. Here, we examine how the dynamics of LTSP genetic adaptation are influenced by varying a single parameter of the experiment—culture volume. We find that culture volume affects survival under LTSP, with viable counts decreasing as volumes increase. Across all volumes, mutations accumulate with time, and the majority of mutations accumulated demonstrate signals of being adaptive. However, positive selection appears to affect mutation accumulation more strongly at higher, compared with lower volumes. Finally, we find that several similar genes are likely involved in adaptation across volumes. However, the specific mutations within these genes that contribute to adaptation can vary in a consistent manner. Combined, our results demonstrate how varying a single parameter of an evolutionary experiment can substantially influence the dynamics of observed adaptation.
Life-Space Mobility and Active Aging as Factors Underlying Quality of Life Among Older People Before and During COVID-19 Lockdown in Finland—A Longitudinal Study
Authors: Rantanen Taina , Eronen Johanna , Kauppinen Markku , Kokko Katja , Sanaslahti Sini , Kajan Niina , Portegijs Erja 
Published: October 2020

Abstract

Background
Social distancing, that is, avoiding places with other people and staying at home, was recommended to prevent viral transmission during the COVID-19 pandemic. Potentially, reduced out-of-home mobility and lower activity levels among older people may lower their quality of life (QOL). We studied cross-sectional and longitudinal associations of and changes in life-space mobility, active aging, and QOL during COVID-19 social distancing compared to 2 years before.

Methods
Altogether 809 community-living participants initially aged 75, 80, or 85 years of our active aging study (AGNES) conducted in 2017–2018 took part in the current AGNES-COVID-19 survey in May and June 2020. Outdoor mobility was assessed with the Life-Space Assessment (range 0–120). Active approach to life was assessed with the University of Jyväskylä Active Aging Scale (range 0–272), and QOL with the shortened Older People’s Quality of Life Questionnaire (range13–65; higher scores better for all). Data were analyzed with General Estimating Equations, General Linear Models, and One-way analysis of variance.

Results
Life-space mobility (B −10.8, SE 0.75, p &lt; .001), the active aging score (B −24.1, SE 0.88, p &lt; .001), and the QOL score (B −1.65, SE 0.21, p &lt; .001) were lower during COVID-19 social distancing versus 2 years before. Concurrent life-space mobility and active aging scores, age, and sex explained 48% of QOL at the baseline and 42% during social distancing. Longitudinally, steeper declines in all 3 variables coincided.

Conclusion
The observed declines indicate compliance with social distancing recommendation, but underline the importance of participation in meaningful life situations as a factor underlying good QOL also during the COVID-19 pandemic.
Development and Evaluation of the Eight-Item Caregiver Self-Efficacy Scale (CSES-8)
Authors: Ritter Philip L , Sheth Khushboo , Stewart Anita L , Gallagher-Thompson Dolores , Lorig Kate 
Published: October 2020

AbstractBackground and ObjectivesThis paper describes the development and evaluation of a short caregiving self-efficacy measure. The self-administered 8-item Caregiver Self-Efficacy Scale (CSES-8) was developed to reflect components of typical caregiver support interventions and to be practical for inclusion in future self-efficacy and caregiving research.Research Design and MethodsWe administered the CSES-8 in 2 samples: participants in an intervention for caregivers of persons with cognitive disabilities, and a voluntary online survey for caregivers of adults. We evaluated the completion rate, item-scale correlations, reliability, descriptive statistics, and preliminary construct validity of the CSES-8 in both samples, and sensitivity to change in the intervention sample.ResultsThe intervention caregivers’ sample (N = 158) was 85% female (mean age = 65 years). The online survey sample (N = 138) was 90% female (mean age = 78). In both samples, the CSES-8 had excellent internal consistency reliability (.89 and .88) and good distribution with sufficient variability to detect change. Test–retest reliability was good in the online sample (.73). As evidence of construct validity, most hypotheses were confirmed in both samples. The CSES-8 was sensitive to change at 6 months for caregivers in the intervention program (p &lt; .001).Discussion and ImplicationsThe CSES-8 is short, comprehensive with respect to common components of interventions to improve caregivers’ quality of life, and sensitive to change. It can serve a useful role exploring mechanisms by which caregiver intervention studies work, and it can be helpful in examining whether self-efficacy mediates the effect of these interventions on various outcomes such as psychological well-being.
Insights into the origin and magnitude of capture and handling-related stress in a coastal elasmobranch Carcharhinus limbatus
Authors: Weber D Nick , Janech Michael G , Burnett Louis E , Sancho Gorka , Frazier Bryan S 
Published: October 2020

Abstract
A suite of blood chemistry parameters (including acid–base indicators and plasma electrolytes) was serially measured in blacktip sharks (Carcharhinus limbatus), captured via rod-and-reel, to gain a more thorough understanding of the physiological stress response to recreational capture. Sharks were caught both from the shore and from fishing vessels and experienced varying degrees of air exposure during handling. While all captured sharks exhibited a metabolic acidosis during the fight on the line (increasing lactate and decreasing pH and bicarbonate), the observed acidosis was compounded by a respiratory component (increasing pCO2) in sharks removed from the water during handling. Vessel-caught sharks handled in the water exhibited significantly greater increases in lactate and glucose (0.73 ± 0.21 mmoll−1 min−1 and 0.81 ± 1.07 mg dl−1 min−1, respectively) than sharks handled out of water (0.21 ± 0.17 mmoll−1 min−1 and −0.32 ± 1.05 mg dl−1 min−1; p &lt; 0.001 and p &lt; 0.05, respectively). These findings provide insights into how differences in recreational capture methods and air exposure can mediate the origin and magnitude of capture-related stress and highlight the importance of considering both sampling time (time from capture to phlebotomy) and sampling location (in water vs. out) in studies conducted on capture-related stress.
Low Influenza Vaccine Effectiveness Against A(H3N2)-Associated Hospitalizations in 2016–2017 and 2017–2018 of the Hospitalized Adult Influenza Vaccine Effectiveness Network (HAIVEN)
Authors: Martin Emily T , Cheng Caroline , Petrie Joshua G , Alyanak Elif , Gaglani Manjusha , Middleton Donald B , Ghamande Shekhar , Silveira Fernanda P , Murthy Kempapura , Zimmerman Richard K , Monto Arnold S , Trabue Christopher , Talbot H Keipp , Ferdinands Jill M ,   HAIVEN Study Investigators, Lamerato Lois E , Lauring Adam , Malosh Ryan E , Murthy Kempapura , McNeal Tresa , Chang Kevin , White Heath , Arroliga Alejandro , Kilpatrick Laurel , Wimberly Meredith , Escobedo Victor , Nichols JoAnn , Clipper Lydia , Raiyani Chandni , Chen Wencong , Robertson Anne , Rao Arundhati , Fader Robert , Walker Kimberly , Volz Marcus , Hughes Kailey , Saul Sean , Stiefel Lori , Susick Michael , Goundappa Balasubramani K , Rinaldo Charles , Williams John , Johnson Monika , Gealey Julie , Eng Heather , Saul Melissa 
Published: October 2020

Abstract

Background
The 2016–2017 and 2017–2018 influenza seasons were notable for the high number of hospitalizations for influenza A(H3N2) despite vaccine and circulating strain match.

Methods
We evaluated vaccine effectiveness (VE) against hospitalization in the test-negative HAIVEN study. Nasal-throat swabs were tested by quantitative reverse transcription polymerase chain reaction (RT-PCR) for influenza and VE was determined based on odds of vaccination by generalized estimating equations. Vaccine-specific antibody was measured in a subset of enrollees.

Results
A total of 6129 adults were enrolled from 10 hospitals. Adjusted VE against A(H3N2) was 22.8% (95% confidence interval [CI], 8.3% to 35.0%), pooled across both years and 49.4% (95% CI, 34.3% to 61.1%) against B/Yamagata. In 2017–2018, the A(H3N2) VE point estimate for the cell-based vaccine was 43.0% (95% CI, −36.3% to 76.1%; 56 vaccine recipients) compared to 24.0% (95% CI, 3.9% to 39.9%) for egg-based vaccines. Among 643 with serology data, hemagglutinin antibodies against the egg-based A(H3N2) vaccine strain were increased in influenza-negative individuals.

Conclusions
Low VE for the A/Hong Kong/4801/2014 vaccine virus in both A(H3N2) seasons emphasizes concerns for continued changes in H3N2 antigenic epitopes, including changes that may impact glycosylation and ultimately reduce VE.
3D Anatomy of the Quail Lumbosacral Spinal Canal—Implications for Putative Mechanosensory Function
Authors: Kamska Viktoriia , Daley Monica , Badri-Spröwitz Alexander 
Published: October 2020

Synopsis
Birds are diverse and agile vertebrates capable of aerial, terrestrial, aquatic, and arboreal locomotion. Evidence suggests that birds possess a novel balance sensing organ in the lumbosacral spinal canal, a structure referred to as the “lumbosacral organ” (LSO), which may contribute to their locomotor agility and evolutionary success. The mechanosensing mechanism of this organ remains unclear. Here we quantify the 3D anatomy of the lumbosacral region of the common quail, focusing on establishing the geometric and biomechanical properties relevant to potential mechanosensing functions. We combine digital and classic dissection to create a 3D anatomical model of the quail LSO and estimate the capacity for displacement and deformation of the soft tissues. We observe a hammock-like network of denticulate ligaments supporting the lumbosacral spinal cord, with a close association between the accessory lobes and ligamentous intersections. The relatively dense glycogen body has the potential to apply loads sufficient to pre-stress denticulate ligaments, enabling external accelerations to excite tuned oscillations in the LSO soft tissue, leading to strain-based mechanosensing in the accessory lobe neurons. Considering these anatomical features together, the structure of the LSO is reminiscent of a mass-spring-based accelerometer.
Presidential Address 2019: How Should Tax Progressivity Respond to Rising Income Inequality?
Authors: Heathcote Jonathan , Storesletten Kjetil , Violante Giovanni L 
Published: October 2020

AbstractWe address the question in the title in a heterogeneous-agent incomplete-market model featuring exogenous idiosyncratic risk, endogenous skill investment, and flexible labor supply. The tax and transfer schedule is restricted to being log-linear in income, a good description of the US system. Rising inequality is modeled as a combination of skill-biased technical change and growth in residual wage dispersion. When facing shifts in the income distribution like those observed in the United States, a utilitarian planner chooses higher progressivity in response to larger residual inequality but lower progressivity in response to widening skill price dispersion reflecting technical change. Overall, optimal progressivity is approximately unchanged between 1980 and 2016. We document that the progressivity of the actual US tax and transfer system has similarly changed little since 1980, in line with the model prescription.
Advanced Breast Cancer Definitions by Staging System Examined in the Breast Cancer Surveillance Consortium
Authors: Kerlikowske Karla , Bissell Michael C. S , Sprague Brian L , Buist Diana S. M , Henderson Louise M , Lee Janie M , Miglioretti Diana L 
Published: October 2020

Abstract

Background
Advanced breast cancer is an outcome used to evaluate screening effectiveness. The advanced cancer definition resulting in the best discrimination of breast cancer death has not been studied in a breast imaging population.

Methods
A total of 52 496 women aged 40-79 years participating in the Breast Cancer Surveillance Consortium diagnosed with invasive cancer were staged using the 8th edition of American Joint Committee on Cancer (AJCC) anatomic and prognostic pathologic systems and Tomosynthesis Mammographic Imaging Screening Trial (TMIST) tumor categories. We calculated the area under the receiver operating characteristic curve for predicting 5-year breast cancer death and the sensitivity and specificity for predicting 5-year breast cancer death for 3 advanced cancer classifications: anatomic stage IIB or higher, prognostic pathologic stage IIA or higher, and TMIST advanced cancer.

Results
The area under the receiver operating characteristic curves for predicting 5-year breast cancer death for AJCC anatomic stage, AJCC prognostic pathologic stage, and TMIST tumor categories were 0.826 (95% confidence interval [CI] = 0.817 to 0.835), 0.856 (95% CI = 0.846 to 0.866), and 0.789 (95% CI = 0.780 to 0.797), respectively. AJCC prognostic pathologic stage had statistically significantly better discrimination than AJCC anatomic stage (difference = 0.030, bootstrap 95% CI = 0.024 to 0.037) and TMIST tumor categories (difference = 0.067, bootstrap 95% CI = 0.059 to 0.075). The sensitivity and specificity for predicting 5-year breast cancer death for AJCC anatomic stage IIB or higher, AJCC prognostic pathologic stage IIA or higher, and TMIST advanced cancer were 72.6%, 76.7%, and 96.1%; and 78.9%, 81.6%, and 41.1%, respectively.

Conclusions
Defining advanced cancer as AJCC prognostic pathologic stage IIA or higher most accurately predicts breast cancer death. Use of this definition by investigators will facilitate comparing breast cancer screening effectiveness studies.
The effect of pre-impact spin on the Moon-forming collision
Authors: Ruiz-Bonilla S , Eke V R , Kegerreis J A , Massey R J , Teodoro L F A 
Published: October 2020

ABSTRACT
We simulate the hypothesized collision between the proto-Earth and a Mars-sized impactor that created the Moon. Among the resulting debris disc in some impacts, we find a self-gravitating clump of material. It is roughly the mass of the Moon, contains $\sim 1{{\ \rm per\ cent}}$ iron like the Moon, and has its internal composition resolved for the first time. The clump contains mainly impactor material near its core but becomes increasingly enriched in proto-Earth material near its surface. The formation of this Moon-sized clump depends sensitively on the spin of the impactor. To explore this, we develop a fast method to construct models of multilayered, rotating bodies and their conversion into initial conditions for smoothed particle hydrodynamical (SPH) simulations. We use our publicly available code to calculate density and pressure profiles in hydrostatic equilibrium and then generate configurations of over a billion particles with SPH densities within 1 per cent of the desired values. This algorithm runs in a few minutes on a desktop computer, for 107 particles, and allows direct control over the properties of the spinning body. In comparison, alternative relaxation or spin-up techniques take hours on a supercomputer and the structure of the rotating body cannot be known beforehand. Collisions that differ only in the impactor’s initial spin reveal a wide variety of outcomes: a merger, a grazing hit-and-run, or the creation of an orbiting proto-Moon.
Self-interacting dark matter and the delay of supermassive black hole growth
Authors: Cruz A , Pontzen A , Volonteri M , Quinn T R , Tremmel M , Brooks A M , Sanchez N N , Munshi F , Di Cintio A 
Published: October 2020

ABSTRACT
Using cosmological hydrodynamic simulations with physically motivated models of supermassive black hole (SMBH) formation and growth, we compare the assembly of Milky Way-mass (Mvir ≈ 7 × 1011 M⊙ at z = 0) galaxies in cold dark matter (CDM) and self-interacting dark matter (SIDM) models. Our SIDM model adopts a constant cross-section of 1 cm2 g−1. We find that SMBH formation is suppressed in the early Universe due to SIDM interactions. SMBH–SMBH mergers are also suppressed in SIDM as a consequence of the lower number of SMBHs formed. Lack of initial merger-driven SMBH growth in turn delays SMBH growth by billions of years in SIDM compared to CDM. Further, we find that this delayed growth suppresses SMBH accretion in the largest progenitors of the main SIDM galaxies during the first 5 Gyr of their evolution. Nonetheless, by z = 0.8 the CDM and SIDM SMBH masses differ only by around 0.2 dex, so that both remain compatible with the MBH–M* relation. We show that the reduced accretion causes the SIDM SMBHs to less aggressively regulate star formation in their host galaxies than their CDM counterparts, resulting in a factor of 3 or more stars being produced over the lifetime of the SIDM galaxies compared to the CDM galaxies. Our results highlight a new way in which SIDM can affect the growth and merger history of SMBHs and ultimately give rise to very different galaxy evolution compared to the classic CDM model.