bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evolutionary and Ecological Correlates of Quiet Flight in Nightbirds, Hawks, Falcons, and Owls
Authors: Clark Christopher J , LePiane Krista , Liu Lori 
Published: May 2020

SynopsisTwo hypotheses have been proposed for the evolution of structures that reduce flight sounds in birds. According to the stealth hypothesis, flying quietly reduces the ability of other animals (e.g., prey) to detect the animal’s approach from its flight sounds. This hypothesis predicts that animals hunting prey with acute hearing evolve silencing features. The self-masking hypothesis posits that reduced flight sounds permit the animal itself to hear better (such as the sounds of its prey, or its own echolocation calls) during flight. This hypothesis predicts that quieting features evolve in predators that hunt by ear, or in species that echolocate. Owls, certain hawks, and nightbirds (nocturnal Caprimulgiformes) have convergently evolved a sound-reducing feature: a velvety coating on the dorsal surface of wing and tail feathers. Here we document a fourth independent origin of the velvet, in the American kestrel (Falco sparverius). Among these four clades (hawks, falcons, nightbirds, and owls), the velvet is longer and better developed in wing and tail regions prone to rubbing with neighboring feathers, apparently to reduce broadband frictional noise produced by rubbing of adjacent feathers. We tested whether stealth or self-masking better predicted which species evolved the velvet. There was no support of echolocation as a driver of the velvet: oilbird(Steatornis caripensis) and glossy swiftlet (Collocalia esculenta) each evolved echolocation but neither had any velvet. A phylogenetic least squares fit of stealth and self-masking (to better hear prey sounds) provided support for both hypotheses. Some nightbirds (nightjars, potoos, and owlet-nightjars) eat flying insects that do not make much sound, implying the velvet permits stealthy approach of flying insects. One nightbird clade, frogmouths (Podargus) have more extensive velvet than other nightbirds and may hunt terrestrial prey by ear, in support of self-masking. In hawks, the velvet is also best developed in species known or suspected to hunt by ear (harriers and kites), supporting the self-masking hypothesis, but velvet is also present in reduced form in hawk species not known to hunt by ear, in support of the stealth hypothesis. American kestrel is not known to hunt by ear, and unlike the other falcons sampled, flies slowly (kite-like) when hunting. Thus the presence of velvet in it supports the stealth hypothesis. All owls sampled (n = 13 species) had extensive velvet, including the buffy fish-owl (Ketupa ketupu), contrary to literature claims that fish-owls had lost the velvet. Collectively, there is support for both the self-masking and stealth hypotheses for the evolution of dorsal velvet in birds.
Effects of temperature and hypoxia on respiration, photorespiration, and photosynthesis of seagrass leaves from contrasting temperature regimes
Authors: Rasmusson Lina M , Buapet Pimchanok , George Rushingisha , Gullström Martin , Gunnarsson Pontus C B , Björk Mats 
Published: May 2020

Abstract
In near-future climate change scenarios, elevated ocean temperatures with higher and more frequent peaks are anticipated than at present. Moreover, increased eutrophication and higher primary and secondary productivity will affect the oxygen levels of shallow-water coastal ecosystems, creating hypoxic conditions that can be experienced regularly, especially in dense vegetated systems. These climate-related events may impose detrimental effects on the primary productivity of seagrass. To evaluate such effects, this study combined gas exchange measurements with pulse amplitude-modulated fluorometry to assess the impact of short-time exposure to a range of water temperatures at ambient and low-oxygen levels on mitochondrial respiration, chlorophyll fluorescence (based on the Fv/F0 ratio), photosynthetic oxygen evolution, and photorespiration in leaf segments of the temperate seagrass Zostera marina and the tropical seagrass Thalassia hemprichii. We found that mitochondrial respiration in both Z. marina and T. hemprichii increased with higher temperatures up to 40°C and that low O2 caused significantly reduced respiration rates, particularly in T. hemprichii. Elevated water temperature had a clear negative effect on the Fv/F0 of both seagrass species, indicating damage or inactivation of the photosynthetic apparatus, even when light is not present. Moreover, damage to the photosynthetic apparatus was observed as an effect of elevated temperature combined with low O2 during darkness, resulting in subsequent lower photosynthesis in light. Photorespiration was present, but not promoted by increased temperature alone and will thus not further contribute to productivity losses during warmer events (when not carbon limited). This study demonstrates the negative impact of hypoxic stress and elevated temperatures on seagrass productivity, which may influence the overall health of seagrass plants as well as oxygen and carbon fluxes of shallow-water coastal ecosystems in warmer climate scenarios.
Bykovskii-Type Theorem for the Picard Manifold
Authors: Balog Antal , Biró András , Cherubini Giacomo , Laaksonen Niko 
Published: May 2020

Abstract
We generalise a result of Bykovskii to the Gaussian integers and prove an asymptotic formula for the prime geodesic theorem in short intervals on the Picard manifold. Previous works show that individually the remainder is bounded by $O(X^{13/8+\epsilon })$ and $O(X^{3/2+\theta +\epsilon })$, where $\theta$ is the subconvexity exponent for quadratic Dirichlet $L$-functions over $\mathbb{Q}(i)$. By combining arithmetic methods with estimates for a spectral exponential sum and a smooth explicit formula, we obtain an improvement for both of these exponents. Moreover, by assuming two standard conjectures on $L$-functions, we show that it is possible to reduce the exponent below the barrier $3/2$ and get $O(X^{34/23+\epsilon })$ conditionally. We also demonstrate a dependence of the remainder in the short interval estimate on the classical Gauss circle problem for shifted centres.
Quasimaps to Zero-Dimensional A∞-Quiver Varieties
Authors: Dinkins Hunter , Smirnov Andrey 
Published: May 2020

Abstract
We consider the moduli spaces of quasimaps to zero-dimensional $A_{\infty }$ Nakajima quiver varieties. An explicit combinatorial formula for the equivariant Euler characteristic of these moduli spaces is obtained and applications to symplectic duality are discussed.
Rabinowitz Floer Homology for Tentacular Hamiltonians
Authors: Pasquotto Federica , Vandervorst Robert , Wiśniewska Jagna 
Published: May 2020

Abstract
This paper extends the definition of Rabinowitz Floer homology to non-compact hypersurfaces. We present a general framework for the construction of Rabinowitz Floer homology in the non-compact setting under suitable compactness assumptions on the periodic orbits and the moduli spaces of Floer trajectories. We introduce a class of hypersurfaces arising as the level sets of specific Hamiltonians: strongly tentacular Hamiltonians for which the compactness conditions are satisfied, cf. [ 21], thus enabling us to define the Rabinowitz Floer homology for this class. Rabinowitz Floer homology in turn serves as a tool to address the Weinstein conjecture and establish existence of closed characteristics for non-compact contact manifolds.
Remembering and Enhancing the Impact of Women in Infectious Diseases
Authors: Gilsdorf Janet R , Zimmer Shanta M 
Published: May 2020

Abstract
Following the establishment of the Infectious Diseases Society of America (IDSA), women played a minor role as IDSA leaders, awards recipients, and presenters at the national meeting. Since the formation of the IDSA Women’s Committee in 1992, women have played an increasing role in all of these domains of the Society. Two subsequent IDSA task forces have emphasized the importance of women, and other unrepresented minorities, to the success of the core missions of the Society. Ongoing efforts to maintain the presence of women and their unique talents, experiences, and understandings in the Society will sustain the strengths of IDSA.
γ-Glutamyltransferase as a Novel Virulence Factor of Acinetobacter baumannii Inducing Alveolar Wall Destruction and Renal Damage in Systemic Disease
Authors: Elhosseiny Noha M , Elhezawy Nada B , Sayed Rehab M , Khattab Marwa S , El Far Miran Y , Attia Ahmed S 
Published: May 2020

Abstract
A thorough understanding of Acinetobacter baumannii pathogenicity is the key to identifying novel drug targets. In the current study, we characterize the γ-glutamyltransferase enzyme (GGT) as a novel virulence factor. A GGT assay showed that the enzyme is secreted via the type II secretion system and results in higher extracellular activity for the hypervirulent AB5075 than the laboratory-adapted strain American Type Culture Collection 17978. Enzyme-linked immunosorbent assay revealed that the former secretes larger amounts of GGT, and a rifampicin messenger RNA stability study showed that one reason for this could be the longer AB5075 ggt transcript half-life. Infection models confirmed that GGT is required for the virulence of A. baumannii. Finally, we show that clinical isolates with significantly higher extracellular GGT activity resulted in more severe infections, and assay of immune response and tissue damage markers confirm this correlation. The current findings establish for the first time the role of the GGT in the pathogenicity of A. baumannii.
How Far Can Rhynchophorus palmarum (Coleoptera: Curculionidae) Fly?
Authors: Hoddle Mark S , Hoddle Christina D , Milosavljević Ivan 
Published: May 2020

Abstract
The palm weevil, Rhynchophorus palmarum (L.), was first recorded in San Diego County, CA in 2011 and breeding populations were recovered from infested Canary Islands date palms, Phoenix canariensis, in San Ysidro, San Diego County, in 2015. This palm pest presents a significant threat to California’s edible date industry as Phoenix dactylifera is a recorded host for this weevil. The flight capabilities of R. palmarum are unknown which limits understanding of rates of natural dispersal. In response to this knowledge deficit, 24-h flight mill trials were conducted with field-collected male and female weevils. A total of 87 weevils (49 females and 38 males) were used in experiments, ~6% failed to fly &gt;1 km in 24 h and were excluded from analyses. Of those 82 weevils flying &gt;1 km in 24 h, the average distance flown by males and females was ~41 and ~53 km, respectively. Approximately 10% of females flew &gt;100 km in 24 h, with two (~4%) females flying &gt;140 km. The maximum recorded distance flown by a male weevil was 95 km. Flight activity was predominantly diurnal and flying weevils exhibited an average weight loss of ~18% while non-flying control weevils lost ~13% body weight in 24 h. The combined flight distances for male and female weevils exhibited a heavy-tailed platykurtic distribution. Flight mill data for R. palmarum are compared to similarly collected flight mill data for two other species of invasive palm weevil, Rhynchophorus ferrugineus (Olivier) and Rhynchophorus vulneratus (Panzer).
An unexpected diagnosis of paediatric subcutaneous sacrococcygeal extraspinal ependymoma: lessons learnt and review of the literature
Authors: Gupta Tanya , Patel Vikesh , El-Medani Faisal , Gupta Sanjay 
Published: May 2020

Abstract
This case describes a 9-year-old male who presented to general surgical clinic with a 3-year history of persistent natal cleft swelling, previously unsuccessfully treated as a pilonidal abscess in the community with multiple courses of antibiotics. In clinic, a 50 × 30-mm soft tissue swelling was found in the natal cleft and a clinical diagnosis of a pilonidal cyst was made. A cream-coloured solid mass measuring 50 × 35 × 30 mm was subsequently excised under general anaesthetic, with specialist histology and immunostaining confirming an unexpected diagnosis of a subcutaneous extraspinal myxopapillary ependymoma, a tumour usually found in the neuraxis. Given the atypical anatomical site of the tumour, the case presented a unique management challenge. Ultimately, the patient underwent a re-operation after specialist multi-disciplinary discussion and is currently disease free at 18 months post-surgery. The authors wish to contribute their experiences of managing this rare extraspinal ependymoma to the few existing reports in the literature.
Survey Costs: Where are We and What is the Way Forward?
Authors: Olson Kristen , Wagner James , Anderson Raeda 
Published: May 2020

Abstract
Survey costs are a major driver of survey design decisions and thought to be related to survey errors. Despite their importance, no common language exists for discussing survey costs, nor are there established criteria for identifying which cost metrics are useful for which purposes. Past efforts to study survey costs may have been hampered by the notion that more reporting is better reporting. This article starts by introducing a typology for survey cost metrics defined by the type of cost (estimated, observed in records, and actually incurred), currency versus non-currency measures, and level of aggregation (total, by components, per unit, relative). We also suggest a set of criteria – errors in costs, generalizability, and the degree to which a cost measure is informative about survey error sources – for evaluating the utility of cost metrics. We illustrate the evaluative criteria with the cost metrics. We argue that clearly articulating types of survey costs and resetting these baseline evaluative criteria for the utility of different types of costs will help us expand research in this critical area. We conclude with recommendations for future research in costs within and across organizations.
Scattered light may reveal the existence of ringed exoplanets
Authors: Sucerquia Mario , Alvarado-Montes Jaime A , Zuluaga Jorge I , Montesinos Matías , Bayo Amelia 
Published: May 2020

ABSTRACT
Rings around giant exoplanets (hereafter ‘exorings’) are still a missing planetary phenomenon among the vast number of discovered planets. Despite the fact that there exist a large number of methods for identifying and characterizing these exorings, none of them has been successful to date. Most of those efforts focus on the photometric signatures produced by rings around transiting exoplanets; thus, little interest has been intended for the detectable signatures that non-transiting ringed planets might cause owing to the excess of scattered starlight from both their atmosphere and the considerably large surface of their (hypothetical) ring system. This extra scattering produced by exorings would occur at an orbital location defined here as ‘the summer solstice’ of a stellar light curve. In this letter, we develop a first-order model to estimate the photometric signatures of non-transiting exorings, and predict their detectability by using present and future facilities. We also show how, besides the discovery itself, our model can be used to constrain orbital and physical parameters of planet–ring systems.
Primed CRISPR DNA uptake in Pyrococcus furiosus
Authors: Garrett Sandra , Shiimori Masami , Watts Elizabeth A , Clark Landon , Graveley Brenton R , Terns Michael P 
Published: May 2020

AbstractCRISPR-Cas adaptive immune systems are used by prokaryotes to defend against invaders like viruses and other mobile genetic elements. Immune memories are stored in the form of ‘spacers’ which are short DNA sequences that are captured from invaders and added to the CRISPR array during a process called ‘adaptation’. Spacers are transcribed and the resulting CRISPR (cr)RNAs assemble with different Cas proteins to form effector complexes that recognize matching nucleic acid and destroy it (‘interference’). Adaptation can be ‘naïve’, i.e. independent of any existing spacer matches, or it can be ‘primed’, i.e. spurred by the crRNA-mediated detection of a complete or partial match to an invader sequence. Here we show that primed adaptation occurs in Pyrococcus furiosus. Although P. furiosus has three distinct CRISPR-Cas interference systems (I-B, I-A and III-B), only the I-B system and Cas3 were necessary for priming. Cas4, which is important for selection and processing of new spacers in naïve adaptation, was also essential for priming. Loss of either the I-B effector proteins or Cas3 reduced naïve adaptation. However, when Cas3 and all crRNP genes were deleted, uptake of correctly processed spacers was observed, indicating that none of these interference proteins are necessary for naïve adaptation.
SNPnexus: a web server for functional annotation of human genome sequence variation (2020 update)
Authors: Oscanoa Jorge , Sivapalan Lavanya , Gadaleta Emanuela , Dayem Ullah Abu Z , Lemoine Nicholas R , Chelala Claude 
Published: May 2020

Abstract
SNPnexus is a web-based annotation tool for the analysis and interpretation of both known and novel sequencing variations. Since its last release, SNPnexus has received continual updates to expand the range and depth of annotations provided. SNPnexus has undergone a complete overhaul of the underlying infrastructure to accommodate faster computational times. The scope for data annotation has been substantially expanded to enhance biological interpretations of queried variants. This includes the addition of pathway analysis for the identification of enriched biological pathways and molecular processes. We have further expanded the range of user directed annotation fields available for the study of cancer sequencing data. These new additions facilitate investigations into cancer driver variants and targetable molecular alterations within input datasets. New user directed filtering options have been coupled with the addition of interactive graphical and visualization tools. These improvements streamline the analysis of variants derived from large sequencing datasets for the identification of biologically and clinically significant subsets in the data. SNPnexus is the most comprehensible web-based application currently available and these new set of updates ensures that it remains a state-of-the-art tool for researchers. SNPnexus is freely available at https://www.snp-nexus.org.
Molecular dynamics study of the recognition of ATP by nucleic acid aptamers
Authors: Xie Ya-chen , Eriksson Leif A , Zhang Ru-bo 
Published: May 2020

AbstractDespite their great success in recognizing small molecules in vitro, nucleic acid aptamers are rarely used in clinical settings. This is partially due to the lack of structure-based mechanistic information. In this work, atomistic molecular dynamics simulations are used to study the static and dynamic supramolecular structures relevant to the process of the wild-type (wt) nucleic acid aptamer recognition and binding of ATP. The effects brought about by mutation of key residues in the recognition site are also explored. The simulations reveal that the aptamer displays a high degree of rigidity and is structurally very little affected by the binding of ATP. Interaction energy decomposition shows that dispersion forces from π-stacking between ATP and the G6 and A23 nucleobases in the aptamer binding site plays a more important role in stabilizing the supramolecular complex, compared to hydrogen-bond interaction between ATP and G22. Moreover, metadynamics simulations show that during the association process, water molecules act as essential bridges connecting ATP with G22, which favors the dynamic stability of the complex. The calculations carried out on three mutated aptamer structures confirm the crucial role of the hydrogen bonds and π-stacking interactions for the binding affinity of the ATP nucleic acid aptamer.
CryoEM structures of human CMG–ATPγS–DNA and CMG–AND-1 complexes
Authors: Rzechorzek Neil J , Hardwick Steven W , Jatikusumo Vincentius A , Chirgadze Dimitri Y , Pellegrini Luca 
Published: May 2020

Abstract
DNA unwinding in eukaryotic replication is performed by the Cdc45–MCM–GINS (CMG) helicase. Although the CMG architecture has been elucidated, its mechanism of DNA unwinding and replisome interactions remain poorly understood. Here we report the cryoEM structure at 3.3 Å of human CMG bound to fork DNA and the ATP-analogue ATPγS. Eleven nucleotides of single-stranded (ss) DNA are bound within the C-tier of MCM2–7 AAA+ ATPase domains. All MCM subunits contact DNA, from MCM2 at the 5′-end to MCM5 at the 3′-end of the DNA spiral, but only MCM6, 4, 7 and 3 make a full set of interactions. DNA binding correlates with nucleotide occupancy: five MCM subunits are bound to either ATPγS or ADP, whereas the apo MCM2-5 interface remains open. We further report the cryoEM structure of human CMG bound to the replisome hub AND-1 (CMGA). The AND-1 trimer uses one β-propeller domain of its trimerisation region to dock onto the side of the helicase assembly formed by Cdc45 and GINS. In the resulting CMGA architecture, the AND-1 trimer is closely positioned to the fork DNA while its CIP (Ctf4-interacting peptide)-binding helical domains remain available to recruit partner proteins.
Native de novo structural determinations of non-canonical nucleic acid motifs by X-ray crystallography at long wavelengths
Authors: Zhang Yashu , El Omari Kamel , Duman Ramona , Liu Sisi , Haider Shozeb , Wagner Armin , Parkinson Gary N , Wei Dengguo 
Published: May 2020

Abstract
Obtaining phase information remains a formidable challenge for nucleic acid structure determination. The introduction of an X-ray synchrotron beamline designed to be tunable to long wavelengths at Diamond Light Source has opened the possibility to native de novo structure determinations by the use of intrinsic scattering elements. This provides opportunities to overcome the limitations of introducing modifying nucleotides, often required to derive phasing information. In this paper, we build on established methods to generate new tools for nucleic acid structure determinations. We report on the use of (i) native intrinsic potassium single-wavelength anomalous dispersion methods (K-SAD), (ii) use of anomalous scattering elements integral to the crystallization buffer (extrinsic cobalt and intrinsic potassium ions), (iii) extrinsic bromine and intrinsic phosphorus SAD to solve complex nucleic acid structures. Using the reported methods we solved the structures of (i) Pseudorabies virus (PRV) RNA G-quadruplex and ligand complex, (ii) PRV DNA G-quadruplex, and (iii) an i-motif of human telomeric sequence. Our results highlight the utility of using intrinsic scattering as a pathway to solve and determine non-canonical nucleic acid motifs and reveal the variability of topology, influence of ligand binding, and glycosidic angle rearrangements seen between RNA and DNA G-quadruplexes of the same sequence.