bluuebunny/crossref_metadata_2025_split huggingface dataset:
Natural disasters and infectious disease in Europe: a literature review to identify cascading risk pathways
Authors: Suk Jonathan E , Vaughan Eleanor C , Cook Robert G , Semenza Jan C 
Published: May 2019

Abstract

Background
Natural disasters are increasing in their frequency and complexity. Understanding how their cascading effects can lead to infectious disease outbreaks is important for developing cross-sectoral preparedness strategies. The review focussed on earthquakes and floods because of their importance in Europe and their potential to elucidate the pathways through which natural disasters can lead to infectious disease outbreaks.

Methods
A systematic literature review complemented by a call for evidence was conducted to identify earthquake or flooding events in Europe associated with potential infectious disease events.

Results
This review included 17 peer-reviewed papers that reported on suspected and confirmed infectious disease outbreaks following earthquakes (4 reports) or flooding (13 reports) in Europe. The majority of reports related to food- and water-borne disease. Eleven studies described the cascading effect of post-disaster outbreaks. The most reported driver of disease outbreaks was heavy rainfall, which led to cross-connections between water and other environmental systems, leading to the contamination of rivers, lakes, springs and water supplies. Exposure to contaminated surface water or floodwater following flooding, exposure to animal excreta and post-disaster living conditions were among other reported drivers of outbreaks.

Conclusions
The cascade effects of natural disasters, such as earthquakes and floods, include outbreaks of infectious disease. The projection that climate change-related extreme weather events will increase in Europe in the coming century highlights the importance of strengthening preparedness planning and measures to mitigate and control outbreaks in post-disaster settings.
The productivity of mixed mountain forests comprised of Fagus sylvatica, Picea abies, and Abies alba across Europe
Authors: Hilmers Torben , Avdagić Admir , Bartkowicz Leszek , Bielak Kamil , Binder Franz , Bončina Andrej , Dobor Laura , Forrester David I , Hobi Martina L , Ibrahimspahić Aida , Jaworski Andrzej , Klopčič Matija , Matović Bratislav , Nagel Thomas A , Petráš Rudolf , del Rio Miren , Stajić Branko , Uhl Enno , Zlatanov Tzvetan , Tognetti Roberto , Pretzsch Hans 
Published: May 2019

Abstract
Mixed mountain forests of European beech (Fagus sylvatica L.), Norway spruce (Picea abies (L.) Karst), and silver fir (Abies alba Mill.) cover a total area of more than 10 million hectares in Europe. Due to altitudinal zoning, these forests are particularly vulnerable to climate change. However, as little is known about the long-term development of the productivity and the adaptation and mitigation potential of these forest systems in Europe, reliable information on productivity is required for sustainable forest management. Using generalized additive mixed models this study investigated 60 long-term experimental plots and provides information about the productivity of mixed mountain forests across a variety of European mountain areas in a standardized way for the first time. The average periodic annual volume increment (PAI) of these forests amounts to 9.3 m3ha−1y−1. Despite a significant increase in annual mean temperature the PAI has not changed significantly over the last 30 years. However, at the species level, we found significant changes in the growth dynamics. While beech had a PAI of 8.2 m3ha−1y−1 over the entire period (1980–2010), the PAI of spruce dropped significantly from 14.2 to 10.8 m3ha−1y−1, and the PAI of fir rose significantly from 7.2 to 11.3 m3ha−1y−1. Consequently, we observed stable stand volume increments in relation to climate change.
Analysis of surface and seismic sources in dense array data with match field processing and Markov chain Monte Carlo sampling
Authors: Gradon Chloé , Moreau Ludovic , Roux Philippe , Ben-Zion Yehuda 
Published: May 2019

SUMMARY
We introduce a methodology based on array processing to detect and locate weak seismic events in a complex fault zone environment. The method is illustrated using data recorded by a dense array of 1108 vertical component geophones in a 600 m × 600 m area on the Clark branch of the San Jacinto Fault. Because surface and atmospheric sources affect weak ground motion, it is necessary to discriminate them from weak seismic sources at depth. Source epicentral positions and associated apparent velocities are extracted from continuous seismic waveforms using Match Field Processing (MFP). We implement MFP at specific frequencies targeting surface and subsurface sources, using for computational efficiency a forward model of acoustic source in a homogenous medium and Markov Chain Monte Carlo sampling. Surface sources such as Betsy gun shots and a moving vehicle are successfully located. Weak seismic events are also detected outside of the array, and their backazimuth angle is retrieved and found to be consistent with the fault geometry. We also show that the homogeneous acoustic model does not yield satisfying results when extracting microseismic event depth, because of the ambiguity between depth and the apparent velocity based on surface data.
Stress-Free Evolution: The Nrf-Coordinated Oxidative Stress Response in Early Diverging Metazoans
Authors: Doonan Liam B , Hartigan Ashlie , Okamura Beth , Long Paul F 
Published: May 2019

AbstractEnvironmental stress from ultraviolet radiation, elevated temperatures or metal toxicity can lead to reactive oxygen species in cells, leading to oxidative DNA damage, premature aging, neurodegenerative diseases, and cancer. The transcription factor nuclear factor (erythroid-derived 2)-like 2 (Nrf2) activates many cytoprotective proteins within the nucleus to maintain homeostasis during oxidative stress. In vertebrates, Nrf2 levels are regulated by the Kelch-family protein Keap1 (Kelch-like ECH-associated protein 1) in the absence of stress according to a canonical redox control pathway. Little, however, is known about the redox control pathway used in early diverging metazoans. Our study examines the presence of known oxidative stress regulatory elements within non-bilaterian metazoans including free living and parasitic cnidarians, ctenophores, placozoans, and sponges. Cnidarians, with their pivotal position as the sister phylum to bilaterians, play an important role in understanding the evolutionary history of response to oxidative stress. Through comparative genomic and transcriptomic analysis our results show that Nrf homologs evolved early in metazoans, whereas Keap1 appeared later in the last common ancestor of cnidarians and bilaterians. However, key Nrf–Keap1 interacting domains are not conserved within the cnidarian lineage, suggesting this important pathway evolved with the radiation of bilaterians. Several known downstream Nrf targets are present in cnidarians suggesting that cnidarian Nrf plays an important role in oxidative stress response even in the absence of Keap1. Comparative analyses of key oxidative stress sensing and response proteins in early diverging metazoans thus provide important insights into the molecular basis of how these lineages interact with their environment and suggest a shared evolutionary history of regulatory pathways. Exploration of these pathways may prove important for the study of cancer therapeutics and broader research in oxidative stress, senescence, and the functional responses of early diverging metazoans to environmental change.
The Role of Developmental Integration and Historical Contingency in the Origin and Evolution of Cypriniform Trophic Novelties
Authors: Hernandez L P , Cohen K E 
Published: May 2019

AbstractWhile functional morphologists have long studied the evolution of anatomical structures, the origin of morphological novelties has received less attention. When such novelties first originate they must become incorporated into an integrated system to be rendered fully functional. Thus, developmental integration is key at the origin of morphological novelties. However, given enough evolutionary time such integration may be broken, allowing for a division of labor that is facilitated by subsequent decoupling of structures. Cypriniformes represent a diverse group of freshwater fishes characterized by several trophic novelties that include: kinethmoid-mediated premaxillary protrusion, a muscular palatal and post-lingual organ, hypertrophied lower pharyngeal jaws that masticate against the base of the neurocranium, novel pharyngeal musculature controlling movement of the hypertrophied lower pharyngeal jaws, and in a few species an incredibly complex epibranchial organ used to aggregate filtered phytoplankton. Here, we use the wealth of such trophic novelties in different cypriniform fishes to present case studies in which developmental integration allowed for the origin of morphological innovations. As proposed in case studies 1 and 2 trophic innovations may be associated with both morphological and lineage diversification. Alternatively, case studies 3 and 4 represent a situation where ecological niche was expanded but with no concomitant increase in species diversity.
Linking Bioenergetics and Parasite Transmission Models Suggests Mismatch Between Snail Host Density and Production of Human Schistosomes
Authors: Malishev Matthew , Civitello David J 
Published: May 2019

Abstract
The consequences of parasite infection for individual hosts depend on key features of host–parasite ecology underpinning parasite growth and immune defense, such as age, sex, resource supply, and environmental stressors. Scaling these features and their underlying mechanisms from the individual host is challenging but necessary, as they shape parasite transmission at the population level. Translating individual-level mechanisms across scales could inherently improve the way we think about feedbacks among parasitism, the mechanisms driving transmission, and the consequences of human impact and disease control efforts. Here, we use individual-based models (IBMs) based on general metabolic theory, Dynamic Energy Budget (DEB) theory, to scale explicit life-history features of individual hosts, such as growth, reproduction, parasite production, and death, to parasite transmission at the population level over a range of resource supplies focusing on the major human parasite, Schistosoma mansoni, and its intermediate host snail, Biomphalaria glabrata. At the individual level, infected hosts produce fewer parasites at lower resources as competition increases. At the population level, our DEB–IBM predicts brief, but intense parasite peaks early during the host growth season when resources are abundant and infected hosts are few. The timing of these peaks challenges the status quo that high densities of infected hosts produce the highest parasite densities. As expected, high resource supply boosts parasite output, but parasite output also peaks at modest to high host background mortality rates, which parallels overcompensation in stage-structured models. Our combined results reveal the crucial role of individual-level physiology in identifying how environmental conditions, time of the year, and key feedbacks within host–parasite ecology interact to define periods of elevated risk. The testable forecasts from this physiologically-explicit epidemiological model can inform disease management to reduce human risk of schistosome infection.
Lethal Organ Donation: Would the Doctor Intend the Donor’s Death?
Authors: Bronner Ben 
Published: May 2019

Abstract
Lethal organ donation is a hypothetical procedure in which vital organs are removed from living donors, resulting in their death. An important objection to lethal organ donation is that it would infringe the prohibition on doctors intentionally causing the death of patients. I present a series of arguments intended to undermine this objection. In a case of lethal organ donation, the donor’s death is merely foreseen, and not intended.
Healthcare Rationing Cutoffs and Sorites Indeterminacy
Authors: Rosoff Philip M 
Published: May 2019

AbstractRationing is an unavoidable mechanism for reining in healthcare costs. It entails establishing cutoff points that distinguish between what is and is not offered or available to patients. When the resource to be distributed is defined by vague and indeterminate terms such as “beneficial,” “effective,” or even “futile,” the ability to draw meaningful boundary lines that are both ethically and medically sound is problematic. In this article, I draw a parallel between the challenges posed by this problem and the ancient Greek philosophical conundrum known as the “sorites paradox.” I argue, like the paradox, that the dilemma is unsolvable by conventional means of logical analysis. However, I propose another approach that may offer a practical solution that could be applicable to real-life situations in which cutoffs must be decided (such as rationing).
A Preliminary Study of U.S. Air Force Pilot Perceptions of the Pilot–Flight Surgeon Relationship
Authors: Nowadly Craig D , Blue Rebecca S , Albaugh Harry M , Mayes Ryan S , Robb Douglas J 
Published: May 2019

Abstract

Introduction
Flight surgeons play a vital role in U.S. Air Force aviation operations by ensuring that pilots are medically prepared to meet the demands of military aviation. However, there is natural tension between pilots and flight surgeons. A pilot may be reluctant to share medical information with a flight surgeon who could negatively impact the pilot’s career or flight status. In this preliminary study, we sought to identify pilot-perceived strengths and weaknesses in the relationship between U.S. Air Force aviators and their flight surgeons.

Materials and Methods
An online survey regarding pilot–flight surgeon confidence and perceived values was distributed electronically to a convenience sample of U.S. Air Force aviators. Participants included U.S. Air Force active duty and Air Reserve Component (Air Force Reserve and Air National Guard) military aviators in addition to U.S. Air Force Academy aviation cadets.

Results
One hundred and seventy-three aviators participated in the survey. Respondents reported variable comfort in approaching flight surgeons with medical concerns and suggested that they believed other pilots might be withholding medical information from flight surgeons or seeking care from civilian physicians for career protection.

Conclusions
We sought to examine the pilot–flight surgeon relationship and its impact on daily flying operations. While limited, results suggest that there may be gaps in trust between pilots and their flight surgeons. These findings could present an opportunity to improve the pilot–flight surgeon relationship by identifying factors that contribute to closer pilot–flight surgeon relationships.
Polarization studies of rotating radio transients
Authors: Caleb M , van Straten W , Keane E F , Jameson A , Bailes M , Barr E D , Flynn C , Ilie C D , Petroff E , Rogers A , Stappers B W , Venkatraman Krishnan V , Weltevrede P 
Published: May 2019

ABSTRACT
We study the polarization properties of 22 known rotating radio transients (RRATs) with the 64-m Parkes radio telescope and present the Faraday rotation measures (RMs) for the 17 with linearly polarized flux exceeding the off-pulse noise by 3σ. Each RM was estimated using a brute-force search over trial RMs that spanned the maximum measurable range $\pm 1.18 \times 10^5 \, \mathrm{rad \, m^2}$ (in steps of 1 $\mathrm{rad \, m^2}$), followed by an iterative refinement algorithm. The measured RRAT RMs are in the range |RM| 1–950 rad m−2 with an average linear polarization fraction of 40 per cent. Individual single pulses are observed to be up to 100 per cent linearly polarized. The RMs of the RRATs and the corresponding inferred average magnetic fields (parallel to the line of sight and weighted by the free electron density) are observed to be consistent with the Galactic plane pulsar population. Faraday rotation analyses are typically performed on accumulated pulsar data, for which hundreds to thousands of pulses have been integrated, rather than on individual pulses. Therefore, we verified the iterative refinement algorithm by performing Monte Carlo simulations of artificial single pulses over a wide range of S/N and RM. At and above an S/N of 17 in linearly polarized flux, the iterative refinement recovers the simulated RM value 100 per cent of the time with a typical mean uncertainty of 5 rad m−2. The method described and validated here has also been successfully used to determine reliable RMs of several fast radio bursts (FRBs) discovered at Parkes.
Trying not to Lose Ground: State and Local Government Advocacy during Passage of the 2017 Tax Cuts and Jobs Act
Authors: Wesley Leckrone J 
Published: May 2019

AbstractThe Tax Cuts and Jobs Act of 2017 (TCJA) was the first major federal tax reform in a generation. This article examines the priority issues of fifty-seven intergovernmental advocacy organizations during the legislation’s passage. These groups played defense from the start, in response to efforts by President Trump and congressional Republicans to streamline the tax code by eliminating tax expenditures. Blocking the potential elimination of the state and local tax (SALT) deduction and preserving the tax exempt status of municipal bond interest represented priorities for most organizations. Ultimately, the TCJA preserved many tax expenditures important to intergovernmental advocacy organizations. However, the SALT deduction was capped at $10,000, representing a big loss. This case study evaluates when and under what conditions the intergovernmental lobby influences federal policy-making. It finds that while state and local groups use a variety of tactics, their ability to navigate partisan politics and harness the self-interest of members of Congress is necessary to success.
Telephone outreach by community workers to improve uptake of NHS Health Checks in more deprived localities and minority ethnic groups: a qualitative investigation of implementation
Authors: Stone T J , Brangan E , Chappell A , Harrison V , Horwood J 
Published: May 2019

Abstract

Background
NHS Health Checks is a national cardiovascular risk assessment and management programme in England. To improve equity of uptake in more deprived, and Black, Asian and minority ethnic (BAME) communities, a novel telephone outreach intervention was developed. The outreach call included an invitation to an NHS Health Check appointment, lifestyle questions, and signposting to lifestyle services. We examined the experiences of staff delivering the intervention.

Methods
Thematic analysis of semi-structured interviews with 10 community Telephone Outreach Workers (TOWs) making outreach calls, and 5 Primary Care Practice (PCP) staff they liaised with. Normalization Process Theory was used to examine intervention implementation.

Results
Telephone outreach was perceived as effective in engaging patients in NHS Health Checks and could reduce related administration burdens on PCPs. Successful implementation was dependent on support from participating PCPs, and tensions between the intervention and other PCP priorities were identified. Some PCP staff lacked clarity regarding the intervention aim and this could reduce the potential to capitalize on TOWs’ specialist skills.

Conclusions
To maximize the potential of telephone outreach to impact equity, purposeful recruitment and training of TOWs is vital, along with support and integration of TOWs, and the telephone outreach intervention, in participating PCPs.
Synthetic design of farnesyl-electrostatic peptides for development of a protein kinase A membrane translocation switch
Authors: Kim Allen K. , Wu Helen D. , Inoue Takanari 
Published: May 2019

AbstractMolecular switches that respond to a biochemical stimulus in cells have proven utility as a foundation for developing molecular sensors and actuators that could be used to address important biological questions. Developing a molecular switch unfortunately remains difficult as it requires elaborate coordination of sensing and actuation mechanisms built into a single molecule. Here, we rationally designed a molecular switch that changes its subcellular localization in response to an intended stimulus such as an activator of protein kinase A (PKA). By arranging the sequence for Kemptide in tandem, we designed a farnesylated peptide whose localization can dramatically change upon phosphorylation by PKA. After testing a different valence number of Kemptide as well as modulating the linker sequence connecting them, we identified an efficient peptide switch that exhibited dynamic translocation between plasma membranes and internal endomembranes in a PKA activity dependent manner. Due to the modular design and small size, our PKA switch can have versatile utility in future studies as a platform for visualizing and perturbing signal transduction pathways, as well as for performing synthetic operations in cells.
Autonomous induction of hepatic polarity to construct single cell liver
Authors: Zhang Yue , de Mets Richard , Monzel Cornelia , Toh Pearlyn , Van Hul Noemi , Ng Soon Seng , Tamir Rashid S. , Viasnoff Virgile 
Published: May 2019

AbstractSymmetry breaking of protein distribution and cytoskeleton organization is an essential aspect for development of apico-basal polarity. In embryonic cells this process is largely cell autonomous, while differentiated epithelial cells collectively polarize during epithelium formation. We report here that the de novo polarization of mature hepatocytes is a cell autonomous process. Single hepatocytes developed bona fide secretory hemi-apical lumens upon adhesion to finely tuned substrates bio-functionalized with cadherin and extra cellular matrix. The creation of this single cell liver allows unprecedented control and imaging resolution of the lumenogenesis process. We demonstrate that the density and localization of cadherins along the initial cell-cell contact acted as a key factor triggering the reorganization from lateral to apical actin cortex. Consequently, we established why hepatocytes could form asymmetric lumens in heterotypic doublets involving another ectopic epithelial cell originating from kidney, breast, or colon.
metaFlye: scalable long-read metagenome assembly using repeat graphs
Authors: Kolmogorov Mikhail , Rayko Mikhail , Yuan Jeffrey , Polevikov Evgeny , Pevzner Pavel 
Published: May 2019

AbstractLong-read sequencing technologies substantially improved assemblies of many isolate bacterial genomes as compared to fragmented assemblies produced with short-read technologies. However, assembling complex metagenomic datasets remains a challenge even for the state-of-the-art long-read assemblers. To address this gap, we present the metaFlye assembler and demonstrate that it generates highly contiguous and accurate metagenome assemblies. In contrast to short-read metagenomics assemblers that typically fail to reconstruct full-length 16S RNA genes, metaFlye captures many 16S RNA genes within long contigs, thus providing new opportunities for analyzing the microbial “dark matter of life”. We also demonstrate that long-read metagenome assemblers significantly improve full-length plasmid and virus reconstruction as compared to short-read assemblers and reveal many novel plasmids and viruses.