bluuebunny/crossref_metadata_2025_split huggingface dataset:
Remarkable floral colour variation in the functionally specialized fly-pollinated iris,Moraea lurida
Authors: Moir Monika , Johnson Steven D , Anderson Bruce 
Published: February 2022

AbstractSapromyophilous flowers are visited by flies seeking carrion or faeces, and flowers of this guild are typically large, purple or red-brown, often speckled and produce a pungent scent. Flowers of the South African iris Moraea lurida conform to this syndrome, but show considerable variation in colour and pattern. We were intrigued by the floral variation within a single population and investigated floral visitors and the effect of body size on pollen loads and whether different colour forms attracted different pollinator assemblages. We found a diverse array of insect visitors, but Diptera comprised the overwhelming majority, with Calliphoridae considered to be the most important for pollination on the basis of their visitation frequency and pollen loads. Effective pollination appeared to be dependent on large-bodied flies that, unlike smaller flies, fit the entire crawl space between the anthers and petals and thus acted like a key in a lock. Choice experiments revealed that the most important fly pollinators showed no colour preferences, and fly vision modelling showed that flies may not be able to discriminate among the different colour forms. This may lead to relaxed selection on colour. Floral scent was dominated by an unusual mix of aliphatic acids and alcohols, characteristic of mammalian skin products and gut microbiome, probably exploiting the perceptual bias of flies to compounds that typify the mammalian microbiome and fermenting carbohydrates.
The PACAP pathway is independent of CGRP in mouse models of migraine: possible new drug target?
Authors: Ernstsen Charlotte , Christensen Sarah L , Rasmussen Rikke H , Nielsen Brian S , Jansen-Olesen Inger , Olesen Jes , Kristensen David M 
Published: February 2022

Abstract
Calcitonin gene-related peptide (CGRP)-antagonizing drugs represent a major advance in migraine treatment. However, up to 50% of patients do not benefit from monoclonal antibodies against CGRP or its receptor. Here, we test the hypothesis that a closely related peptide, pituitary adenylate cyclase-activating peptide (PACAP-38), works independently of CGRP and thus might represent a new, alternative drug target.
To understand differences in CGRP- and PACAP-mediated migraine pain, we used mouse models of provoked migraine-like pain based on multiple stimulations and subsequent measurement of tactile sensitivity response with von Frey filaments. Genetically modified mice lacking either functional CGRP receptors (Ramp1 knockout) or TRPA1 channels (Trpa1 knockout) were used together with CGRP-targeting antibodies and chemical inhibitors in wild-type mice (ntotal = 299). Ex vivo myograph studies were used to measure dilatory responses to CGRP and PACAP-38 in mouse carotid arteries.
PACAP-38 provoked significant hypersensitivity and dilated the carotid arteries independently of CGRP. In contrast, glyceryl trinitrate-induced hypersensitivity is dependent on CGRP. Contrary to previous results with the migraine-inducing substances glyceryl trinitrate, cilostazol and levcromakalim, PACAP-38-induced hypersensitivity worked only partially through inhibition of ATP-sensitive potassium channels.
Using multiple migraine-relevant models, these findings establish the PACAP-38 pathway as distinct from other migraine provoking pathways such as CGRP and glyceryl trinitrate. PACAP antagonism may therefore be a novel therapeutic target of particular interest in patients unresponsive to CGRP-antagonizing drugs.
Optimized Sequencing Adaptors Enable Rapid and Real-Time Metagenomic Identification of Pathogens during Runtime of Sequencing
Authors: Zhang Dong , Zhang Jingjia , Du Juan , Zhou Yiwen , Wu Pengfei , Liu Zidan , Sun Zhunzhun , Wang Jianghao , Ding Wenchao , Chen Junjie , Wang Jun , Xu Yingchun , Ouyang Chuan , Yang Qiwen 
Published: February 2022

AbstractBackgroundMetagenomic next-generation sequencing (mNGS) offers the promise of unbiased detection of emerging pathogens. However, in indexed sequencing, the sequential paradigm of data acquisition, demultiplexing, and analysis restrain read assignment in advance and real-time analysis, resulting in lengthy turnaround time for clinical metagenomic detection.MethodsWe described the utility of internal-index adaptors with different lengths of barcode in multiplex sequencing. The base composition for each position within these adaptors was well-balanced to ensure nucleotide diversity and optimal sequencing performance and to achieve the early assignment of reads by first sequencing the barcodes. Combined with an automated library preparation device, we delivered a rapid and real-time bioinformatics pathogen identification solution for the Illumina NextSeq platform. The diagnostic performance was evaluated by testing 153 lower respiratory tract specimens using mNGS in comparison to culture, 16S/internal transcribed spacer amplicon sequencing, and additional PCR-based tests.ResultsBy calculating the average F1 scores of all read lengths under different threshold values, we established the optimal threshold for pathogens identification, and found that 36 bp was the optimal shortest read length for rapid mNGS analysis. Rapid detection had a negative percentage agreement and positive percentage agreement of 100% and 85.1% for bacteria and 97.4% and 80.3% for fungi, when compared to a composite standard. The rapid mNGS solution enabled accurate pathogen identification in about 9.1 to 10.1 h sample-to-answer turnaround time.ConclusionsOptimized internal index adaptors combined with a real-time analysis pipeline provide a potential tool for a first-line test in critically ill patients.
Fate of remaining dissected aorta after descending thoracic or thoracoabdominal aorta replacement for chronic dissection
Authors: Jung Joon Chul , Chang Hyoung Woo , Lee Jae Hang , Park Kay-Hyun 
Published: February 2022

Abstract

OBJECTIVES
After performing descending thoracic or thoraco-abdominal aorta replacement for chronic aortic dissection, the fate of the remaining dissected aorta, without significant enlargement, is not well known. This study aimed to investigate the changes in the remaining aorta and the risk factors for late composite aortic events.

METHODS
In 98 patients with chronic type A or B aortic dissection who underwent descending thoracic or thoraco-abdominal aorta replacement, the immediate postoperative and last follow-up computed tomography scans were reviewed. Aortic area-derived diameter was measured using the centreline reconstruction method at the levels of the 10 zones of the aorta and iliac arteries. The incidence of and risk factors for late composite aortic events (aortic death, rupture, reoperation, last follow-up aortic area-derived diameter &gt;60 mm) were analysed.

RESULTS
The median follow-up and computed tomography follow-up durations were 88.5 and 63.7 months, respectively. Nine late deaths occurred. The median growth rate of the remaining aorta was the greatest in the dissected infrarenal abdominal aorta at 0.8 mm/year. Of 16 late composite aortic events, the majority (2 ruptures and 8 reoperations) occurred in the distal contiguous segment. The 5- and 10-year cumulative incidence of events in the distal contiguous segment were 4.9% and 16.1%, respectively. Young age and Marfan syndrome were significant risk factors.

CONCLUSIONS
Late composite aortic events were not negligible, especially in the distal contiguous segment. In young or Marfan syndrome patients, a greater distal extent of replacement may have to be considered at experienced aortic centres.
Orthologs of Saccharomyces cerevisiae SFH2, genes encoding Sec14 family proteins, implicated in utilization of n-alkanes and filamentous growth in response to n-alkanes in Yarrowia lipolytica
Authors: Watanabe Natsuhito , Iwama Ryo , Murayama Reiko , Suzawa Tetsuki , He Zhiyong , Mizuike Aya , Shiwa Yuh , Yoshikawa Hirofumi , Horiuchi Hiroyuki , Fukuda Ryouichi 
Published: February 2022

Abstract
The dimorphic yeast Yarrowia lipolytica has an ability to assimilate n-alkanes as carbon and energy sources. In this study, the roles of orthologs of Saccharomyces cerevisiae SEC14 family gene SFH2, which we named SFH21, SFH22, SFH23 and SFH24, of Y. lipolytica were investigated. The transcript levels of SFH21, SFH22 and SFH23, determined by RNA-seq analysis, qRT-PCR analysis and northern blot analysis, were found to increase in the presence of n-alkanes. The deletion mutant of SFH21, but not that of SFH22, SFH23 or SFH24, showed defects in growth in the media containing n-alkanes and in filamentous growth on the solid media containing n-alkanes. Additional deletions of SFH22 and SFH23 significantly exaggerated the defect in filamentous growth of the deletion mutant of SFH21, and expression of SFH22 or SFH24 using the SFH21 promoter partially suppressed the growth defect of the deletion mutant of SFH21 on n-alkanes. These results suggest that SFH2 orthologs are involved in the utilization of n-alkanes and filamentous growth in response to n-alkanes in Y. lipolytica.
Reducing disease risks to British forests: an exploration of costs and benefits of nursery best practices
Authors: Valatin Gregory , Price Colin , Green Sarah 
Published: February 2022

AbstractTrade-disseminated Phytophthora species are implicated in a recent upsurge of Phytophthora diseases in the UK and the establishment and spread of these pathogens in the wider UK environment via diseased propagation material. The costs and benefits of introducing best practices in the nursery sector and for society at large were explored in relation to avoiding potential impacts of introductions of new pathogens in the wider woodland environment. The analysis formed part of a wider project on the drivers of introduction and spread of Phytophthora species and opportunities for mitigation by plant nurseries. The effect in reducing the risk of introductions of new pathogens is not easily quantified, but the shorter the interval between avoided outbreaks, the greater the benefit of introducing best practices. The maximum interval between avoided outbreaks for the benefits to exceed the costs from a nursery perspective can be estimated. The results indicate that the benefits of introducing nursery best practices are unlikely to outweigh the costs from a nursery perspective where Phytophthora alone is considered. The analysis is extended by also considering benefits in reducing risks of Xylella. Scenario analysis based upon modelling harvested wood and carbon impacts is then used to investigate potential costs that would be expected to be borne by society in the event of the introduction and spread of a new Phytophthora species affecting either oak or Sitka spruce stands in Britain. The results indicate the magnitude of the externality involved, with the cost of an outbreak affecting oak estimated at around £500 million and one affecting Sitka spruce at £11 300 million. While approaches taken in the paper are exploratory, there seems a strong case for some social incentives or control in the nursery sector, to reduce the probability of new diseases infecting British forests.
GABAA α subunit control of hyperactive behavior in developing zebrafish
Authors: Barnaby Wayne , Dorman Barclay Hanna E , Nagarkar Akanksha , Perkins Matthew , Teicher Gregory , Trapani Josef G , Downes Gerald B 
Published: February 2022

Abstract
GABAA receptors mediate rapid responses to the neurotransmitter gamma-aminobutyric acid and are robust regulators of the brain and spinal cord neural networks that control locomotor behaviors, such as walking and swimming. In developing zebrafish, gross pharmacological blockade of these receptors causes hyperactive swimming, which is also a feature of many zebrafish epilepsy models. Although GABAA receptors are important to control locomotor behavior, the large number of subunits and homeostatic compensatory mechanisms have challenged efforts to determine subunit-selective roles. To address this issue, we mutated each of the 8 zebrafish GABAA α subunit genes individually and in pairs using a CRISPR-Cas9 somatic inactivation approach and, then, we examined the swimming behavior of the mutants at 2 developmental stages, 48 and 96 h postfertilization. We found that disrupting the expression of specific pairs of subunits resulted in different abnormalities in swimming behavior at 48 h postfertilization. Mutation of α4 and α5 selectively resulted in longer duration swimming episodes, mutations in α3 and α4 selectively caused excess, large-amplitude body flexions (C-bends), and mutation of α3 and α5 resulted in increases in both of these measures of hyperactivity. At 96 h postfertilization, hyperactive phenotypes were nearly absent, suggesting that homeostatic compensation was able to overcome the disruption of even multiple subunits. Taken together, our results identify subunit-selective roles for GABAA α3, α4, and α5 in regulating locomotion. Given that these subunits exhibit spatially restricted expression patterns, these results provide a foundation to identify neurons and GABAergic networks that control discrete aspects of locomotor behavior.
Estimating SNP heritability in presence of population substructure in biobank-scale datasets
Authors: Lin Zhaotong , Seal Souvik , Basu Saonli 
Published: February 2022

Abstract
Single nucleotide polymorphism heritability of a trait is measured as the proportion of total variance explained by the additive effects of genome-wide single nucleotide polymorphisms. Linear mixed models are routinely used to estimate single nucleotide polymorphism heritability for many complex traits, which requires estimation of a genetic relationship matrix among individuals. Heritability is usually estimated by the restricted maximum likelihood or method of moments approaches such as Haseman–Elston regression. The common practice of accounting for such population substructure is to adjust for the top few principal components of the genetic relationship matrix as covariates in the linear mixed model. This can get computationally very intensive on large biobank-scale datasets. Here, we propose a method of moments approach for estimating single nucleotide polymorphism heritability in presence of population substructure. Our proposed method is computationally scalable on biobank datasets and gives an asymptotically unbiased estimate of heritability in presence of discrete substructures. It introduces the adjustments for population stratification in a second-order estimating equation. It allows these substructures to vary in their single nucleotide polymorphism allele frequencies and in their trait distributions (means and variances) while the heritability is assumed to be the same across these substructures. Through extensive simulation studies and the application on 7 quantitative traits in the UK Biobank cohort, we demonstrate that our proposed method performs well in the presence of population substructure and much more computationally efficient than existing approaches.
Wavefield reconstruction and wave equation inversion for seismic surface waves
Authors: Shaiban A , de Ridder S A L , Curtis A 
Published: February 2022

SUMMARY
Surface waves are a particular type of seismic wave that propagate around the surface of the Earth, but which oscillate over depth ranges beneath the surface that depend on their frequency of oscillation. This causes them to travel with a speed that depends on their frequency, a property called dispersion. Estimating surface wave dispersion is of interest for many geophysical applications using both active and passive seismic sources, not least because the speed–frequency relationship can be used to infer the subsurface velocity structure at depth beneath the surface. We present an inversion scheme that exploits spatial and temporal relationships in the scalar Helmholtz (wave) equation to estimate dispersion relations of the elastic surface wave data in both active and passive surveys, while also reconstructing the wavefield continuously in space (i.e. between the receivers at which the wavefield was recorded). We verify the retrieved dispersive phase velocity by comparing the results to dispersion analysis in the frequency-slowness domain, and to the local calculation of dispersion using modal analysis. Synthetic elastic examples demonstrate the method under a variety of recording scenarios. The results show that despite the scalar approximation made to represent these intrinsically elastic waves, the proposed method reconstructs both the wavefield and the phase dispersion structure even in the case of strong aliasing and irregular sampling.
Ground motion simulations in Quito (Ecuador) due to major earthquakes from the subduction zone
Authors: Courboulex Francoise , Castro-Cruz David Alejandro , Laurendeau Aurore , Bonilla Luis Fabian , Alvarado Alexandra , Bertrand Etienne 
Published: February 2022

SUMMARY
In 1906, an earthquake with a magnitude estimated between Mw 8.4 and 8.8 occurred in the subduction zone along the coast of Ecuador and Colombia. This earthquake caused extensive damage on the coast but had a rather small impact on the capital city of Quito, situated 180 km away. At that time, the city of Quito extended over a small area with a few thousand inhabitants, while today it stretches over 40 km and has a population of over 3 million, with most of the city built without paraseismic regulations. The aim of this study is to obtain new insights on the impact that large earthquakes from the subduction zone would have on the city today. This question is crucial since we know that the city of Quito is prone to site effects and that the southern part of the city amplifies seismic waves at low frequencies, around 0.3–0.4 Hz. In April 2016, an Mw 7.8 earthquake occurred on the subduction interface in the Pedernales area. This event was the first large earthquake in the city of Quito to be well recorded by 13 stations of the permanent accelerometric network (RENAC). In this study, we take advantage of this data set (main shock and large aftershock recordings) to (1) test an empirical Green's function blind simulation approach where the input stress drop is taken from a global catalogue of source time functions, (2) compare the synthetic accelerograms and ground motion values we obtain for an Mw 7.8 earthquake with the actual recordings of the Pedernales earthquake and then (3) simulate larger earthquakes of Mw 8.2 and 8.5 from the subduction zone. For Mw 7.8 simulations, our approach allows a good reproduction of the ground motions in the whole frequency bands and properly takes into account site effects. For Mw 8.2 and 8.5 simulations, we obtain for the stations in the southern part of the basin, larger values at low frequencies than the predicted motion given by ground motion models. These values, although high, should be supported by new or recent buildings if they are constructed respecting the building code that applies in Quito. Therefore, for this type of strong but distant earthquake, the seismic standards appear to be well suited and it is imperative to ensure that they are well considered in the design of the new buildings to be constructed, especially in the southern part of the expanding city.
Seasonal temperature regulates network connectivity of salmon louse
Authors: Huserbråten M B O , Johnsen I A 
Published: February 2022

Abstract
Chronically high infestation of salmon louse (Lepeophtheirus salmonis) questions the sustainability of the Norwegian Atlantic salmon (Salmo salar) aquaculture industry. The confinement of millions of hosts, within hundreds of farms with overlapping larval dispersal kernels create the structure for extremely persistent parasite meta-populations. However, the processes regulating the temporal variation in cross-contamination of pelagic salmon louse stages among farms (i.e. connectivity), a vital process driving louse population dynamics, are not well described. Here, we employ a data driven biophysical dispersal model that reproduces three-and-a-half years of production histories of 132 salmon farms in western Norway and quantifies the connectivity of infective pelagic lice stages among the farms with the ocean currents. We show that although the complex geography of western Norwegian fjords governs the long-term topology of the connectivity network, there was a strong seasonal component to network fragmentation. The main de-structuring agent was the delayed infectivity of the pelagic lice stages at cooler temperatures increasing dispersal distances, enhanced by occasional large scale wind forcing events. Coordinated fallowing strategies and de-lousing treatments only played a marginal role in network fragmentation, suggesting that novel lice restraining strategies that consider the environmentally sensitive transport distances must be developed to successfully break up the connectivity network.
Does early extubation after cardiac surgery lead to a reduction in intensive care unit length of stay?
Authors: Taylor Marcus , Apparau Denish , Mosca Roberto , Nwaejike Nnamdi 
Published: February 2022

Summary
A best evidence topic in cardiac surgery was written according to a structured protocol. The question addressed was whether early extubation (EE) after cardiac surgery leads to a reduction in intensive care unit (ICU) length of stay (LOS)? A total of 564 papers were found using the reported search, of which 4 were randomized trials and hence represented the best evidence to answer the clinical question. The authors, journal, date and country of publication, patient group studied, study type, relevant outcomes and results of these papers are tabulated. EE was defined as extubation in theatre (n = 2), within 6 h of surgery (n = 1) and within 8 h of surgery (n = 1). EE was associated with significantly reduced ICU LOS in all studies. Despite the Society of Thoracic Surgeons using extubation &lt;6 h after surgery as a measure of quality, this study has demonstrated that no standardized definition for EE currently exists. The body of evidence identified in this work has demonstrated that for appropriately selected patients (avoiding patients with multiple comorbidities, advanced age and undergoing complex non-elective surgery) early tracheal extubation is associated with a reduction in ICU LOS without an increase in the rate of postoperative complications.