bluuebunny/crossref_metadata_2025_split huggingface dataset:
Asymptomatic carriage rates and case fatality of SARS-CoV-2 infection in residents and staff in Irish nursing homes
Authors: Kennelly Sean P , Dyer Adam H , Noonan Claire , Martin Ruth , Kennelly Siobhan M , Martin Alan , O’Neill Desmond , Fallon Aoife 
Published: September 2020

Abstract

Background
SARS-CoV-2 has disproportionately affected nursing homes (NH). In Ireland, the first NH case COVID-19 occurred on 16 March 2020. A national point-prevalence testing programme of all NH residents and staff took place (18 April 2020 to 5 May 2020).

Aims
to examine characteristics of NHs across three Irish Community Health Organisations, proportions with COVID-19 outbreaks, staff and resident infection rates symptom profile and resident case fatality.

Methods
in total, 45 NHs surveyed, requesting details on occupancy, size, COVID-19 outbreak, outbreak timing, total symptomatic/asymptomatic cases and outcomes for residents from 29 February 2020 to 22 May 2020.

Results
surveys were returned from 62.2% (28/45) of NHs (2,043 residents, 2,303 beds). Three-quarters (21/28) had COVID-19 outbreaks (1,741 residents, 1,972 beds). Median time from first COVID-19 case in Ireland to first case in these NHs was 27.0 days. Resident incidence was 43.9% (764/1,741)—40.8% (710/1,741) laboratory confirmed, with 27.2% (193/710) asymptomatic and 3.1% (54/1,741) clinically suspected. Resident case fatality was 27.6% (211/764) for combined laboratory-confirmed/clinically suspected COVID-19. Similar proportions of residents in NHs with ‘early-stage’ (&lt;28 days) versus ‘later-stage’ outbreaks developed COVID-19. Lower proportions of residents in ‘early’ outbreak NHs had recovered compared with those with ‘late’ outbreaks (37.4 versus 61.7%; χ2 = 56.9, P &lt; 0.001). Of 395 NH staff across 12 sites with confirmed COVID-19, 24.7% (99/398) were asymptomatic. There was a significant correlation between the proportion of staff with symptomatic COVID-19 and resident numbers with confirmed/suspected COVID-19 (Spearman’s rho = 0.81, P &lt; 0.001).

Conclusion
this study demonstrates the significant impact of COVID-19 on the NH sector. Systematic point-prevalence testing is necessary to reduce risk of transmission from asymptomatic carriers and manage outbreaks in this setting.
Capturing Profit from Disaster: The Assets Company Ltd and the Afterlife of the City of Glasgow Bank
Authors: O’Reilly Sean 
Published: September 2020

Abstract
The City of Glasgow Bank’s collapse in 1878 was the largest bank failure of its time. The causes of the crash and its impact on joint-stock banking and the Scottish and British economy have been well-studied, but how its liquidation was concluded remains under-explored. At the same time, the legal and commercial milieu of nineteenth-century Britain spawned a new type of commercial entity—the investment trust. At the intersection of these two historical moments lies the Assets Company Ltd, which is both the legal device that finally concluded the liquidation of the City of Glasgow Bank and a fascinating case study of an early investment trust. Employing little-used archival sources—primarily the Assets Company’s records kept by the Board of Trade and published court judgments—this article investigates the significance and legacy of the Assets Company, from its incorporation in 1882 to its winding-up in 1956. Beyond merely concluding the legal process of liquidation, the Assets Company would go on to manage and profit from the recovery of the City of Glasgow Bank’s assets as well as conduct its own investment activities well into the twentieth century. This article concludes that the Assets Company provides a noteworthy example of how the Bank’s shareholders responded to the winding-up of a large failed bank, particularly, one with unlimited liability, and how an investment trust can be used to maximise the proceeds of liquidation. The winding-up of the City of Glasgow Bank was thus unique relative to previous bank failures in how its shareholders were able to avoid the prolonged liquidation experienced by other Scottish banks. Finally, the Assets Company is an interesting case study of the diversity of the early investment trust industry, and a company that would go on to inspire numerous successor enterprises.
The logic of partial supposition
Authors: Eva Benjamin , Hartmann Stephan 
Published: September 2020

AbstractAccording to orthodoxy, there are two basic moods of supposition: indicative and subjunctive. The most popular formalizations of the corresponding norms of suppositional judgement are given by Bayesian conditionalization and Lewisian imaging, respectively. It is well known that Bayesian conditionalization can be generalized (via Jeffrey conditionalization) to provide a model for the norms of partial indicative supposition. This raises the question of whether imaging can likewise be generalized to model the norms of ‘partial subjunctive supposition’. The present article casts doubt on whether the most natural generalizations of imaging are able to provide a plausible account of the norms of partial subjunctive supposition .
Finding long tandem repeats in long noisy reads
Authors: Morishita Shinichi , Ichikawa Kazuki , Myers Eugene W 
Published: September 2020

Abstract

Motivation
Long tandem repeat expansions of more than 1000 nt have been suggested to be associated with diseases, but remain largely unexplored in individual human genomes because read lengths have been too short. However, new long-read sequencing technologies can produce single reads of 10 000 nt or more that can span such repeat expansions, although these long reads have high error rates, of 10–20%, which complicates the detection of repetitive elements. Moreover, most traditional algorithms for finding tandem repeats are designed to find short tandem repeats (&lt;1000 nt) and cannot effectively handle the high error rate of long reads in a reasonable amount of time.

Results
Here, we report an efficient algorithm for solving this problem that takes advantage of the length of the repeat. Namely, a long tandem repeat has hundreds or thousands of approximate copies of the repeated unit, so despite the error rate, many short k-mers will be error-free in many copies of the unit. We exploited this characteristic to develop a method for first estimating regions that could contain a tandem repeat, by analyzing the k-mer frequency distributions of fixed-size windows across the target read, followed by an algorithm that assembles the k-mers of a putative region into the consensus repeat unit by greedily traversing a de Bruijn graph. Experimental results indicated that the proposed algorithm largely outperformed Tandem Repeats Finder, a widely used program for finding tandem repeats, in terms of sensitivity.

Availability and implementation
https://github.com/morisUtokyo/mTR.
MSCquartets 1.0: quartet methods for species trees and networks under the multispecies coalescent model in R
Authors: Rhodes John A , Baños Hector , Mitchell Jonathan D , Allman Elizabeth S 
Published: September 2020

Abstract

Summary
MSCquartets is an R package for species tree hypothesis testing, inference of species trees and inference of species networks under the Multispecies Coalescent model of incomplete lineage sorting and its network analog. Input for these analyses are collections of metric or topological locus trees which are then summarized by the quartets displayed on them. Results of hypothesis tests at user-supplied levels are displayed in a simplex plot by color-coded points. The package implements the QDC and WQDC algorithms for topological and metric species tree inference, and the NANUQ algorithm for level-1 topological species network inference, all of which give statistically consistent estimators under the model.

Availability and implementation
MSCquartets is available through the Comprehensive R Archive Network: https://CRAN.R-project.org/package=MSCquartets.
Supratidal existence drives phenotypic divergence, but not speciation, in tropical rocky-shore snails
Authors: Marshall David J , Taha Hussein , Brahim Amalina , Abdelhady Ahmed Awad 
Published: September 2020

AbstractThe mechanisms underlying the evolutionary adaptation of animals that transcend the ecological barrier separating the intertidal and supratidal zones of rocky shores are poorly understood. Different wetting frequencies in these zones in tropical regions (daily vs. seasonally, respectively) impose different physical stressors, which should drive phenotypic variation and ultimately speciation in the animals that inhabit them. We studied morphological, physiological and genetic variation in a tropical high-shore gastropod that transcends these zones [Echinolittorina malaccana (Philippi, 1847)]. Variation in melanization, shell features and evaporative water loss was linked to regular seawater wetting, frequent activity and feeding, and solar exposure in intertidal snails, and to inactivity and prolonged aestivation in the shade during continuous air exposure in supratidal snails. Despite selective pressure for phenotypic divergence, and reproductive isolation of the populations in either zone, their mitochondrial COI gene sequences confirmed that they represent a single species. Speciation in our study case is probably constrained by the limitation on activity, mating and reproduction of supratidal snails, such that their populations can only be sustained through intertidal pelagic larval recruitment. Comparisons with other studies suggest that supratidal speciation and specialization for life in this zone probably require moderation of the abiotic (desiccative) conditions, to facilitate greater activity and interaction of animals during air exposure.
Latitudinal variation in sexual dimorphism in a freshwater fish group
Authors: Sumarto Bayu K A , Kobayashi Hirozumi , Kakioka Ryo , Tanaka Rieko , Maeda Ken , Tran Hau D , Koizumi Noriyuki , Morioka Shinsuke , Bounsong Vongvichith , Watanabe Katsutoshi , Musikasinthorn Prachya , Tun Sein , Yun L K C , Anoop V K , Raghavan Rajeev , Masengi Kawilarang W A , Fujimoto Shingo , Yamahira Kazunori 
Published: September 2020

AbstractTropical animals are characterized by showy ornaments and conspicuous body colours as compared with their temperate relatives. Some recent studies have hypothesized that sexual selection pressures are stronger in the tropics than in the temperate zone. Although negative correlations between latitude and the degree of sexual dimorphism would support this hypothesis, phylogeny should be taken into account in such comparative studies. Comparisons of the degree of sexual dimorphism in body size and fin lengths among species of the Adrianichthyidae, a freshwater fish family having a wide geographical range throughout Southeast and East Asia, revealed that lower latitude species are sexually more dimorphic in all characters than higher latitude species. Phylogenetic generalized least squares analyses using a mitochondrial DNA phylogeny demonstrated that the negative correlations between latitude and the degree of sexual dimorphism become non-significant when phylogeny is considered, but that the variance in the degree of sexual dimorphism is explained not only by phylogeny but also almost equally by latitude. Ancestral state reconstruction indicated that sexual dimorphisms have evolved independently even within major clades. These findings are consistent with the view that tropical species are exposed to stronger sexual selection pressures than temperate species. We discuss possible causes of the latitudinal variation in sexual selection pressure.
Different ontogenetic trajectories of body colour, pattern and crypsis in two sympatric intertidal crab species
Authors: Duarte Rafael C , Dias Gustavo M , Flores Augusto A V , Stevens Martin 
Published: September 2020

AbstractAnimals frequently exhibit great variation in appearance, especially in heterogeneous habitats where individuals can be concealed differentially against backgrounds. Although background matching is a common anti-predator strategy, gaps exist in our understanding of within- and among-species variation. Specifically, the drivers of changes in appearance associated with habitat use and occurring through ontogeny are poorly understood. Using image analysis, we tested how individual appearance and camouflage in two intertidal crab species, the mud crab Panopeus americanus and the mottled crab Pachygrapsus transversus, relate to ontogeny and habitat use. We predicted that both species would change appearance with ontogeny, but that resident mud crabs would exhibit higher background similarity than generalist mottled crabs. Both species showed ontogenetic changes; the mud crabs became darker, whereas mottled crabs became more green. Small mud crabs were highly variable in colour and pattern, probably stemming from the use of camouflage in heterogeneous habitats during the most vulnerable life stage. Being habitat specialists, mud crabs were better concealed against all backgrounds than mottled crabs. Mottled crabs are motile and generalist, occupying macroalgae-covered rocks when adults, which explains why they are greener and why matches to specific habitats are less valuable. Differential habitat use in crabs can be associated with different coloration and camouflage strategies to avoid predation.
Emotion and Brain Oscillations: High Arousal is Associated with Decreases in Alpha- and Lower Beta-Band Power
Authors: Schubring David , Schupp Harald T 
Published: September 2020

AbstractThe study of brain oscillations associated with emotional picture processing has revealed conflicting findings. Although many studies observed a decrease in power in the alpha- and lower beta band, some studies observed an increase. Accordingly, the main aim of the present research series was to further elucidate whether emotional stimulus processing is related to an increase or decrease in alpha/beta power. In Study 1, participants (N = 16) viewed briefly presented (150 ms) high-arousing erotic and low-arousing people pictures. Picture presentation included a passive viewing condition and an active picture categorization task. Study 2 (N = 16) replicated Study 1 with negative valence stimuli (mutilations). In Study 3 (N = 18), stimulus materials of Study 1 and 2 were used. The main finding is that high-arousing pictures (erotica and mutilations) are associated with a decrease of power in the alpha/beta band across studies and task conditions. The effect peaked in occipitoparietal sensors between 400 and 800 ms after stimulus onset. Furthermore, a late (&gt;1000 ms) alpha/beta power increase to mutilation pictures was observed, possibly reflecting top–down inhibitory control processes. Overall, these findings suggest that brain oscillations in the alpha/beta-band may serve as a useful measure of emotional stimulus processing.
Factors Associated With Candida auris Colonization and Transmission in Skilled Nursing Facilities With Ventilator Units, New York, 2016–2018
Authors: Rossow John , Ostrowsky Belinda , Adams Eleanor , Greenko Jane , McDonald Robert , Vallabhaneni Snigdha , Forsberg Kaitlin , Perez Stephen , Lucas Todd , Alroy Karen A , Jacobs Slifka Kara , Walters Maroya , Jackson Brendan R , Quinn Monica , Chaturvedi Sudha , Blog Debra ,   New York Candida auris Investigation Workgroup, Southwick Karen , Denis Ronald Jean , Erazo Richard , Fernandez Rafael , Bucher Coralie , Leach Lynn , Zhu Yan , Lutterloh Emily 
Published: September 2020

Abstract

Background
Candida auris is an emerging, multidrug-resistant yeast that spreads in healthcare settings. People colonized with C. auris can transmit this pathogen and are at risk for invasive infections. New York State (NYS) has the largest US burden (&gt;500 colonized and infected people); many colonized individuals are mechanically ventilated or have tracheostomy, and are residents of ventilator-capable skilled nursing facilities (vSNF). We evaluated the factors associated with C. auris colonization among vSNF residents to inform prevention interventions.

Methods
During 2016–2018, the NYS Department of Health conducted point prevalence surveys (PPS) to detect C. auris colonization among residents of vSNFs. In a case-control investigation, we defined a case as C. auris colonization in a resident, and identified up to 4 residents with negative swabs during the same PPS as controls. We abstracted data from medical records on patient facility transfers, antimicrobial use, and medical history.

Results
We included 60 cases and 218 controls identified from 6 vSNFs. After controlling for potential confounders, the following characteristics were associated with C. auris colonization: being on a ventilator (adjusted odds ratio [aOR], 5.9; 95% confidence interval [CI], 2.3–15.4), receiving carbapenem antibiotics in the prior 90 days (aOR, 3.5; 95% CI, 1.6–7.6), having ≥1 acute care hospital visit in the prior 6 months (aOR, 4.2; 95% CI, 1.9–9.6), and receiving systemic fluconazole in the prior 90 days (aOR, 6.0; 95% CI, 1.6–22.6).

Conclusions
Targeted screening of patients in vSNFs with the above risk factors for C. auris can help identify colonized patients and facilitate the implementation of infection control measures. Antimicrobial stewardship may be an important factor in the prevention of C. auris colonization.
Population Trends of the Sugarcane Borer (Lepidoptera: Crambidae) in Louisiana Sugarcane
Authors: Wilson B E , White W H , Richard R T , Johnson R M 
Published: September 2020

Abstract
The sugarcane borer, Diatraea saccharalis (F.) (Lepidoptera: Crambidae), is the primary pest of sugarcane, Saccharum spp., in Louisiana. Spring populations are not considered economically damaging, but quantifying infestations can provide an indication of the spatial and temporal character of the damaging summer populations. Statewide surveys quantified the density of sugarcane tillers killed by D. saccharalis (deadhearts) from sugarcane fields across the state in spring from 2003 to 2020. Deadheart density varied greatly among years with a high of 1,318/ha in 2003 to a low of 0/ha in 2018. Linear regressions of the 3-yr rolling average showed declines in spring D. saccharalis populations and the percentage of acreage treated with insecticides over 17 yr. Weather factors including minimum winter temperatures and average spring temperatures were poor predictors of D. saccharalis populations. Only total precipitation in the month of April was positively correlated with numbers of deadhearts per hectare. Results suggest overwintering mortality is not a key factor influencing populations of the first generation of D. saccharalis in Louisiana. Total precipitation in the month of July was positively associated with percentage of treated acreage. Spring deadheart density was directly related to percentage of acreage treated with insecticides during the summer. Quantifying first-generation D. saccharalis populations by recording deadheart density can aid in predicting pest pressure later in the growing season.
Extracorporeal life support rewarming rate is associated with survival with good neurological outcome in accidental hypothermia
Authors: Saczkowski Richard , Kuzak Nick , Grunau Brian , Schulze Costas 
Published: September 2020

AbstractOBJECTIVESFavourable outcomes have been demonstrated after extracorporeal life support (ECLS) facilitated rewarming for severe accidental hypothermia. The clinical impact of varying rewarming rates however is unclear. We sought to quantify the change in the probability of good neurological outcome with ECLS rewarming rate and identify the optimal rewarming rate threshold.METHODSWe performed a secondary analysis of the International ACcidental Hypothermia Extracorporeal Life Support Collaborators, an individual patient data data set (n = 658) for ECLS-assisted rewarming for accidental hypothermia. The independent variable of interest was rewarming rate. The primary outcome was survival with good neurological status. We applied an adjusted marginal effects model to quantify the probability of good neurological outcome over clinically observed rewarming rates. We examined strata defined by sex, initial potassium level and history of asphyxiation.RESULTSOf 658 cases, the median age and initial core temperature were 36 years (22–55) and 24.5°C (22.1–26.2) respectively; 190 (29%) were female, and 547 (83%) had a non-perfusing initial cardiac rhythm. The mean rewarming rate was 7.0°C/h. The median ECLS duration was 5.8 h (range: 0.5–158 h). The overall survival was 46% (n = 303/658), and good neurological outcome was 40% (n = 265/658). The median intensive care unit and hospital length of stay was 5 days (range: 1–35 days) and 18 days (range: 1–106 days), respectively. Marginal effects analysis demonstrated a 1.9% decrease in the probability of survival with good neurological outcome for each 1°C/h increase in rewarming. Across the reported range of rewarming rates (0.05–30.8°C/h), the probability of good neurological outcome declined from 49.6% to 4.1% for an average patient. The relationship was similar within various subgroups. The optimal cut-off threshold for the rate of rewarming to distinguish between a good and poor neurological outcome was ≤5.0°C/h.CONCLUSIONSAmong cases with severe accidental hypothermia treated with ECLS, slower rewarming rates are associated with improved survival with good neurological outcomes. Slow rewarming, at rates ≤5.0°C/h, may improve clinical outcomes.
Interdisciplinary management of acute ischaemic stroke: Current evidence training requirements for endovascular stroke treatment: Position Paper from the ESC Council on Stroke and the European Association for Percutaneous Cardiovascular Interventions with the support of the European Board of Neurointervention
Authors: Nardai Sandor , Lanzer Peter , Abelson Mark , Baumbach Andreas , Doehner Wolfram , Hopkins L Nelson , Kovac Jan , Meuwissen Martijn , Roffi Marco , Sievert Horst , Skrypnik Dmitry , Sulzenko Jakub , van Zwam Wim , Gruber Andreas , Ribo Marc , Cognard Christophe , Szikora Istvan , Flodmark Olof , Widimsky Petr 
Published: September 2020

Abstract
This ESC Council on Stroke/EAPCI/EBNI position paper summarizes recommendations for training of cardiologists in endovascular treatment of acute ischaemic stroke. Interventional cardiologists adequately trained to perform endovascular stroke interventions could complement stroke teams to provide the 24/7 on call duty and thus to increase timely access of stroke patients to endovascular treatment. The training requirements for interventional cardiologists to perform endovascular therapy are described in details and should be based on two main principles: (i) patient safety cannot be compromised, (ii) proper training of interventional cardiologists should be under supervision of and guaranteed by a qualified neurointerventionist and within the setting of a stroke team. Interdisciplinary cooperation based on common standards and professional consensus is the key to the quality improvement in stroke treatment.