bluuebunny/crossref_metadata_2025_split huggingface dataset:
What factors predict path tortuosity of Great Basin pocket mice in shrub-steppe habitat invaded by cheatgrass?
Authors: Melaschenko Natalie C , Hodges Karen E 
Published: December 2019

Abstract
Foraging animals choose habitats based on characteristics that often cannot be satisfied simultaneously, such as easy mobility, abundant or high-quality foods, and safety from predators. Invasive plants may alter habitat structure and provide novel foods; thus, measuring how animals forage in invaded landscapes offers insights into these new ecological relationships. We examined the movements of Great Basin pocket mice (Perognathus parvus) in sage-steppe habitats invaded by cheatgreass (Bromus tectorum) in southcentral British Columbia, Canada. The pathway tortuosity (fractal D) of pocket mice increased with vegetative cover and population density and decreased with open habitat, but these variables explained little of the variation in tortuosity. The fractal dimension of movement pathways of pocket mice was consistent over spatial scales ranging from 0.5 m to two-thirds of the home range size, unlike in other species where fractal dimensions are not consistent over multiple spatial scales. Collectively, our results indicate that foraging movements of pocket mice were not affected by the low densities of cheatgrass in this system.
Stylistic analysis of the French presidential speeches: Is Macron really different?
Authors: Labbé Dominique , Savoy Jacques 
Published: December 2019

AbstractPresidential speeches indicate the government’s intentions and justifications supported by a dedicated style and rhetoric oscillating between explanation and controversy. Over a period of 60 years, can we observe stylistic variations by the different French presidents of the Fifth Republic (1958–2018)? Based on official transcripts of all their allocutions, this article illustrates the stylistic evolution and presents the underlying main trends. This study shows that de Gaulle’s rhetoric is not mainly dedicated to his own person, or that the two terms of J. Chirac are not fully similar. According to several overall stylistic indicators, Macron’s style does not appear as complex compared to his predecessors (F. Hollande or N. Sarkozy) but a more careful analysis clearly demonstrates his noticeable new style. Compared to the recent US presidents, the French ones present some similarities (e.g. similar mean sentence length) and dissimilarities (more I-words, less we-words). In this comparative analysis, Macron’s style is also clearly distinctive from both the US and former French presidents. Opting for a more abstract discourse, less anchored in space, using less numbers, E. Macron tends to use long sentences. These various stylistic and rhetorical features could explain his being misunderstood by the French people and his recurrent low approval ratings.
Properties of a fungicidal product formed from a reaction between L-cystine and pyridoxal
Authors: Johnston Elizabeth A , Lloyd Spencer B , Granger Donald L 
Published: December 2019

AbstractPreviously we found that three components of a commonly used mammalian cell culture medium incorporated into agar killed cryptococci (Granger and Call 2019). The components were L-cystine, iron [Fe(III)], and pyridoxal (CIP). We now report on a buffered solution at neutral pH of the three components, which was highly fungicidal without agar. We showed that CIP fungicidal activity, identical to the findings with cell culture medium, was inactivated by visible light and was unstable with storage in the dark. Congeners replacing either pyridoxal or L-cystine in CIP revealed structural requirements for fungicidal activity. Replacing pyridoxal in CIP with 2-hydroxy-5-nitrobenzaldehyde produced a solution that was equally fungicidal and maintained fungicidal activity upon storage in the dark for up to 50 days. We employed methods for excluding iron from CIP and found that fungicidal activity was not affected. Upon mixing L-cystine and pyridoxal in buffer at pH 7.0, diode array spectroscopy revealed a red-shift of absorbance maximum from 391 nm to 398 nm. Our findings point to Schiff base reaction between the pyridoxal aldehyde group of C1 with the alpha amino group(s) of cystine to yield a fungicidal compound. Light at wave length approximately 400 nm inactivates this complex accompanied by bleaching of the pyridine ring of pyridoxal. Our findings may be useful for design of a class of fungicidal compounds formed through Schiff base reaction of disulfide compounds with aromatic ring-bearing aldehydes.
Cosmology with galaxy–galaxy lensing on non-perturbative scales: emulation method and application to BOSS LOWZ
Authors: Wibking Benjamin D , Weinberg David H , Salcedo Andrés N , Wu Hao-Yi , Singh Sukhdeep , Rodríguez-Torres Sergio , Garrison Lehman H , Eisenstein Daniel J 
Published: December 2019

ABSTRACTWe describe our non-linear emulation (i.e. interpolation) framework that combines the halo occupation distribution (HOD) galaxy bias model with N-body simulations of non-linear structure formation, designed to accurately predict the projected clustering and galaxy–galaxy lensing signals from luminous red galaxies in the redshift range 0.16 &lt; z &lt; 0.36 on comoving scales 0.6 &lt; rp &lt; 30 $h^{-1} \, \text{Mpc}$. The interpolation accuracy is ≲ 1–2 per cent across the entire physically plausible range of parameters for all scales considered. We correctly recover the true value of the cosmological parameter S8 = (σ8/0.8228)(Ωm/0.3107)0.6 from mock measurements produced via subhalo abundance matching (SHAM)-based light-cones designed to approximately match the properties of the SDSS LOWZ galaxy sample. Applying our model to Baryon Oscillation Spectroscopic Survey (BOSS) Data Release 14 (DR14) LOWZ galaxy clustering and galaxy-shear cross-correlation measurements made with Sloan Digital Sky Survey (SDSS) Data Release 8 (DR8) imaging, we perform a prototype cosmological analysis marginalizing over wCDM cosmological parameters and galaxy HOD parameters. We obtain a 4.4 per cent measurement of S8 = 0.847 ± 0.037, in 3.5σ tension with the Planck cosmological results of 1.00 ± 0.02. We discuss the possibility of underestimated systematic uncertainties or astrophysical effects that could explain this discrepancy.
The effect of fluctuating fuzzy axion haloes on stellar dynamics: a stochastic model
Authors: El-Zant Amr A , Freundlich Jonathan , Combes Françoise , Halle Anaelle 
Published: December 2019

ABSTRACT
Fuzzy dark matter of ultralight axions has gained attention, largely in light of the galactic scale problems associated with cold dark matter. But the large de Broglie wavelength, believed to possibly alleviate these problems, also leads to fluctuations that place constraints on ultralight axions. We adapt and extend a method, previously devised to describe the effect of gaseous fluctuations on cold dark matter cusps, in order to determine the imprints of ultralight axion haloes on the motion of classical test particles. We first evaluate the effect of fluctuations in a statistically homogeneous medium of classical particles, then in a similar system of ultralight axions. In the first case, one recovers the classical two body relaxation time (and diffusion coefficients) from white noise density fluctuations. In the second situation, the fluctuations are not born of discreteness noise but from the finite de Broglie wavelength; correlation therefore exists over this scale, while white noise is retained on larger scales, elucidating the correspondence with classical relaxation. The resulting density power spectra and correlation functions are compared with those inferred from numerical simulations, and the relaxation time arising from the associated potential fluctuations is evaluated. We then apply our results to estimate the heating of discs embedded in axion dark haloes. We find that this implies an axion mass $m \gtrsim 2 \times 10^{-22} \, {\rm eV}$. We finally apply our model to the case of the central cluster of Eridanus II, confirming that far stronger constraints on m may in principle be obtained, and discussing the limitations associated with the assumptions leading to these.
Ozone chemistry on tidally locked M dwarf planets
Authors: Yates Jack S , Palmer Paul I , Manners James , Boutle Ian , Kohary Krisztian , Mayne Nathan , Abraham Luke 
Published: December 2019

ABSTRACT
We use the Met Office Unified Model to explore the potential of a tidally locked M dwarf planet, nominally Proxima Centauri b irradiated by a quiescent version of its host star, to sustain an atmospheric ozone layer. We assume a slab ocean surface layer, and an Earth-like atmosphere of nitrogen and oxygen with trace amounts of ozone and water vapour. We describe ozone chemistry using the Chapman mechanism and the hydrogen oxide (HOx, describing the sum of OH and HO2) catalytic cycle. We find that Proxima Centauri radiates with sufficient UV energy to initialize the Chapman mechanism. The result is a thin but stable ozone layer that peaks at 0.75 parts per million at 25 km. The quasi-stationary distribution of atmospheric ozone is determined by photolysis driven by incoming stellar radiation and by atmospheric transport. Ozone mole fractions are smallest in the lowest 15 km of the atmosphere at the substellar point and largest in the nightside gyres. Above 15 km the ozone distribution is dominated by an equatorial jet stream that circumnavigates the planet. The nightside ozone distribution is dominated by two cyclonic Rossby gyres that result in localized ozone hotspots. On the dayside the atmospheric lifetime is determined by the HOx catalytic cycle and deposition to the surface, with nightside lifetimes due to chemistry much longer than time-scales associated with atmospheric transport. Surface UV values peak at the substellar point with values of 0.01 W m−2, shielded by the overlying atmospheric ozone layer but more importantly by water vapour clouds.
Genomic Evidence for Complex Domestication History of the Cultivated Tomato in Latin America
Authors: Razifard Hamid , Ramos Alexis , Della Valle Audrey L , Bodary Cooper , Goetz Erika , Manser Elizabeth J , Li Xiang , Zhang Lei , Visa Sofia , Tieman Denise , van der Knaap Esther , Caicedo Ana L 
Published: December 2019

Abstract
The process of plant domestication is often protracted, involving underexplored intermediate stages with important implications for the evolutionary trajectories of domestication traits. Previously, tomato domestication history has been thought to involve two major transitions: one from wild Solanum pimpinellifolium L. to a semidomesticated intermediate, S. lycopersicum L. var. cerasiforme (SLC) in South America, and a second transition from SLC to fully domesticated S. lycopersicum L. var. lycopersicum in Mesoamerica. In this study, we employ population genomic methods to reconstruct tomato domestication history, focusing on the evolutionary changes occurring in the intermediate stages. Our results suggest that the origin of SLC may predate domestication, and that many traits considered typical of cultivated tomatoes arose in South American SLC, but were lost or diminished once these partially domesticated forms spread northward. These traits were then likely reselected in a convergent fashion in the common cultivated tomato, prior to its expansion around the world. Based on these findings, we reveal complexities in the intermediate stage of tomato domestication and provide insight on trajectories of genes and phenotypes involved in tomato domestication syndrome. Our results also allow us to identify underexplored germplasm that harbors useful alleles for crop improvement.
Enhancers Facilitate the Birth of De Novo Genes and Gene Integration into Regulatory Networks
Authors: Majic Paco , Payne Joshua L 
Published: December 2019

AbstractRegulatory networks control the spatiotemporal gene expression patterns that give rise to and define the individual cell types of multicellular organisms. In eumetazoa, distal regulatory elements called enhancers play a key role in determining the structure of such networks, particularly the wiring diagram of “who regulates whom.” Mutations that affect enhancer activity can therefore rewire regulatory networks, potentially causing adaptive changes in gene expression. Here, we use whole-tissue and single-cell transcriptomic and chromatin accessibility data from mouse to show that enhancers play an additional role in the evolution of regulatory networks: They facilitate network growth by creating transcriptionally active regions of open chromatin that are conducive to de novo gene evolution. Specifically, our comparative transcriptomic analysis with three other mammalian species shows that young, mouse-specific intergenic open reading frames are preferentially located near enhancers, whereas older open reading frames are not. Mouse-specific intergenic open reading frames that are proximal to enhancers are more highly and stably transcribed than those that are not proximal to enhancers or promoters, and they are transcribed in a limited diversity of cellular contexts. Furthermore, we report several instances of mouse-specific intergenic open reading frames proximal to promoters showing evidence of being repurposed enhancers. We also show that open reading frames gradually acquire interactions with enhancers over macroevolutionary timescales, helping integrate genes—those that have arisen de novo or by other means—into existing regulatory networks. Taken together, our results highlight a dual role of enhancers in expanding and rewiring gene regulatory networks.
HdaB: a novel and conserved DnaA-related protein that targets the RIDA process to stimulate replication initiation
Authors: Frandi Antonio , Collier Justine 
Published: December 2019

Abstract
Exquisite control of the DnaA initiator is critical to ensure that bacteria initiate chromosome replication in a cell cycle-coordinated manner. In many bacteria, the DnaA-related and replisome-associated Hda/HdaA protein interacts with DnaA to trigger the Regulatory Inactivation of DnaA (RIDA) and prevent over-initiation events. In the Caulobacter crescentus Alphaproteobacterium, the RIDA process also targets DnaA for its rapid proteolysis by Lon. The impact of the RIDA process on adaptation of bacteria to changing environments remains unexplored. Here, we identify a novel and conserved DnaA-related protein, named HdaB, and show that homologs from three different Alphaproteobacteria can inhibit the RIDA process, leading to over-initiation and cell death when expressed in actively growing C. crescentus cells. We further show that HdaB interacts with HdaA in vivo, most likely titrating HdaA away from DnaA. Strikingly, we find that HdaB accumulates mainly during stationary phase and that it shortens the lag phase upon exit from stationary phase. Altogether, these findings suggest that expression of hdaB during stationary phase prepares cells to restart the replication of their chromosome as soon as conditions improve, a situation often met by free-living or facultative intracellular Alphaproteobacteria.
Understanding Buprenorphine for Use in Chronic Pain: Expert Opinion
Authors: Webster Lynn , Gudin Jeffrey , Raffa Robert B , Kuchera Jay , Rauck Richard , Fudin Jeffrey , Adler Jeremy , Mallick-Searle Theresa 
Published: December 2019

AbstractObjectiveAn expert panel convened to reach a consensus on common misconceptions surrounding buprenorphine, a Schedule III partial µ-opioid receptor agonist indicated for chronic pain. The panel also provided clinical recommendations on the appropriate use of buprenorphine and conversion strategies for switching to buprenorphine from a full µ-opioid receptor agonist for chronic pain management.MethodsThe consensus panel met on March 25, 2019, to discuss relevant literature and provide recommendations on interpreting buprenorphine as a partial µ-opioid receptor agonist, prescribing buprenorphine before some Schedule II, III, or IV options, perioperative/trauma management of patients taking buprenorphine, and converting patients from a full µ-opioid receptor agonist to buprenorphine.ResultsThe panel recommended that buprenorphine’s classification as a partial µ-opioid receptor agonist not be clinically translated to mean partial analgesic efficacy. The panel also recommended that buprenorphine be considered before some Schedule II, III, or IV opioids in patients with a favorable risk/benefit profile on the basis of metabolic factors, abuse potential, and tolerability and that buprenorphine be continued during the perioperative/trauma period. In addition, switching patients from a full µ-opioid receptor agonist to buprenorphine should be considered with no weaning period at starting doses that are based on the previous opioid dose.ConclusionsThese recommendations provide a framework for clinicians to address most clinical scenarios regarding buprenorphine use. The overall consensus of the panel was that buprenorphine is a unique Schedule III opioid with favorable pharmacologic properties and a safety profile that may be desirable for chronic pain management.
Miswiring of Frontostriatal Projections in Schizophrenia
Authors: Levitt James J , Nestor Paul G , Kubicki Marek , Lyall Amanda E , Zhang Fan , Riklin-Raviv Tammy , O′Donnell Lauren J , McCarley Robert W , Shenton Martha E , Rathi Yogesh 
Published: December 2019

Abstract
We investigated brain wiring in chronic schizophrenia and healthy controls in frontostriatal circuits using diffusion magnetic resonance imaging tractography in a novel way.
We extracted diffusion streamlines in 27 chronic schizophrenia and 26 healthy controls connecting 4 frontal subregions to the striatum. We labeled the projection zone striatal surface voxels into 2 subtypes: dominant-input from a single cortical subregion, and, functionally integrative, with mixed-input from diverse cortical subregions.
We showed: 1) a group difference for total striatal surface voxel number (P = .045) driven by fewer mixed-input voxels in the left (P  = .007), but not right, hemisphere; 2) a group by hemisphere interaction for the ratio quotient between voxel subtypes (P  = .04) with a left (P  = .006), but not right, hemisphere increase in schizophrenia, also reflecting fewer mixed-input voxels; and 3) fewer mixed-input voxel counts in schizophrenia (P  = .045) driven by differences in left hemisphere limbic (P  = .007) and associative (P  = .01), but not sensorimotor, striatum.
These results demonstrate a less integrative pattern of frontostriatal structural connectivity in chronic schizophrenia. A diminished integrative pattern yields a less complex input pattern to the striatum from the cortex with less circuit integration at the level of the striatum. Further, as brain wiring occurs during early development, aberrant brain wiring could serve as a developmental biomarker for schizophrenia.
Wide spectrum and high frequency of genomic structural variation, including transposable elements, in large double-stranded DNA viruses
Authors: Loiseau Vincent , Herniou Elisabeth A , Moreau Yannis , Lévêque Nicolas , Meignin Carine , Daeffler Laurent , Federici Brian , Cordaux Richard , Gilbert Clément 
Published: December 2019

AbstractOur knowledge of the diversity and frequency of genomic structural variation segregating in populations of large double-stranded (ds) DNA viruses is limited. Here, we sequenced the genome of a baculovirus (Autographa californica multiple nucleopolyhedrovirus [AcMNPV]) purified from beet armyworm (Spodoptera exigua) larvae at depths &gt;195,000× using both short- (Illumina) and long-read (PacBio) technologies. Using a pipeline relying on hierarchical clustering of structural variants (SVs) detected in individual short- and long-reads by six variant callers, we identified a total of 1,141 SVs in AcMNPV, including 464 deletions, 443 inversions, 160 duplications, and 74 insertions. These variants are considered robust and unlikely to result from technical artifacts because they were independently detected in at least three long reads as well as at least three short reads. SVs are distributed along the entire AcMNPV genome and may involve large genomic regions (30,496 bp on average). We show that no less than 39.9 per cent of genomes carry at least one SV in AcMNPV populations, that the vast majority of SVs (75%) segregate at very low frequency (&lt;0.01%) and that very few SVs persist after ten replication cycles, consistent with a negative impact of most SVs on AcMNPV fitness. Using short-read sequencing datasets, we then show that populations of two iridoviruses and one herpesvirus are also full of SVs, as they contain between 426 and 1,102 SVs carried by 52.4–80.1 per cent of genomes. Finally, AcMNPV long reads allowed us to identify 1,757 transposable elements (TEs) insertions, 895 of which are truncated and occur at one extremity of the reads. This further supports the role of baculoviruses as possible vectors of horizontal transfer of TEs. Altogether, we found that SVs, which evolve mostly under rapid dynamics of gain and loss in viral populations, represent an important feature in the biology of large dsDNA viruses.
Quality Assurance in Higher Education: Evaluation of Adjunct Clinical Faculty
Authors: Barker Nancy 
Published: December 2019

Abstract
The clinical experience is often thought of as an opportunity to tie theory to practice. However, with the current shortage of full-time nursing faculty and the increased dependence on adjunct faculty, how do administrators ensure quality? The purpose of this exploratory descriptive study was to determine the evaluation practices of administrators from accredited universities. Administrators’ (n = 26) methods of evaluation were collected via survey with follow-up interviews. Several themes emerged that may assist with the identification of issues in the evaluation of adjunct clinical faculty.
Targeted therapies in melanoma beyond BRAF: targeting NRAS-mutated and KIT-mutated melanoma
Authors: Delyon Julie , Lebbe Céleste , Dumaz Nicolas 
Published: December 2019

Purpose of review
Melanoma treatment have been revolutionized since 2010 by the development of immune checkpoint inhibitors, and, for BRAF-mutated melanoma, targeted therapies based on BRAF and MEK inhibitors, which is a model of effective targeted therapy in cancer. However, patients with BRAF wild type cannot benefit for such treatments. In this review, we will focus on the current clinical development of targeted therapies beyond BRAF, in NRAS-mutated and KIT-altered melanoma.

Recent findings
In NRAS-mutated melanoma, targeted therapies based on MEK inhibition are being developed as monotherapy or in combination with MAPK, PI3K or CDK4/6 inhibitor. Targeted therapies of KIT-altered melanoma patients is based in KIT inhibitor (mostly imatinib, nilotinib), although for both melanoma subtypes, results are for now disappointing as compared with BRAF and MEK inhibitors in BRAF-mutated melanoma.

Summary
Combined therapeutic targeted strategies are awaited in NRAS-mutated and KIT-altered melanoma and could provide additional benefit.