bluuebunny/crossref_metadata_2025 huggingface dataset:
DolphinNext: A graphical user interface for creating, deploying and executing Nextflow pipelines
Authors: Yukselen Onur , Turkyilmaz Osman , Ozturk Ahmet Rasit , Garber Manuel , Kucukural Alper
Published: July 2019

The emergence of high throughput technologies that produce vast amounts of genomic data, such as next-generation sequencing (NGS) are transforming biological research. The dramatic increase in the volume of data makes analysis the main bottleneck for scientific discovery. The processing of high throughput datasets typically involves many different computational programs, each of which performs a specific step in a pipeline. Given the wide range of applications and organizational infrastructures, there is a great need for a highly-parallel, flexible, portable, and reproducible data processing frameworks. Flexibility ensures that pipelines can support a variety of applications without requiring one-off modifications. Portability ensures that users can leverage computationally available resources and work within economic constraints. Reproducibility warrants credibility to the results and is particularly challenging in the face of the sheer volume of data and the complexity of processing pipelines that vary widely between users.

Several platforms currently exist for the design and execution of complex pipelines (e.g. Galaxy, GenePattern, GeneProf). Unfortunately, these platforms lack the necessary combination of parallelism, portability, flexibility and/or reproducibility that are required by the current research environment. To address these shortcomings, Nextflow was implemented to simplify portable, scalable, and reproducible scientific pipelines using containers. We have used Nextflow capabilities as leverage and developed a user interface, DolphinNext, for creating, deploying, and executing complex Nextflow pipelines for high throughput data processing. The guiding principle of DolphinNext is to facilitate the building and deployment of complex pipelines using a modular approach implemented in a graphical interface. DolphinNext provides: 1. A drag and drop user interface that abstracts pipelines and allows users to create pipelines without familiarity in underlying programming languages. 2. A user interface to monitor pipeline execution that allows the re-initiation of pipelines at intermediate steps 3. Reproducible pipelines with version tracking and stand-alone versions that can be run independently. 4. Seamless portability to distributed computational environments such as high-performance clusters or cloud computing environments.
Mechanism of µ-Opioid Receptor-Magnesium Interaction and Positive Allosteric Modulation
Authors: Hu X. , Provasi D. , Filizola M.
Published: July 2019

In the era of opioid abuse epidemics, there is an increased demand for understanding how opioid receptors can be allosterically modulated to guide the development of more effective and safer opioid therapies. Among the modulators of the µ-opioid (MOP) receptor, which is the pharmacological target for the majority of clinically used opioid drugs, are monovalent and divalent cations. Specifically, the monovalent sodium cation (Na+) has been known for decades to affect MOP receptor signaling by reducing agonist binding, whereas the divalent magnesium cation (Mg2+) has been shown to have the opposite effect, notwithstanding the presence of sodium chloride. While ultra-high resolution opioid receptor crystal structures have revealed a specific Na+ binding site and molecular dynamics (MD) simulation studies have supported the idea that this monovalent ion reduces agonist binding by stabilizing the receptor inactive state, the putative binding site of Mg2+ on the MOP receptor, as well as the molecular determinants responsible for its positive allosteric modulation of the receptor, are unknown. In this work, we carried out tens of microseconds of all-atom MD simulations to investigate the simultaneous binding of Mg2+ and Na+ cations to inactive and active crystal structures of the MOP receptor embedded in an explicit lipid/water environment. Analyses of these simulations shed light on (a) the preferred binding sites of Mg2+ on the MOP receptor, (b) details of the competition between Mg2+ and Na+ cations for specific sites, (c) estimates of binding affinities, and (d) testable hypotheses of the molecular mechanism underlying the positive allosteric modulation of the MOP receptor by the Mg2+ cation.

Statement of Significance

Overprescription of opioid drugs in the late 1990s, followed by abuse of both prescription and illicit opioid drugs, has led to what is nowadays called “opioid overdose crisis” or “opioid epidemic”, with more than 130 Americans dying daily from opioid overdose at the time of writing. To reduce opioid doses, and thereby prevent or treat overdose and opioid use disorders, attention has recently shifted to the use of co-analgesics. Understanding how opioid receptor targets can be allosterically modulated by these elements, including cations, is key to the development of improved therapeutics. Here, we provide an atomic-level understanding of the mechanism by which magnesium binds to the µ-opioid receptor and enhances opioid drug efficacy by stabilizing the receptor activated state.
Unraveling the hexaploid sweetpotato inheritance using ultra-dense multilocus mapping
Authors: Mollinari Marcelo , Olukolu Bode A. , da S. Pereira Guilherme , Khan Awais , Gemenet Dorcus , Yencho Craig , Zeng Zhao-Bang
Published: July 2019

The hexaploid sweetpotato (Ipomoea batatas(L.) Lam., 2n = 6x = 90) is an important staple food crop worldwide and has a vital role in alleviating famine in developing countries. Due to its high ploidy level, genetic studies in sweetpotato lag behind major diploid crops significantly. We built an ultra-dense multilocus integrated genetic map and characterized the inheritance system in a sweetpotato full-sib family using our newly implemented software, MAPpoly. The resulting genetic map revealed 96.5% collinearity betweenI. batatasand its diploid relativeI. trifida.We computed the genotypic probabilities across the whole genome for all individuals in the mapping population and inferred their complete hexaploid haplotypes. We provide evidence that most of the meiotic configurations (73.3%) were resolved in bivalents, although a small portion of multivalent signatures (15.7%), among other inconclusive configurations (11.0%) were also observed. Except for low levels of preferential pairing in linkage group 2, we observed a hexasomic inheritance mechanism in all linkage groups. We propose that the hexasomic-bivalent inheritance promotes stability to the allelic transmission in sweetpotato.
Inhibition of adhesive nanofibrillar mediatedStreptococcus gordonii - Candida albicansmono- and dual-species biofilms
Authors: Veerapandian Raja , Vediyappan Govindsamy
Published: July 2019

Dental caries and periodontitis are the most common oral disease of all age groups, affecting billions of people worldwide. These oral diseases are mostly associated with the microbial biofilms in the oral cavity.Streptococcus gordonii, an early tooth colonizing bacterium andCandida albicans, an opportunistic pathogenic fungus, are the two abundant oral microbes form mixed biofilms and augment their virulence properties affecting oral health negatively. Understanding the molecular mechanisms of their interactions and blocking the growth of these biofilms by nontoxic compounds could help develop effective therapeutic approaches. We report in this study, inhibition of mono- or dual-species biofilms ofS. gordoniiandC. albicans, and biofilm eDNAin vitroby Gymnemic Acids (GAs), a nontoxic small molecule inhibitor of fungal hyphae. Scanning electron microscopic images of biofilms revealed attachment ofS. gordoniicells to the hyphal and on saliva-coated hydroxyapatite (sHA) surfaces via nanofibrils only in the untreated control but not in the GAs treated biofilms. Interestingly,C. albicansproduced fibrillar adhesive structures from hyphae when grown withS. gordoniias mixed biofilm and addition of GAs to this biofilm abrogates the nanofibrils, reduces the growth of hyphae, and biofilms. To our knowledge, this is a first report thatC. albicansproduces adhesive fibrils from hyphae in response toS. gordoniimixed biofilm growth. A semi-quantitative PCR data of selected genes related to biofilms of both microbes show their differential expression. Further evaluation of one of the gene products ofS. gordoniirevealed that GAs could inhibit its recombinant glyceraldehyde-3-phosphate dehydrogenase (GAPDH) enzyme activity. Taken together, our results suggest thatS. gordoniistimulates expression of adhesive materials inC. albicansby direct interaction and or by signaling mechanism(s), and these mechanisms can be inhibited by GAs. Further studies on global gene expression of these biofilms and their biochemical studies may reveal the molecular mechanism of their inhibition.
Spatial attention enhances cortical tracking of quasi-rhythmic visual stimuli
Authors: Tabarelli D. , Keitel C. , Gross J. , Baldauf D.
Published: July 2019

Successfully interpreting and navigating our natural visual environment requires us to track its dynamics constantly. Additionally, we focus our attention on behaviorally relevant stimuli to enhance their neural processing. Little is known, however, about how sustained attention affects the ongoing tracking of stimuli with rich natural temporal dynamics. Here, we used MRI-informed source reconstructions of magnetoencephalography (MEG) data to map to what extent various cortical areas track concurrent continuous quasi-rhythmic visual stimulation. Further, we tested how top-down visuo-spatial attention influences this tracking process. Our bilaterally presented quasi-rhythmic stimuli covered a dynamic range of 4 – 20Hz, subdivided into three distinct bands. As an experimental control, we also included strictly rhythmic stimulation (10 vs 12 Hz). Using a spectral measure of brain-stimulus coupling, we were able to track the neural processing of left vs. right stimuli independently, even while fluctuating within the same frequency range. The fidelity of neural tracking depended on the stimulation frequencies, decreasing for higher frequency bands. Both attended and non-attended stimuli were tracked beyond early visual cortices, in ventral and dorsal streams depending on the stimulus frequency. In general, tracking improved with the deployment of visuo-spatial attention to the stimulus location. Our results provide new insights into how human visual cortices process concurrent dynamic stimuli and provide a potential mechanism – namely increasing the temporal precision of tracking – for boosting the neural representation of attended input.
Metabolic Recovery and Compensatory Shell Growth of Juvenile Pacific Geoduck Panopea Generosa Following Short-Term Exposure to Acidified Seawater
Authors: Gurr Samuel J. , Vadopalas Brent , Roberts Steven B. , Putnam Hollie M.
Published: July 2019

While acute stressors can be detrimental, environmental stress conditioning can improve performance. To test the hypothesis that physiological status is altered by stress conditioning, we subjected juvenile Pacific geoduck, Panopea generosa, to repeated exposures of elevated pCO2 in a commercial hatchery setting followed by a period in ambient common garden. Respiration rate and shell length were measured for juvenile geoduck periodically throughout short-term repeated reciprocal exposure periods in ambient (~550 µatm) or elevated (~2400 µatm) pCO2 treatments and in common, ambient conditions, five months after exposure. Short-term exposure periods comprised an initial 10-day exposure followed by 14 days in ambient before a secondary 6-day reciprocal exposure. The initial exposure to elevated pCO2 significantly reduced respiration rate by 25% relative to ambient conditions, but no effect on shell growth was detected. Following 14 days in common garden, ambient conditions, reciprocal exposure to elevated or ambient pCO2 did not alter juvenile respiration rates, indicating ability for metabolic recovery under subsequent conditions. Shell growth was negatively affected during the reciprocal treatment in both exposure histories, however clams exposed to the initial elevated pCO2 showed compensatory growth with 5.8% greater shell length (on average between the two secondary exposures) after five months in ambient conditions. Additionally, clams exposed to the secondary elevated pCO2 showed 52.4% increase in respiration rate after five months in ambient conditions. Early exposure to low pH appears to trigger carry-over effects suggesting bioenergetic re-allocation facilitates growth compensation. Life stage-specific exposures to stress can determine when it may be especially detrimental, or advantageous, to apply stress conditioning for commercial production of this long-lived burrowing clam.

Lay summary

Commercial shellfish hatcheries provide essential food security, but often production can be hampered by sensitivity of shellfish at early life stages. Repeated short-term exposures can increase tolerance and performance of the geoduck clam with implications for sustainable aquaculture.
Causal associations between potentially modifiable risk factors and the Alzheimer’s disease phenome: A Mendelian randomization study
Authors: Andrews Shea J , Fulton-Howard Brian , O’Reilly Paul , Farrer Lindsay A , Haines Jonathan L , Mayeux Richard , Naj Adam C , Pericak-Vance Margaret A , Schellenberg Gerard D , Wang Li-San , Marcora Edoardo , Goate Alison M
Published: July 2019

Objective

To evaluate the causal association of 22 previously reported risk factors for Alzheimer’s disease (AD) on the “AD phenome”: AD, AD age of onset (AAOS), hippocampal volume, cortical surface area and thickness, cerebrospinal fluid (CSF) levels of Aβ42, tau, and ptau181, and the neuropathological burden of neuritic plaques, neurofibrillary tangles, and vascular brain injury (VBI).

Methods

Polygenic risk scores (PRS) for the 22 risk factors were computed in 26,431 AD cases/controls and the association with AD was evaluated using logistic regression. Two-sample Mendelian randomization was used to evaluate the causal effect of risk factors on the AD phenome.

Results

PRS for increased education and diastolic blood pressure were associated with reduced risk for AD. PRS for increased total cholesterol and moderate-vigorous physical activity were associated with an increased risk of AD. MR indicated that only Education was causally associated with reduced risk of AD, delayed AAOS, and increased cortical surface area and thickness. Total-and LDL-cholesterol levels were causally associated with increased neuritic plaque burden, while diastolic blood pressure and pulse pressure are causally associated with increased risk of VBI. Furthermore, total cholesterol was associated with decreased hippocampal volume; smoking initiation and BMI with decreased cortical thickness; and sleep duration with increased cortical thickness.

Interpretation

Our comprehensive examination of the genetic evidence for the causal roles of previously reported risk factors in AD using PRS and MR, supports a causal role for education, blood pressure, cholesterol levels, smoking, and BMI with the AD phenome.
Tracking the mind’s eye: Primate gaze behavior during virtual visuomotor navigation reflects belief dynamics
Authors: Lakshminarasimhan Kaushik J , Avila Eric , Neyhart Erin , DeAngelis Gregory C , Pitkow Xaq , Angelaki Dora E
Published: July 2019

To take the best actions, we often need to maintain and update beliefs about variables that cannot be directly observed. To understand the principles underlying such belief updates, we need tools to uncover subjects’ belief dynamics from natural behaviour. We tested whether eye movements could be used to infer subjects’ beliefs about latent variables using a naturalistic, visuomotor navigation task. We observed eye movements that appeared to continuously track the goal location even when no visible target was present there. Accurate goal-tracking was associated with improved task performance, and inhibiting eye movements in humans impaired navigation precision. By using passive stimulus playback and manipulating stimulus reliability, we show that subjects’ eye movements are likely voluntary, rather than reflexive. These results suggest that gaze dynamics play a key role in action-selection during challenging visuomotor behaviours, and may possibly serve as a window into the subject’s dynamically evolving internal beliefs.
Leveraging peptide substrate libraries to design inhibitors of bacterial Lon protease
Authors: Babin Brett M. , Kasperkiewicz Paulina , Janiszewski Tomasz , Yoo Euna , Drąg Marcin , Bogyo Matthew
Published: July 2019

Lon is a widely-conserved housekeeping protease found in all domains of life. Bacterial Lon is involved in the recovery from various types of stress, including tolerance to fluoroquinolone antibiotics, and is linked to pathogenesis in a number of organisms. However, detailed functional studies of Lon have been limited by the lack of selective, cell-permeable inhibitors. Here we describe the use of positional scanning libraries of hybrid peptide substrates to profile the primary sequence specificity of bacterial Lon. In addition to identifying optimal natural amino acid binding preferences, we identified several non-natural residues that were leveraged to develop optimal peptide substrates as well as a potent peptidic boronic acid inhibitor of Lon. Treatment ofE. coliwith this inhibitor promotes UV-induced filamentation and reduces tolerance to ciprofloxacin, phenocopying establishedlon-deletion phenotypes. It is also non-toxic to mammalian cells due to its increased selectivity for Lon over the proteasome. Our results provide new insight into the primary substrate specificity of Lon and identify substrates and an inhibitor that will serve as useful tools for dissecting the diverse cellular functions of Lon.
Evidence that inconsistent gene prediction can mislead analysis of algal genomes
Authors: Chen Yibi , González-Pech Raúl A. , Stephens Timothy G. , Bhattacharya Debashish , Chan Cheong Xin
Published: July 2019

Comparative algal genomics often relies on predicted gene models from de novo assembled genomes. However, the artifacts introduced by different gene-prediction approaches, and their impact on comparative genomic analysis, remain poorly understood. Here, using available genome data from six dinoflagellate species in Symbiodiniaceae, we identified potential methodological biases in the published gene models that were predicted using different approaches. We developed and applied a comprehensive customized workflow to predict genes from these genomes. The observed variation among predicted gene models resulting from our workflow agreed with current understanding of phylogenetic relationships among these taxa, whereas those published earlier were largely biased by the distinct approaches used in each instance. Importantly, these biases mislead the inference of homologous gene families and synteny among genomes, thus impacting biological interpretation of these data. Our results demonstrate that a consistent gene-prediction approach is critical for comparative genomics, particularly for non-model algal genomes.
Regulation of nucleolar dominance inDrosophila melanogaster
Authors: Warsinger-Pepe Natalie , Li Duojia , Yamashita Yukiko M.
Published: July 2019

In eukaryotic genomes, ribosomal RNA (rRNA) genes exist as tandemly repeated clusters, forming ribosomal DNA (rDNA) loci. Each rDNA locus typically contains hundreds of rRNA genes to meet the high demand of ribosome biogenesis. Nucleolar dominance is a phenomenon, whereby individual rDNA loci are entirely silenced or transcribed, and is believed to be a mechanism to control rRNA dosage. Nucleolar dominance was originally noted to occur in interspecies hybrids, and has been shown to occur within a species (i.e. non-hybrid contexts). However, studying nucleolar dominance within a species has been challenging due to the highly homogenous sequence across rDNA loci. By utilizing single nucleotide polymorphisms (SNPs) between X rDNA vs. Y rDNA loci in males, as well as sequence variations between two X rDNA loci in females, we conducted a thorough characterization of nucleolar dominance throughout development ofD. melanogaster. We demonstrate that nucleolar dominance is a developmentally-regulated program, where Y rDNA dominance is established during male embryogenesis, whereas females normally do not exhibit dominance between two X rDNA loci. By utilizing various chromosomal complements (e.g. X/Y, X/X, X/X/Y) and a chromosome rearrangement, we show that Y chromosome rDNA likely containsciselements that dictate its dominance over the X chromosome rDNA. Our study begins to reveal the mechanisms underlying the selection of rDNA loci for activation/silencing in nucleolar dominance.
Challenges in the calibration of large-scale ordinary differential equation models
Authors: Kapfer Eva-Maria , Stapor Paul , Hasenauer Jan
Published: July 2019

Mathematical models based on ordinary differential equations have been employed with great success to study complex biological systems. With soaring data availability, more and more models of increasing size are being developed. When working with these large-scale models, several challenges arise, such as high computation times or poor identifiability of model parameters. In this work, we review and illustrate the most common challenges using a published model of cellular metabolism. We summarize currently available methods to deal with some of these challenges while focusing on reproducibility and reusability of models, efficient and robust model simulation and parameter estimation.
Phase variation of a signal transduction system controlsClostridioides difficilecolony morphology, motility, and virulence
Authors: Garrett Elizabeth M. , Sekulovic Ognjen , Wetzel Daniela , Jones Joshua B. , Edwards Adrianne N. , Vargas-Cuebas Germán , McBride Shonna M. , Tamayo Rita
Published: July 2019

Recent work has revealed thatClostridioides difficile, a major cause of nosocomial diarrheal disease, exhibits phenotypic heterogeneity within a clonal population as a result of phase variation. ManyC. difficilestrains representing multiple ribotypes develop two colony morphotypes, termed rough and smooth, but the biological implications of this phenomenon have not been explored. Here, we examine the molecular basis and physiological relevance of the distinct colony morphotypes produced by this bacterium. We show thatC. difficilereversibly differentiates into rough and smooth colony morphologies, and that bacteria derived from the isolates display opposing surface and swimming motility behaviors. We identified an atypical phase-variable signal transduction system consisting of a histidine kinase and two response regulators, named herein CmrRST, which mediates the switch in colony morphology and motility behaviors. The CmrRST-regulated surface motility is independent of Type IV pili, suggesting a novel mechanism of surface expansion inC. difficile. Microscopic analysis of cell and colony structure indicates that CmrRST promotes the formation of elongated bacteria arranged in bundled chains, which may contribute to bacterial migration. In a hamster model of acuteC. difficiledisease, colony morphology correlates with virulence, and the CmrRST system is required for disease development. Furthermore, we provide evidence that CmrRST phase varies during infection, suggesting that the intestinal environment impacts the proportion of CmrRST-expressingC. difficile. Our findings indicate thatC. difficileemploys phase variation of the CmrRST signal transduction system to generate phenotypic heterogeneity during infection, with concomitant effects on bacterial physiology and pathogenesis.

Significance Statement

Phenotypic heterogeneity within a genetically clonal population allows many mucosal pathogens to survive within their hosts, balancing the need to produce factors that promote colonization and persistence with the need to avoid the recognition of those factors by the host immune system. Recent work suggests that the human intestinal pathogenClostridium difficileemploys phase variation during infection to generate a heterogeneous population differing in swimming motility, toxin production, and more. This study identifies a signal transduction system that broadly impactsC. difficilephysiology and behaviorin vitroand in an animal model. Phase variation of this system is therefore poised to modulate the coordinated expression of multiple mechanisms influencingC. difficiledisease development.
Niche partitioning as a selective pressure for the evolution of theDrosophilanervous system
Authors: Keesey Ian W. , Grabe Veit , Knaden Markus , Hansson Bill S.
Published: July 2019

The ecological and developmental selective pressures associated with evolution have shaped most animal traits, such as behavior, morphology and neurobiology. As such, the examination of phylogenetic characteristics of the nervous system can be utilized as a means to assess these traits, and thus, to evaluate the underlying selective pressures that produce evolutionary variation between species. Recent studies across a multitude ofDrosophilahave hypothesized the existence of a fundamental tradeoff between two primary sensory organs, the eye and the antenna. However, the identification of any potential ecological mechanisms for this observed tradeoff have not been firmly established. Our current study examines two monophyletic species within theobscuragroup, and asserts that despite their close relatedness and overlapping ecology, they deviate strongly in both visual and olfactory investment. Here we contend that both courtship and microhabitat preferences mirror and support the observed inverse variation in these sensory traits. Moreover, that this variation in visual and olfactory investment between closely-related species seems to provide relaxed competition, a process by which similar species can use a shared environment differently and in ways that help them both coexist. The nervous system has a unique role in evolution as it provides the functional connection between morphology, physiology, and behavior. As such, characterizing any tradeoffs between costs and benefits for the nervous system may be essential to our understanding of animal diversity, as well as vital to our understanding of the selective forces that have shaped the natural world.
Crystal structure analysis of the biologically active drug molecule riluzole and riluzolium chloride
Authors: Mondal Pradip Kumar , T Athulbabu , Rao Varun , Chopra Deepak
Published: July 2019

This study is an investigation into the crystal structure of the biologically active drug molecule riluzole [RZ, 6-(trifluoromethoxy)-1,3-benzothiazol-2-amine], C8H5F3N2OS, and its derivative, the riluzolium chloride salt [RZHCl, 2-amino-6-(trifluoromethoxy)-1,3-benzothiazol-3-ium chloride], C8H6F3N2OS+·Cl−. In spite of repeated efforts to crystallize the drug, its crystal structure has not been reported to date, hence the current study provides a method for obtaining crystals of both riluzole and its corresponding salt, riluzolium hydrochloride. The salt was obtained by grinding HCl with the drug and crystallizing the obtained solid from dichloromethane. The crystals of riluzole were obtained in the presence of L-glutamic acid and D-glutamic acid in separate experiments. In the crystal structure of RZHCl, the –OCF3 moiety is perpendicular to the molecular plane containing the riluzolium ion, as can be seen by the torsion angle of 107.4 (3)°. In the case of riluzole, the torsion angles of the four different molecules in the asymmetric unit show that in three cases the trifluoromethoxy group is perpendicular to the riluzole molecular plane and only in one molecule does the –OCF3 group lie in the same molecular plane. The crystal structure of riluzole primarily consists of strong N—H...N hydrogen bonds along with weak C—H...F, C—H...S, F...F, C...C and C...S interactions, while that of its salt is stabilized by strong [N—H]+...Cl− and weak C—H...Cl−, N—H...S, C—H...F, C...C, S...N and S...Cl− interactions.
Species‐specific strategies increase unpredictability of escape flight in eared moths
Authors: Hügel Theresa , Goerlitz Holger R.
Published: July 2019

Many prey species overlap in time and space and are hunted by the same predators. A common anti‐predator behaviour is using evasive manoeuvres to escape an attacking predator. The escape‐tactic diversity hypothesis postulates that species‐specific differences in evasive behaviour will increase the overall unpredictability experienced by predators within a predator–prey community. Evolutionary, escape‐tactic diversity would be driven by the enhanced predator protection for each prey individual in the community. However, escape‐tactic diversity could also be a functional consequence of morphological differences that correlate with evasive capabilities.

Echolocating bats and eared moths are a textbook example of predator–prey interactions. Moths exhibit evasive flight with diverse tactics; however, the variability of their evasive flight within and between species and individuals has never been quantified systematically. In addition, moth species show variation in size, which correlates with their flight capability.

We recorded flight strength during tethered flight of eight sympatric moth species in response to the same level of simulated bat predation. Our method allowed us to record kinematic parameters that are correlated with evasive flight in a controlled way to investigate species‐specific differences in escape tactics.

We show species‐specific and size‐independent differences in both overall flight strength and change of flight strength over time, supporting the escape‐tactic diversity hypothesis for eared moths. Additionally, we show strong interindividual differences in evasive flight within some species. This diversity in escape tactic between eared moths increases the overall unpredictability of evasive flight experienced by bat predators, likely providing increased protection against predatory bats for the single individual.
Some remarks on Q‐compensated sparse deconvolution without knowing the quality factor Q
Authors: Chai Xintao , Peng Ronghua , Tang Genyang , Chen Wei , Li Jingnan
Published: July 2019

The subsurface media are not perfectly elastic, thus anelastic absorption, attenuation and dispersion (aka Q filtering) effects occur during wave propagation, diminishing seismic resolution. Compensating for anelastic effects is imperative for resolution enhancement. Q values are required for most of conventional Q‐compensation methods, and the source wavelet is additionally required for some of them. Based on the previous work of non‐stationary sparse reflectivity inversion, we evaluate a series of methods for Q‐compensation with/without knowing Q and with/without knowing wavelet. We demonstrate that if Q‐compensation takes the wavelet into account, it generates better results for the severely attenuated components, benefiting from the sparsity promotion. We then evaluate a two‐phase Q‐compensation method in the frequency domain to eliminate Q requirement. In phase 1, the observed seismogram is disintegrated into the least number of Q‐filtered wavelets chosen from a dictionary by optimizing a basis pursuit denoising problem, where the dictionary is composed of the known wavelet with different propagation times, each filtered with a range of possible values. The elements of the dictionary are weighted by the infinity norm of the corresponding column and further preconditioned to provide wavelets of different values and different propagation times equal probability to entry into the solution space. In phase 2, we derive analytic solutions for estimates of reflectivity and Q and solve an over‐determined equation to obtain the final reflectivity series and Q values, where both the amplitude and phase information are utilized to estimate the Q values. The evaluated inversion‐based Q estimation method handles the wave‐interference effects better than conventional spectral‐ratio‐based methods. For Q‐compensation, we investigate why sparsity promoting does matter. Numerical and field data experiments indicate the feasibility of the evaluated method of Q‐compensation without knowing Q but with wavelet given.
Predicting the fundamental thermal niche of crop pests and diseases in a changing world: A case study on citrus greening
Authors: Taylor Rachel A. , Ryan Sadie J. , Lippi Catherine A. , Hall David G. , Narouei‐Khandan Hossein A. , Rohr Jason R. , Johnson Leah R.
Published: July 2019

Predicting where crop pests and diseases can occur, both now and in the future under different climate change scenarios, is a major challenge for crop management. One solution is to estimate the fundamental thermal niche of the pest/disease to indicate where establishment is possible. Here, we develop methods for estimating and displaying the fundamental thermal niche of pests and pathogens and apply these methods to Huanglongbing (HLB), a vector‐borne disease that is currently threatening the citrus industry worldwide.

We derive a suitability metric based on a mathematical model of HLB transmission between tree hosts and its vector Diaphorina citri, and incorporate the effect of temperature on vector traits using data from laboratory experiments performed at different temperatures. We validate the model using data on the historical range of HLB.

Our model predicts that transmission of HLB is possible between 16 and 33°C with peak transmission at ~25°C. The greatest uncertainty in our suitability metric is associated with the mortality of the vectors at peak transmission, and fecundity at the edges of the thermal range, indicating that these parameters need further experimental work.

We produce global thermal niche maps by plotting how many months each location is suitable for establishment of the pest/disease. This analysis reveals that the highest suitability for HLB occurs near the equator in large citrus‐producing regions, such as Brazil and South‐East Asia. Within the Northern Hemisphere, the Iberian peninsula and California are HLB suitable for up to 7 months of the year and are free of HLB currently.

Policy implications. We create a thermal niche map which indicates the places at greatest risk of establishment should a crop disease or pest enter these regions. This indicates where surveillance should be focused to prevent establishment. Our mechanistic method can be used to predict new areas for Huanglongbing transmission under different climate change scenarios and is easily adapted to other vector‐borne diseases and crop pests.
Lisbon After the Crisis: From Credit‐fuelled Suburbanization to Tourist‐driven Gentrification
Authors: Lestegás Iago
Published: July 2019

This article examines Lisbon's post‐crisis transition from a once dominant process of suburban expansion enabled by abundant credit to one of ongoing gentrification of its historic centre. In my research, I draw on quantitative and qualitative data to illustrate the remarkable growth of the metropolitan area's population and dwelling stock until the global financial crisis—which affected the Portuguese economy in the course of a process of financialization that relied heavily on the housing industry—and the intensity of urban rehabilitation in subsequent years. However, there is evidence that the latter has not halted nor reduced the loss of long‐term residents in the historic centre, as tourists and other international gentrifiers occupy the upgraded dwelling stock amid an escalation of house prices and rents. The specific contribution of this research lies in the link that it establishes between Lisbon's ongoing process of inner‐city gentrification and the lack of suburban expansion after 2007. By showing that the credit crunch triggered a shift in the geographic location of real‐estate capital that materialized in a new urban development model, this research adds an empirical layer to the study of the spatial effects of the crisis and contributes to the literature on the subsequent restructuring of southern European housing markets.
The consequences of supply gaps in two‐dimensional policy spaces for voter turnout and political support: The case of economically left‐wing and culturally right‐wing citizens in Western Europe
Authors: HILLEN SVEN , STEINER NILS D.
Published: July 2019

Parties with left‐wing positions on economic issues and right‐wing (i.e., authoritarian) positions on cultural issues have been historically largely absent from the supply side of the policy space of Western European democracies. Yet, many citizens hold such left‐authoritarian issue attitudes. This article addresses the hypotheses that left‐authoritarian citizens are less likely to vote, less satisfied with the democratic process and have lower levels of political trust when there is a left‐authoritarian supply gap. Using data for 14 Western European countries from the European Social Survey 2008 in the main analysis, it is shown that left‐authoritarians are less likely to vote and exhibit lower levels of satisfaction with democracy and political trust. A supplementary analysis of national election studies from Finland before and after the electoral breakthrough of the left‐authoritarian True Finns Party in 2011 indicates that whether left‐authoritarians participate less and believe less in the efficacy of voting is contingent on the presence of a strong left‐authoritarian party. This study illuminates how constrained party supply in a two‐dimensional policy space can affect voter turnout as well as political support, and has broader implications for the potential further rise of left‐authoritarian challenger parties.
The Infant Injury Database: A Tool for the Study of Injury Patterns in Medicolegal Investigations of Child Abuse
Authors: Soto Martinez Miriam E. , Love Jennifer C. , Pinto Deborrah C. , Wiersema Jason M. , Derrick Sharon M. , Bachim Angela , Greeley Christopher , Donaruma‐Kwoh Marcella , Truong Van Thi Thanh , Gao Si , Crowder Christian M.
Published: July 2019

In 2012, the Harris County Institute of Forensic Sciences began prospectively collecting injury data from pediatric autopsies. These data and associated case information from 635 pediatric cases are archived in the Infant Injury Database (IID). This paper introduces the IID to the forensic community and demonstrates its potential utility for child abuse and infant fatality investigations. The database is intended to be a source of evidence‐based research for coroners/medical examiners and clinicians in the recognition and diagnosis of child abuse. RR estimates were employed to quantify the relationship between individual autopsy findings to trauma‐related and nontrauma‐related causes of death. For example, unsurprisingly, the RR of trauma cases with multiple injury types is significantly greater than other causes of death, but the RR results provide a quantitative representation of the relationship. ROC curve modeling of the presence/absence of various injury types performed well at discriminating trauma from other causes of death (AUC = 0.96).
Endotracheal intubation by a specialised paediatric retrieval team
Authors: Glasheen John , Holmes Paul , Rampersad Neeta , Raman Sainath
Published: July 2019

Objectives

Intubation of critically ill children is an infrequent procedure, and is associated with significant risk. We set out to describe intubations carried out by the Children's Health Queensland Retrieval Service (CHQRS), with the intention to identify areas for improvement in the performance of intubation in the retrieval setting.

Methods

Paediatric patients undergoing transport while intubated were identified, and cases where intubation occurred after the arrival of the CHQRS team were examined.

Results

Over the study period of January 2015 to September 2018, 498 intubated retrievals were undertaken; 85 patients were intubated after the arrival of CHQRS; the age range was 1 day to 16.5 years (median 0.5, interquartile range [IQR] 0.11–3 years). The median weight was 6.2 kg (IQR 3.7–16.5 kg). The pathology requiring intubation included respiratory 36 (42.3%), sepsis 21 (24.7%), neurological 11 (12.9%) and trauma 7 (8.2%). A total of 470 of 498 (94.4%) of intubated patients were from regional referral or tertiary hospitals, 28 of 498 (5.6%) were from rural and remote facilities. Of 85 patients, 57 (67.1%) were intubated by CHQRS and 28 (32.9%) were intubated by a doctor from the referring facility. The CHQRS team was more likely to perform the intubation in smaller children (median weight 5.0 vs 9.9 kg, P = 0.03). The mean scene time was 2.8 h. The scene time was shorter if the intubation was performed by CHQRS (mean 2.6 h, median 2.5, IQR 1.8–3.3; median 3, IQR 2.2–3.9; P = 0.048). The scene time was shorter when the intubation was predicted from tasking information (2.6 vs 3.1 h; P = 0.03).

Conclusion

Paediatric endotracheal intubation is an infrequent procedure in our service. An airway registry could improve documentation and gather information to identify specific training requirements and areas for practice improvement.
Elucidation of The Anti‐Inflammatory Effect of Vanillin In Lps‐Activated THP‐1 Cells
Authors: Zhao Dongrui , Jiang Yunsong , Sun Jinyuan , Li Hehe , Huang Mingquan , Sun Xiaotao , Zhao Mouming
Published: July 2019

Vanillin, a kind of phenolic compound, is naturally found in food and beverage and widely used as a flavoring agent. In view of the safety and universality of vanillin, exploring the functions of vanillin on human is of great value. Thus, lipopolysaccharide (LPS)‐activated THP‐1 cells were selected as the cell model to evaluate the anti‐inflammatory effect of vanillin in this study. On the basis of the results, vanillin markedly suppressed the expression of inflammatory cytokines (that is, TNF‐α, IL‐1β, IL‐6, and IL‐8), mediators (NO, iNOS, PGE2, and COX‐2), and NLRP3 inflammasome (that is, NLRP3, ASC, and caspase‐1), blocked the LPS‐induced activation of the NF‐κB/IκBα/AP‐1 signaling pathway, and activated the gene expression of the Nrf2/HO‐1 signaling pathway. In addition, it was confirmed that vanillin was unable to react with LPS due to the results of quantification by HS‐SPME‐GC‐MS. Hence, vanillin could effectively attenuate LPS‐induced inflammatory response by regulating the expression of intracellular signaling pathways in THP‐1 cells. It is a potent anti‐inflammatory component found in food and beverage. These findings might contribute to the overall understanding of the potential health benefits of vanillin for food application.

Practical Application

In this study, the anti‐inflammatory effect of vanillin (VA) was evaluated by ELISA, real‐time PCR, and western blot in LPS‐induced THP‐1 cells. The hypothesis that VA could react with LPS was excluded due to the results of quantification by HS‐SPME‐GC‐MS. On the basis of the result, vanillin could effectively attenuate LPS‐induced inflammatory response in THP‐1 cells and was a potent anti‐inflammatory component natural in food and beverage. These findings might contribute to the overall understanding of the potential health benefits of vanillin for food application.
Clinical relevance of metal artefact reduction in computed tomography (iMAR) in the pelvic and head and neck region: Multi‐institutional contouring study of gross tumour volumes and organs at risk on clinical cases
Authors: Hagen Marius , Kretschmer Matthias , Würschmidt Florian , Gauer Tobias , Giro Christian , Karsten Elias , Lorenzen Jörn
Published: July 2019

Introduction

Artefacts caused by dental implants and hip replacements may impede target volume definition and dose calculation accuracy. The iterative metal artefact reduction (iMAR) algorithm can provide a solution for this problem. The present study compares delineation of gross tumour volumes (GTVs) and organs at risk (OARs) in the pelvic and the head and neck (H & N) regions using computed tomography (CT) with and without iMAR, and thus the practical applicability of iMAR for routine clinical use.

Methods

The native planning CT and CT‐iMAR data of two typical clinical cases with image‐distorting artefacts were used for multi‐institutional contouring and analysis using the Dice similarity coefficient (DSC). GTV/OAR contours were compared with an intraobserver approach and compared to predefined reference structures.

Results

Mean volume for GTVprostate in the intraobserver approach decreased from 87 ± 44 cm3 (native CT) to 75 ± 22 cm3 (CT‐iMAR) (P = 0.168). Compared to the reference, DSC values for GTVProstate increased from 0.68 ± 0.15 to 0.78 ± 0.07 (CT vs. iMAR) (P < 0.05). In the H & N region, the reference for GTVTongue (34 cm3) was underestimated on both data sets. No significant improvement in DSC values (0.83 ± 0.06 (native CT) versus 0.86 ± 0.06 (CT‐iMAR)) was observed.

Conclusion

The use of iMAR improves the anatomical delineation at the transition of prostate and bladder in cases of bilateral hip replacement. In the H & N region, anatomical residual structures and experience were apparently sufficient for precise contouring.
Determinants of women's dissatisfaction with anaesthesia care in labour and delivery
Authors: Yurashevich M. , Carvalho B. , Butwick A. J. , Ando K. , Flood P. D.
Published: July 2019

Patient‐centred care and factors associated with patient satisfaction with anaesthesia have been widely studied. However, the most important considerations in the setting of obstetric anaesthesia are uncertain. Identification of, and addressing, factors that contribute to patient dissatisfaction may improve quality of care. We sought to identify factors associated with < 100% satisfaction with obstetric anaesthesia care. At total of 4297 women treated by anaesthetists provided satisfaction data 24 h after vaginal and 48 h after caesarean delivery. As 78% of women were 100% satisfied, we studied factors associated with the dichotomous variable, 100% satisfied vs. < 100% satisfied. We evaluated patient characteristics and peripartum factors using multivariable sequential logistic regression. The following factors were strongly associated with maternal dissatisfaction after vaginal delivery: pain intensity during the first stage of labour; pain intensity during the second stage of labour; postpartum pain intensity; delay > 15 min in providing epidural analgesia and postpartum headache (all p < 0.0001). Pruritus (p = 0.005) also contributed to dissatisfaction after vaginal delivery, whereas non‐Hispanic ethnicity was negatively associated with dissatisfaction (p = 0.01). After caesarean delivery, the intensity of postpartum pain (p < 0.0001), headache (p = 0.001) and pruritus (p = 0.001) were linked to dissatisfaction. Hispanic ethnicity also had a negative relationship with dissatisfaction after caesarean delivery (p = 0.005). Thus, inadequate or delayed analgesia and treatment‐related side‐effects are associated with maternal dissatisfaction with obstetric anaesthesia care. Development of protocols to facilitate identification of ineffective analgesia and provide an appropriate balance between efficacy and side‐effects, are important goals to optimise maternal satisfaction.