bluuebunny/crossref_metadata_2025_split huggingface dataset:
Lessons learnt from incidents involving the airway and breathing reported from Australasian emergency departments
Authors: Crock Carmel , Hansen Kim , Fogg Toby , Cahill Angela , Deakin Anita , Runciman William B 
Published: August 2017

AbstractObjectiveTo review incident reports relating to problems encountered during the ED management of patients with ‘airway or breathing’ problems, with the aim of finding and highlighting common themes within these rare events, and making recommendations to further improve patient safety in the areas in which deficiencies have been identified.MethodsThematic analysis of 36 incidents reported from Australasian EDs, which were related to problems with airway and breathing.ResultsIn all, 51 problems were identified among the 36 incidents related to airway and/or breathing. Fourteen involved clinical decision‐making, 11 equipment, nine communication, seven intubation, five surgical access and five pneumothorax. Eight incidents involved children and there were nine deaths within hours or days.ConclusionsRecommendations for improving preparedness of ED staff and facilities have been made for each of the problem areas identified with respect to clinical practice, equipment, communication and clinical process. Analysis of incidents from the Australasian Emergency Medicine Events Register allows clusters of like‐events to be identified and characterised, providing the possibility of getting a better idea of how problems present and progress, with some information about contributing factors, characteristics and context. This will pave the way for earlier and better detection of life‐threatening problems and the development and reinforcement of preventive and corrective strategies.
Disentangling the role of management, vegetation structure, and plant quality for Orthoptera in lowland meadows
Authors: Schirmel Jens , Gerlach Rebekka , Buhk Constanze 
Published: August 2017

AbstractSeminatural grasslands provide habitats for various species and are important for biodiversity conservation. The understanding of the diverse responses of species and traits to different grassland management methods is therefore urgently needed. We disentangled the role of grassland management (fertilization and irrigation), vegetation structure (biomass, sward height) and plant quality (protein and fiber content) for Orthoptera communities in lowland hay meadows in Germany. We found vegetation structure to be the most important environmental category in explaining community structure of Orthoptera (species richness, total individuals, functional diversity and species composition). Intensively used meadows (fertilized, irrigated, high plant biomass) were characterized by assemblages with few species, low functional diversity, and low conservation value. Thereby, the relatively moderate fertilizer inputs in our study system of up to ∼75 kg N/ha/year reduced functional diversity of Orthoptera, while this negative effect of fertilization was not detectable when solely considering taxonomic aspects. We found strong support for a prominent role of plant quality in shaping Orthoptera communities and especially the trait composition. Our findings demonstrate the usefulness of considering both taxonomic and functional components (functional diversity) in biodiversity research and we suggest a stronger involvement of plant quality measures in Orthoptera studies.
Assembly and RNA‐free annotation of highly heterozygous genomes: The case of the thick‐billed murre (Uria lomvia)
Authors: Tigano Anna , Sackton Timothy B. , Friesen Vicki L. 
Published: August 2017

AbstractThanks to a dramatic reduction in sequencing costs followed by a rapid development of bioinformatics tools, genome assembly and annotation have become accessible to many researchers in recent years. Among tetrapods, birds have genomes that display many features that facilitate their assembly and annotation, such as small genome size, low number of repeats and highly conserved genomic structure. However, we found that high genomic heterozygosity could have a great impact on the quality of the genome assembly of the thick‐billed murre (Uria lomvia), an arctic colonial seabird. In this study, we tested the performance of three genome assemblers, ray/sscape, soapdenovo2 and platanus, in assembling the highly heterozygous genome of the thick‐billed murre. Our results show that platanus, an assembler specifically designed for heterozygous genomes, outperforms the other two approaches and produces a highly contiguous (N50 = 15.8 Mb) and complete genome assembly (93% presence of genes from the Benchmarking Universal Single Copy Ortholog [BUSCO] gene set). Additionally, we annotated the thick‐billed murre genome using a homology‐based approach that takes advantage of the genomic resources available for birds and other taxa. Our study will be useful for those researchers who are approaching assembly and annotation of highly heterozygous genomes, or genomes of species of conservation concern, and/or who have limited financial resources.
A novel post hoc method for detecting index switching finds no evidence for increased switching on the Illumina HiSeq X
Authors: Owens Gregory L. , Todesco Marco , Drummond Emily B. M. , Yeaman Sam , Rieseberg Loren H. 
Published: August 2017

AbstractHigh‐throughput sequencing using the Illumina HiSeq platform is a pervasive and critical molecular ecology resource, and has provided the data underlying many recent advances. A recent study has suggested that “index switching,” where reads are misattributed to the wrong sample, may be higher in new versions of the HiSeq platform. This has the potential to invalidate both published and in‐progress work across the field. Here, we test for evidence of index switching in an exemplar whole‐genome shotgun data set sequenced on both the Illumina HiSeq 2500, which should not have the problem, and the Illumina HiSeq X, which may. We leverage unbalanced heterozygotes, which may be produced by index switching, and ask whether the undersequenced allele is more likely to be found in other samples in the same lane than expected based on the allele frequency. Although we validate the sensitivity of this method using simulations, we find that neither the HiSeq 2500 nor the HiSeq X has evidence of index switching. This suggests that, thankfully, index switching may not be a ubiquitous problem in HiSeq X sequence data. Lastly, we provide scripts for applying our method so that index switching can be tested for in other data sets.
Quantifying and modelling decay in forecast proficiency indicates the limits of transferability in land‐cover classification
Authors: Gavish Yoni , O'Connell Jerome , Benton Tim G. 
Published: August 2017

Abstract

The ability to provide reliable projections for the current and future distribution of land‐cover is fundamental if we wish to protect and manage our diminishing natural resources. Two inter‐related revolutions make map productions feasible at unprecedented resolutions—the availability of high‐resolution remotely sensed data and the development of machine‐learning algorithms. However, ground‐truthed data needed for training models is in most cases spatially and temporally clustered. Therefore, map production requires extrapolation of models from one place to another and the uncertainty cost of such extrapolation is rarely explored. In other words, the focus has mainly been on projections, and less on quantifying their reliability.

Using the concept of “forecast horizon”, we suggest that the predictability of land‐cover classification models should be quantitatively explored as a continuum against distances measured along multiple dimensions—space, time, environmental and spectral. Focusing on ten agricultural sites from England and using models specifically designed to predict multivariate decay‐curves, we ask: how does a model's predictive performance decay with distance? More specifically, we explored if we could predict the proficiency (kappa statistics) of a model trained in one site when making predictions in another site based on the spatial, temporal, spectral and environmental distances between sites.

We found that model proficiency decays with distance between sites in each dimension. More importantly, we found for the first time, that it is possible to predict the performance a model transferred to or from a novel site will have, based on its distances from known sites. The spectral distance variables were the most important when predicting model transferability.

Exploring model transferability as a continuum may have multiple usages including predicting uncertainty values in space and time, prioritisation of strategies for ground‐truth data collection, and optimising model characteristics for defined tasks.
Single‐tube library preparation for degraded DNA
Authors: Carøe Christian , Gopalakrishnan Shyam , Vinner Lasse , Mak Sarah S. T. , Sinding Mikkel Holger S. , Samaniego José A. , Wales Nathan , Sicheritz‐Pontén Thomas , Gilbert M. Thomas P. 
Published: August 2017

Abstract

In recent years, massive parallel sequencing has revolutionised the study of degraded DNA, thus enabling the field of ancient DNA to evolve into that of paleogenomics. Despite these advances, the recovery and sequencing of degraded DNA remains challenging due to limitations in the manipulation of chemically damaged and highly fragmented DNA molecules. In particular, the enzymatic reactions and DNA purification steps during library preparation can result in DNA template loss and sequencing biases, affecting downstream analyses. The development of library preparation methods that circumvent these obstacles and enable higher throughput are therefore of interest to researchers working with degraded DNA.

In this study, we compare four Illumina library preparation protocols, including two “single‐tube” methods developed for this study with the explicit aim of improving data quality and reducing preparation time and expenses. The methods are tested on grey wolf (Canis lupus) museum specimens.

We found single‐tube protocols increase library complexity, yield more reads that map uniquely to the reference genome, reduce processing time, and may decrease laboratory costs by 90%.

Given the advantages of single‐tube library preparations, we anticipate these methods will be of considerable interest to the growing field of paleogenomics and other applications investigating degraded DNA.
Modelling unbiased dispersal kernels over continuous space by accounting for spatial heterogeneity in marking and observation efforts
Authors: Chadœuf Joël , Millon Alexandre , Bourrioux Jean‐Luc , Printemps Thierry , van Hecke Benoît , Lecoustre Vincent , Bretagnolle Vincent 
Published: August 2017

AbstractAlthough a key demographic trait determining the spatial dynamics of wild populations, dispersal is notoriously difficult to estimate in the field. Indeed, dispersal distances obtained from the monitoring of marked individuals typically lead to biased estimations of dispersal kernels as a consequence of (i) restricted spatial scale of the study areas compared to species potential dispersal and (ii) heterogeneity in marking and observation efforts and therefore in detection probability across space.Here, we propose a novel method to circumvent these issues that does not require data on observation effort per se, to correct for the variability in detection of marked individuals across space. Observed dispersal events were weighted by the distribution of departure points and an eroded spatial window approach was applied so as to deal with border effect. We conducted a set of simulations which indicated that our method was successful in correcting the effect of spatially heterogeneous detectability and produce unbiased dispersal kernels.We applied this method to a real dataset on the Montagu's harrier (>5,000 chicks tagged), providingc. 6,000 resightings collected in entire France by a network of 1,200 volunteers within a citizen‐science programme. The median dispersal distance observed was 32 km (range: 0.1–627 km). Once corrected for spatial heterogeneity in marking and observation efforts and border effect, the modelled dispersal kernel indicated a median dispersal distance of 78–123 km depending on the spatial scale considered (constrained within French borders or not, respectively).Synthesis and applications: The current rise of citizen‐science programmes is likely to stretch our estimate of the ecologically relevant spatial scale at which dispersal takes place for many taxa. Our method is particularly suited for such large‐scale data that typically suffer from high spatial heterogeneity in marking and observation efforts and offers the possibility to derive unbiased dispersal kernels, a key component for modelling population dynamics and species distribution in a context of environmental change. Currently, our method assumes homogeneity in both habitat and dispersal behaviour across individuals. We discuss, however, how to relax these hypotheses to further investigate the effect of, e.g. local conspecific density or habitat quality on dispersal propensity.
Combinatorial effect of nicotine and black tea on heart rate variability: Useful or harmful?
Authors: Joukar S. , Sheibani M. 
Published: August 2017

Summary

The effect of nicotine on heart rate variability (HRV) is controversial. Autonomic nervous system is the main regulator of heart rhythm, and heart rate variability is an appropriate index to assessment of the effects of the autonomic system on heart.

In this study, the combination effect of nicotine and black tea consumption on sympatho‐vagal balance and heart rate variability was investigated in rats.

Male Wistar rats were randomized into four groups as control, tea (2.5 g/100 cc, daily), nicotine (2 mg/kg/d) and tea plus nicotine groups which treated for 28 days, and in the 29th day, their electrocardiograms (lead II) were recorded.

The mean of high‐frequency power (HF) in tea, nicotine and tea plus nicotine groups was significantly more than control group (P < .05), and low‐frequency power/high‐frequency power (LF/HF) ratio in the nicotine and tea + nicotine groups was significantly less than control group (P < .05). LF values did not differ significantly among groups. Mean of standard deviation of normal RR intervals (SDNN) and square root of the mean squared differences of successive RR intervals (RMSSD) increased significantly in tea, nicotine and tea + nicotine groups in comparison with control group (P < .05)

Overall, 4‐week administration of black tea, nicotine or their combination with dosages used in this study can increase the heart rate variability and improve the sympatho‐vagal balance in rat.
A multimethod computational simulation approach for investigating mitochondrial dynamics and dysfunction in degenerative aging
Authors: Hoffman Timothy E. , Barnett Katherine J. , Wallis Lyle , Hanneman William H. 
Published: August 2017

SummaryResearch in biogerontology has largely focused on the complex relationship between mitochondrial dysfunction and biological aging. In particular, the mitochondrial free radical theory of aging (MFRTA) has been well accepted. However, this theory has been challenged by recent studies showing minimal increases in reactive oxygen species (ROS) as not entirely deleterious in nature, and even beneficial under the appropriate cellular circumstances. To assess these significant and nonintuitive observations in the context of a functional system, we have taken an in silico approach to expand the focus of the MFRTA by including other key mitochondrial stress response pathways, as they have been observed in the nematode Caenorhabditis elegans. These include the mitochondrial unfolded protein response (UPRmt), mitochondrial biogenesis and autophagy dynamics, the relevant DAF‐16 and SKN‐1 axes, and NAD+‐dependent deacetylase activities. To integrate these pathways, we have developed a multilevel hybrid‐modeling paradigm, containing agent‐based elements among stochastic system‐dynamics environments of logically derived ordinary differential equations, to simulate aging mitochondrial phenotypes within a population of energetically demanding cells. The simulation experiments resulted in accurate predictions of physiological parameters over time that accompany normal aging, such as the declines in both NAD+ and ATP and an increase in ROS. Additionally, the in silico system was virtually perturbed using a variety of pharmacological (e.g., rapamycin, pterostilbene, paraquat) and genetic (e.g., skn‐1, daf‐16, sod‐2) schemes to quantitate the temporal alterations of specific mechanistic targets, supporting insights into molecular determinants of aging as well as cytoprotective agents that may improve neurological or muscular healthspan.
Cost‐effectiveness of emergency department‐initiated treatment for opioid dependence
Authors: Busch Susan H. , Fiellin David A. , Chawarski Marek C. , Owens Patricia H. , Pantalon Michael V. , Hawk Kathryn , Bernstein Steven L. , O'Connor Patrick G. , D'Onofrio Gail 
Published: August 2017

AbstractBackground and AimsIn a recent randomized trial, patients with opioid dependence receiving brief intervention, emergency department (ED)‐initiated buprenorphine and ongoing follow‐up in primary care with buprenorphine (buprenorphine) were twice as likely to be engaged in addiction treatment compared with referral to community‐based treatment (referral) or brief intervention and referral (brief intervention). Our aim was to evaluate the relative cost‐effectiveness of these three methods of intervening on opioid dependence in the ED.DesignMeasured health‐care use was converted to dollar values. We considered a health‐care system perspective and constructed cost‐effectiveness acceptability curves that indicate the probability each treatment is cost‐effective under different thresholds of willingness‐to‐pay for outcomes studied.SettingAn urban ED in the United States.ParticipantsOpioid‐dependent patients aged 18 years or older.MeasurementsSelf‐reported 30‐day assessment data were used to construct cost‐effectiveness acceptability curves for patient engagement in formal addiction treatment at 30 days and the number of days illicit opioid‐free in the past week.FindingsConsidering only health‐care system costs, cost‐effectiveness acceptability curves indicate that at all positive willingness‐to‐pay values, ED‐initiated buprenorphine treatment was more cost‐effective than brief intervention or referral. For example, at a willingness‐to‐pay threshold of $1000 for 30‐day treatment engagement, we are 79% certain ED‐initiated buprenorphine is most cost‐effective compared with other studied treatments. Similar results were found for days illicit opioid‐free in the past week. Results were robust to secondary analyses that included patients with missing cost data, included crime and patient time costs in the numerator, and to changes in unit price estimates.ConclusionIn the United States, emergency department‐initiated buprenorphine intervention for patients with opioid dependence provides high value compared with referral to community‐based treatment or combined brief intervention and referral.
Caledopsalta gen. nov., a new genus for the New Caledonian cicadas previously assigned to Pauropsalta Goding & Froggatt, plus the description of four new species (Hemiptera: Cicadoidea: Cicadidae)
Authors: Delorme Quentin 
Published: August 2017

AbstractSpecies currently assigned to Pauropsalta Goding & Froggatt in New Caledonia are reviewed. Molecular and morphological studies indicate that New Caledonian cicadas placed in this genus belong in a different genus. The genus Caledopsalta gen. nov. is therefore erected to accommodate Caledopsalta johanae comb. nov., and Caledopsalta judithae. comb. nov., as well as the following four new species: Caledopsalta ouitchamboensis sp. nov., C. canteminvantum sp. nov., C. garrula sp. nov. and C. sciaphila sp. nov. Male calling songs of all species are analysed and described from field recordings. A key to the species of Caledopsalta gen. nov. is provided. This new genus is included within the tribe Cicadettini, with Pauropsalta johanae designated as the type species.
Atypical fibroxanthoma management: Recurrence, metastasis and disease‐specific death
Authors: Polcz Margit Marisa , Sebaratnam Deshan Frank , Fernández‐Peñas Pablo 
Published: August 2017

AbstractAtypical fibroxanthoma (AFX) is a rare spindle cell neoplasm predominantly found on the head and neck of elderly individuals with sun‐damaged skin, with no evidence‐based guidelines for their management. A systematic retrospective review of the literature focusing on treatment modality found a recurrence and metastasis rate of 8.0% (5.6% when adjusted for incomplete excisions) and 0.5% for local excision and 4.6% and 3.2% for Mohs micrographic surgery, respectively. Our results suggest that with clear surgical margins, AFX is unlikely to recur and metastases are rare, with significantly higher rates in the immunosuppressed population.
Chinko/Mbari drainage basin represents a conservation hotspot for Eastern Derby eland in Central Africa
Authors: Brandlová Karolína , Gloneková Markéta , Hejcmanová Pavla , Jůnková Vymyslická Pavla , Aebischer Thierry , Hickisch Raffael , Mallon David 
Published: August 2017

AbstractOne of the largest of antelopes, Derby eland (Taurotragus derbianus), is an important ecosystem component of African savannah. While the western subspecies is Critically Endangered, the eastern subspecies is classified as least concern. Our study presents the first investigation of population dynamics of the Derby eland in the Chinko/Mbari Drainage Basin, Central African Republic, and assesses the conservation role of this population. We analysed data from 63 camera traps installed in 2012. The number of individuals captured within a single camera event ranged from one to 41. Herds were mostly mixed by age and sex, mean group size was 5.61, larger during the dry season. Adult (AD) males constituted only 20% of solitary individuals. The overall sex ratio (M:F) was 1:1.33, while the AD sex ratio shifted to 1:1.52, reflecting selective hunting pressure. Mean density ranged from 0.04 to 0.16 individuals/km2, giving an estimated population size of 445–1,760 individuals. Chinko harbours one of the largest documented populations of Derby eland in Central Africa, making Chinko one of its potential conservation hotspots.