bluuebunny/crossref_metadata_2025_split huggingface dataset:
The role of fire and a long‐lived soil seed bank in maintaining persistence, genetic diversity and connectivity in a fire‐prone landscape
Authors: Bradbury Donna , Tapper Sarah‐Louise , Coates David , McArthur Shelley , Hankinson Margaret , Byrne Margaret 
Published: September 2015

AbstractAimTerrestrial plant ecology and evolution is significantly influenced by the phenomenon of fire, but studies of its potential impact on intraspecific genetic variation and phylogeography are rare. This understanding will be important for predicting the biogeographical consequences of changing fire regimes under global climate change. Here, we asked whether changing historical fire regimes, together with climatic and geological history, have influenced phylogeographical patterns in a fire‐ephemeral vine. We also asked whether demographic stochasticity associated with a fire‐ephemeral life history results in nuclear genetic drift as expected from spatio‐temporal patchiness, or if this effect is buffered by the connectivity and diversity afforded by a persistent soil seed bank.LocationThe fire‐prone, mediterranean‐type climate region of south‐western Australia.MethodsWe used Bayesian phylogeny reconstruction and statistical tests of demographic expansion based on variation at three non‐coding chloroplast sequence regions (atpF, ndhF–rpl32, psbD–trnT) to reconstruct phylogeographical history. Nuclear diversity and population structure at 11 microsatellite loci were investigated for evidence of genetic drift.ResultsEvidence for prolonged persistence and a lack of vicariance within the species range was found, together with strong evidence of historical demographic expansion. Contrary to expectations, there was little evidence of nuclear genetic drift despite strong, above‐ground spatio‐temporal population patchiness.Main conclusionsOur findings suggest that a late Pleistocene increase in fire frequency may have led to demographic expansion in this fire‐ephemeral species; alternatively, the expansion signal may be an inherent feature of fire ephemerals with a persistent soil seed bank. Prolonged climatic stability has likely fostered persistence within the species range in contrast to contraction and vicariance. The notable lack of genetic drift implies a role for ample pollen dispersal and a long‐lived soil seed bank in the maintenance of diversity and connectivity in an otherwise stochastic, fire‐driven system.
Femoral Access PCI in a Default Radial Center Identifies High‐Risk Patients With Poor Outcomes
Authors: Uddin Muezz , Bundhoo Shantu , Mitra Rito , Ossei‐Gerning Nicholas , Morris Keith , Anderson Richard , Kinnaird Tim 
Published: September 2015

BackgroundIncreasingly the trans‐radial route (TRR) is preferred over the trans‐femoral route (TFR) for PCI. However, even in high volume default TRR centers a cohort of patients undergo TFR PCI. We examined the demographics, procedural characteristics, and outcomes of patients undergoing PCI via the TF.MethodsThe patient demographics, procedural data, and outcomes of 5,379 consecutive patients undergoing PCI at a default radial center between 2009 and 2012 were examined. Major bleeding (MB) was classified by ACUITY and BARC definitions.ResultsA total of 559 (10.4%) patients underwent PCI via the TFR and 4,820 patients via the TRR (89.6%). Baseline variables associated with TFR were shock, previous CABG, chronic total occlusion intervention, rotablation/laser use, female sex, and renal failure. Sixty‐five patients of the TFR cohort (11.6%) experienced MB with 27 (41.5%) being access site related. MB was significantly more frequent than in the radial cohort. The variables independently associated with MB in the TFR cohort were renal failure, acute presentation, shock, and age. In the TFR, patients with MB mortality was high at 30 days (17.2% vs 2.6% for no MB, P < 0.0001) and at 1 year (37.6% vs 5.0%, P < 0.0001). Shock and MB were highly predictive of 30 day and 12 month mortality.ConclusionIn a default radial PCI center 10% of patients undergo PCI via the femoral artery. These patients have high baseline bleeding risk and undergo complex interventions. As a result the incidence of major bleeding, transfusion and death are high. Alternative strategies are required to optimize outcomes in this select group. (J Interven Cardiol 2015;28:485–492)
Rural Enrollment in the Federally Facilitated Marketplace
Authors: Drake Coleman , Abraham Jean M. , McCullough Jeffrey S. 
Published: September 2015

AbstractPurposeWe sought to examine the demographic, market, and policy‐related factors influencing first year enrollment rates for the population targeted by the Health Insurance Marketplaces (HIMs) established as part of the Affordable Care Act. In particular, we analyzed differences in enrollment rates across urban and rural counties in 32 states served by the Federally Facilitated Marketplace.MethodsWe used enrollment data from the Assistant Secretary for Planning and Evaluation of the US Department of Health and Human Services and demographic data from the American Community Survey, supplemented with other market and policy‐related information. Using multivariate regression, we investigated how county‐level enrollment rates are associated with demographic, market and policy‐related characteristics, including rurality.FindingsRelative to an adjusted mean enrollment rate of 17.1% for large metropolitan counties, small metropolitan counties have a 2.8% lower enrollment rate and rural counties have a 2.7% lower enrollment rate. States’ decisions to expand Medicaid and to have the federal government fully manage the HIM are both negatively associated with enrollment rates. Partnership HIMs exhibit a positive association with enrollment rates as do navigator grants, but the latter relationship is only present in counties located in Medicaid expansion states.ConclusionsEnrollment rates vary by rurality, but differences are statistically significant only between large metropolitan counties and all other types of counties—small metropolitan, micropolitan, and noncore. State‐level policies, particularly Medicaid expansion, have the largest association with enrollment rates among the explanatory variables examined in the model.
Abstraction and its Limits: Finding Space For Novel Explanation
Authors: Knox Eleanor 
Published: September 2015

AbstractSeveral modern accounts of explanation acknowledge the importance of abstraction and idealization for our explanatory practice. However, once we allow a role for abstraction, questions remain. I ask whether the relation between explanations at different theoretical levels should be thought of wholly in terms of abstraction, and argue that changes of the quantities in terms of which we describe a system can lead to novel explanations that are not merely abstractions of some more detailed picture. I use the example of phase transitions as described by statistical mechanics and thermodynamics to illustrate this, and to demonstrate some details of the relationship between abstraction, idealization, and novel explanation.
Know How to Transmit Knowledge?
Authors: Poston Ted 
Published: September 2015

AbstractIntellectualism about knowledge‐how is the view that practical knowledge is a species of propositional knowledge. I argue that this view is undermined by a difference in properties between knowledge‐how and both knowledge‐that and knowledge‐wh. More specifically, I argue that both knowledge‐that and knowledge‐wh are easily transmitted via testimony while knowledge‐how is not easily transmitted by testimony. This points to a crucial difference in states of knowledge. I also consider Jason Stanley's attempt to subsume knowledge‐how under an account of de se knowledge. I argue that there are crucial differences between de se knowledge and knowledge‐how. Thus, this paper advances both the discussion of intellectualism and the literature on the nature of de se knowledge.
How do vertebrates respond to mast seeding?
Authors: Bogdziewicz Michał , Zwolak Rafał , Crone Elizabeth E. 
Published: September 2015

Mast‐seeding is the synchronized and intermittent production of a large seed crop by a population of plants. The cascading effects of masting on wildlife have been well documented in granivorous rodents. Yet, the effects of mast‐seeding are potentially further reaching, since a number of generalist species can take advantage of mast years. We employed a full‐text search algorithm to identify all papers that discussed effects of mast‐seeding on wildlife, in addition to typical searches of titles and abstracts. We aimed to evaluate the breadth of wildlife species for which mast years are thought to be important drivers. In addition, we tested three hypotheses derived from past reviews: 1) species with lower reproductive potential (lower average litter size) are more likely to show aggregative responses to mast‐seeding, 2) species with lower body sizes (lower mobility) are more likely to show reproductive responses, and 3) indirect consumers of mast (predators) are more likely to show aggregative responses than direct consumers. We found 186 articles including reports of response of 122 species of vertebrates to mast‐seeding. Expectations were partly confirmed: relationships 1) and 2) held for mammals, but not for birds. However, 3) direct consumers were more likely than indirect consumers to show aggregative responses. Our tests of the first two hypotheses question the generality of past predictions for taxa other than mammals. Our test of the third hypothesis suggests that responses of direct and indirect consumers might depend on the type of resource pulse. Many of the examples in our analysis come from systems in which wildlife responses to mast have been less rigorously documented than the examples in past reviews. They suggest the range of wildlife responses to mast‐seeding are more taxonomically and ecologically diverse than past reviews have widely recognized and point to directions for future research.SynthesisMast seeding is a pulsed resource with numerous cascading effects on wildlife. Yet, because masting is largely unpredictable, it is inherently difficult to study. We developed a full‐text search algorithm to identify incidental reports as well as deliberate studies of vertebrate reactions to masting. We found that the type of response to mast seeding (reproductive or through immigration) varies predictably as a function of life history traits (litter size and body mass) in mammals, but not in birds. Our literature search also shows that responses to mast‐seeding are more taxonomically and ecologically diverse than past reviews have recognized.
Social support moderates the relationship between sleep and inflammation in a population at high risk for developing cardiovascular disease
Authors: Tomfohr Lianne M. , Edwards Kate M. , Madsen Joshua W. , Mills Paul J. 
Published: September 2015

AbstractPoor sleep and low social support have each been associated with mortality and morbidity from chronic illness, and a small body of research suggests that the two interact to influence systemic inflammation whereby good social relationships may buffer the relationship between poor sleep and increased inflammation. The current study investigated interactions between sleep and social support in the prediction of inflammation in a clinical population (prehypertensive and hypertensive individuals) at high risk for the development of cardiovascular disease. Using a standardized subjective measure of sleep quality, we found that social support moderated the association between sleep and circulating levels of both IL‐6 and CRP, such that poor sleep appeared to confer a risk of increased inflammation only in those participants who also reported low social support. In women, the same relationship was observed for TNF‐α. These results extend previous findings into a clinical population and also demonstrate that sleep quality and social support interact in the prediction of two previously uninvestigated clinically relevant inflammatory markers (CRP and TNF‐α). High levels of perceived social support may compensate for the negative health impact of poor sleep quality and vice versa.
Francisella philomiragia Bacteremia in a Patient with Acute Respiratory Insufficiency and Acute-on-Chronic Kidney Disease
Authors: Relich Ryan F. , Humphries Romney M. , Mattison H. Reid , Miles Jessica E. , Simpson Edward R. , Corbett Ian J. , Schmitt Bryan H. , May M. 
Published: September 2015

ABSTRACT

Francisella philomiragia
is a very uncommon pathogen of humans. Diseases caused by it are protean and have been reported largely in near-drowning victims and those with chronic granulomatous disease. We present a case of
F. philomiragia
pneumonia with peripheral edema and bacteremia in a renal transplant patient and review the diverse reports of
F. philomiragia
infections.
Characterization of Achromobacter Species in Cystic Fibrosis Patients: Comparison of
bla
OXA-114
PCR Amplification, Multilocus Sequence Typing, and Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry
Authors: Rodrigues Elenice R. A. , Ferreira Alex G. , Leão Robson S. , Leite Cassiana C. F. , Carvalho-Assef Ana Paula , Albano Rodolpho M. , Marques Elizabeth A. 
Published: September 2015

ABSTRACT

Molecular methodologies were used to identify 28
Achromobacter
spp. from patients with cystic fibrosis (CF). Multilocus sequence typing (MLST) identified 17
Achromobacter xylosoxidans
isolates (all
bla
OXA-114
positive), nine
Achromobacter ruhlandii
isolates (all
bla
OXA-114
positive), one
Achromobacter dolens
isolate, and one
Achromobacter insuavis
isolate. All less common species were misidentified as
A. xylosoxidans
by matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS). Chronic colonization by clonally related
A. ruhlandii
isolates was demonstrated.
Testing for Herpes Simplex Virus in Low-Volume Cerebrospinal Fluid Samples: Comparison of Three Protocols To Optimize Detection
Authors: Espy Mark J. , Irish Cole L. , Binnicker Matthew J. 
Published: September 2015

ABSTRACT
Detection of herpes simplex virus 1 and 2 (HSV-1 and HSV-2) in cerebrospinal fluid (CSF) is a medical emergency and requires rapid, sensitive testing. However, the volume of CSF received for microbiological studies may be limited, especially from young children. In this study, we compared three testing protocols to our routine real-time PCR method to determine the most sensitive approach for detecting HSV-1 and HSV-2 in low-volume (≤100 μl) CSF.
Response of Mammalian Macrophages to Challenge with the Chlorovirus Acanthocystisturfacea Chlorella Virus 1
Authors: Petro Thomas M. , Agarkova Irina V. , Zhou You , Yolken Robert H. , Van Etten James L. , Dunigan David D. 
Published: September 2015

ABSTRACT

It was recently reported that 44% of the oropharyngeal samples from the healthy humans in a study cohort had DNA sequences similar to that of the chlorovirus ATCV-1 (
Acanthocystis
turfacea
chlorella virus 1, family
Phycodnaviridae
) and that these study subjects had decreases in visual processing and visual motor speed compared with individuals in whom no virus was detected. Moreover, mice inoculated orally with ATCV-1 developed immune responses to ATCV-1 proteins and had decreases in certain cognitive domains. Because heightened interleukin-6 (IL-6), nitric oxide (NO), and ERK mitogen-activated protein (MAP) kinase activation from macrophages are linked to cognitive impairments, we evaluated cellular responses and viral PFU counts in murine RAW264.7 cells and primary macrophages after exposure to ATCV-1
in
vitro
for up to 72 h after a virus challenge. Approximately 8% of the ATCV-1 inoculum was associated with macrophages after 1 h, and the percentage increased 2- to 3-fold over 72 h. Immunoblot assays with rabbit anti-ATCV-1 antibody detected a 55-kDa protein consistent with the viral capsid protein from 1 to 72 h and increasing
de
novo
synthesis of a previously unidentified 17-kDa protein beginning at 24 h. Emergence of the 17-kDa protein did not occur and persistence of the 55-kDa protein declined over time when cells were exposed to heat-inactivated ATCV-1. Moreover, starting at 24 h, RAW264.7 cells exhibited cytopathic effects, annexin V staining, and cleaved caspase 3. Activation of ERK MAP kinases occurred in these cells by 30 min postchallenge, which preceded the expression of IL-6 and NO. Therefore, ATCV-1 persistence in and induction of inflammatory factors by these macrophages may contribute to declines in the cognitive abilities of mice and humans.

IMPORTANCE
Virus infections that persist in and stimulate inflammatory factors in macrophages contribute to pathologies in humans. A previous study showed that DNA sequences homologous to the chlorovirus ATCV-1 were found in a significant fraction of oropharyngeal samples from a healthy human cohort. We show here that ATCV-1, whose only known host is a eukaryotic green alga (
Chlorella
heliozoae
) that is an endosymbiont of the heliozoon
Acanthocystis
turfacea
, can unexpectedly persist within murine macrophages and trigger inflammatory responses including factors that contribute to immunopathologies. The inflammatory factors that are produced in response to ATCV-1 include IL-6 and NO, whose induction is preceded by the activation of ERK MAP kinases. Other responses of ATCV-1-challenged macrophages include an apoptotic cytopathic effect, an innate antiviral response, and a metabolic shift toward aerobic glycolysis. Therefore, mammalian encounters with chloroviruses may contribute to chronic inflammatory responses from macrophages.
A Synthetic Porcine Reproductive and Respiratory Syndrome Virus Strain Confers Unprecedented Levels of Heterologous Protection
Authors: Vu Hiep L. X. , Ma Fangrui , Laegreid William W. , Pattnaik Asit K. , Steffen David , Doster Alan R. , Osorio Fernando A. 
Published: September 2015

ABSTRACTCurrent vaccines do not provide sufficient levels of protection against divergent porcine reproductive and respiratory syndrome virus (PRRSV) strains circulating in the field, mainly due to the substantial variation of the viral genome. We describe here a novel approach to generate a PRRSV vaccine candidate that could confer unprecedented levels of heterologous protection against divergent PRRSV isolates. By using a set of 59 nonredundant, full-genome sequences of type 2 PRRSVs, a consensus genome (designated PRRSV-CON) was generated by aligning these 59 PRRSV full-genome sequences, followed by selecting the most common nucleotide found at each position of the alignment. Next, the synthetic PRRSV-CON strain was generated through the use of reverse genetics. PRRSV-CON replicates as efficiently as our prototype PRRSV strain FL12, bothin vitroandin vivo. Importantly, when inoculated into pigs, PRRSV-CON confers significantly broader levels of heterologous protection than does wild-type PRRSV. Collectively, our data demonstrate that PRRSV-CON can serve as an excellent candidate for the development of a broadly protective PRRSV vaccine.IMPORTANCEThe extraordinary genetic variation of RNA viruses poses a monumental challenge for the development of broadly protective vaccines against these viruses. To minimize the genetic dissimilarity between vaccine immunogens and contemporary circulating viruses, computational strategies have been developed for the generation of artificial immunogen sequences (so-called “centralized” sequences) that have equal genetic distances to the circulating viruses. Thus far, the generation of centralized vaccine immunogens has been carried out at the level of individual viral proteins. We expand this concept to PRRSV, a highly variable RNA virus, by creating a synthetic PRRSV strain based on a centralized PRRSV genome sequence. This study provides the first example of centralizing the whole genome of an RNA virus to improve vaccine coverage. This concept may be significant for the development of vaccines against genetically variable viruses that require active viral replication in order to achieve complete immune protection.
Genetic Diversity within Alphaherpesviruses: Characterization of a Novel Variant of Herpes Simplex Virus 2
Authors: Burrel Sonia , Désiré Nathalie , Marlet Julien , Dacheux Laurent , Seang Sophie , Caumes Eric , Bourhy Hervé , Agut Henri , Boutolleau David 
Published: September 2015

ABSTRACT
Very low levels of variability have been reported for the herpes simplex virus 2 (HSV-2) genome. We recently described a new genetic variant of HSV-2 (HSV-2v) characterized by a much higher degree of variability for the UL30 gene (DNA polymerase) than observed for the HG52 reference strain. Retrospective screening of 505 clinical isolates of HSV-2 by a specific real-time PCR assay targeting the UL30 gene led to the identification of 13 additional HSV-2v isolates, resulting in an overall prevalence of 2.8%. Phylogenetic analyses on the basis of microsatellite markers and gene sequences showed clear differences between HSV-2v and classical HSV-2. Thirteen of the 14 patients infected with HSV-2v originated from West or Central Africa, and 9 of these patients were coinfected with HIV. These results raise questions about the origin of this new virus. Preliminary results suggest that HSV-2v may have acquired genomic segments from chimpanzee alphaherpesvirus (ChHV) by recombination.

IMPORTANCE
This article deals with the highly topical question of the origin of this new HSV-2 variant identified in patients with HIV coinfection originating mostly from West or Central Africa. HSV-2v clearly differed from classical HSV-2 isolates in phylogenetic analyses and may be linked to simian ChHV. This new HSV-2 variant highlights the possible occurrence of recombination between human and simian herpesviruses under natural conditions, potentially presenting greater challenges for the future.
Workplace training for senior trainees: a systematic review and narrative synthesis of current approaches to promote patient safety
Authors: Walton Merrilyn , Harrison Reema , Burgess Annette , Foster Kirsty 
Published: September 2015

ABSTRACT

Background
Preventable harm is one of the top six health problems in the developed world. Developing patient safety skills and knowledge among advanced trainee doctors is critical. Clinical supervision is the main form of training for advanced trainees. The use of supervision to develop patient safety competence has not been established.

Objective
To establish the use of clinical supervision and other workplace training to develop non-technical patient safety competency in advanced trainee doctors.

Data sources
Keywords, synonyms and subject headings were used to search eight electronic databases in addition to hand-searching of relevant journals up to 1 March 2014.

Method
Titles and abstracts of retrieved publications were screened by two reviewers and checked by a third. Full-text articles were screened against the eligibility criteria. Data on design, methods and key findings were extracted. Clinical supervision documents were assessed against components common to established patient safety frameworks. Findings from the reviewed articles and document analysis were collated in a narrative synthesis.

Results
Clinical supervision is not identified as an avenue for embedding patient safety skills in the workplace and is consequently not evaluated as a method to teach trainees these skills. Workplace training in non-technical patient safety skills is limited, but one-off training courses are sometimes used.

Conclusions
Clinical supervision is the primary avenue for learning in postgraduate medical education but the most overlooked in the context of patient safety learning. The widespread implementation of short courses is not matched by evidence of rigorous evaluation. Supporting supervisors to identify teaching moments during supervision and to give weight to non-technical skills and technical skills equally is critical.