bluuebunny/crossref_metadata_2025_split huggingface dataset:
Towns and Trails Drive Carnivore Connectivity using a Step Selection Approach
Authors: Whittington Jesse , Baron Robin , Hebblewhite Mark , Ford Adam T. , Paczkowski John 
Published: February 2021

AbstractGlobal increases in human activity threaten connectivity of animal populations. Protection and restoration of animal movement corridors requires robust models to forecast the effects of human activity on connectivity. Recent advances in the field of animal movement ecology and step selection functions offer new approaches for estimating connectivity. We show how a combination of hidden Markov movement models and step selection functions can be used to simulate realistic movement paths with multiple behavioral states. Simulated paths can be used to generate utilization distributions and estimate changes in connectivity for multiple land use scenarios. We applied movement models to 20 years of grizzly bear (Ursus arctos) and gray wolf (Canis lupus) data collected in and around Banff National Park, Canada. These carnivores avoided areas near towns in all seasons, avoided areas of high trail density in most seasons, and campgrounds during summer and fall. We simulated movement paths for three landscape scenarios: reference conditions with no anthropogenic development, current conditions, and future conditions with expanded town footprints and trail networks. We counted the number of paths that crossed valley-wide, digital transects through mountain tourist towns of Banff and Canmore, Alberta. We divided current and future crossing rates by the reference crossing rates to estimate connectivity. Current connectivity rates ranged between 7 and 45% of reference values with an average of 21% for grizzly bears and 25% for wolves. Potential town expansion and increased development of trails further decreased connectivity an average of 6% in future scenarios. Anthropogenic developments reduced the amount of available high quality large carnivore habitat in the Bow Valley by an average of 14% under current conditions and 16% under future conditions. Our approach for estimating connectivity provides a robust and flexible method for combining movement models with step selection analyses to estimate connectivity for a variety of species.
Natural Selection as the Sum over all Histories
Authors: Neal-Sturgess C E 
Published: February 2021

AbstractAs evolution can be connected to the principle of least action, and if it is depicted in evolution-space versus time then it corresponds to the direction of ultimate causation. As an organism evolves and follows a path of proximate causation, if the vector is closely parallel to that of the Ultimate Causation then the changes will confer desirable attributes which will lead to further development. If, however, the variations do not occur in a direction close to that of the ultimate causation vector the evolved organism will quickly die out. Therefore Natural Selection may be viewed as similar to Feynman’s “sum over all histories”. This approach is compatible with both Neutral Theory and Selection, as it includes both positive and negative mutations and selection. Therefore, the principle of least action gives a direction, but not a purpose, to evolution.
Extracellular S100B alters spontaneous Ca2+fluxes in dopaminergic neurons via L-type voltage gated calcium channels: Implications for Parkinson’s disease
Authors: Bancroft Eric A. , Pandey Gauri , Zarate Sara M. , Srinivasan Rahul 
Published: February 2021

AbstractParkinson’s disease (PD) is associated with an abnormal increase in S100B within the midbrain and cerebrospinal fluid. In addition, overexpression of S100B in mice accelerates the loss of substantia nigra pars compacta (SNc) dopaminergic (DA) neurons, suggesting a role for this protein in PD pathogenesis. We found that in the mouse SNc, S100B labeled astrocytic processes completely envelop the somata of tyrosine hydroxylase (TH) positive DA neurons. Based on this finding, we rationalized that abnormal increases in extracellularly secreted S100B by astrocytic processes in the SNc could alter DA neuron activity, thereby causing dysregulated midbrain function. To test this hypothesis, we measured the effect of bath perfused S100B peptide on the frequency and amplitude of spontaneous calcium fluxes in identified TH+and TH−midbrain neurons from 3-week old mouse primary midbrain cultures. Acute exposure to 50 pM S100B caused a 2-fold increase in calcium flux frequency only in TH+DA neurons. The L-type voltage gated calcium channel (VGCC) inhibitor, diltiazem eliminated S100B-mediated increases in DA neuron calcium flux frequency, while the T-type specific VGCC blocker mibefradil failed to inhibit the stimulatory effect of S100B. Chronic exposure to S100B caused a 3-fold reduction in calcium flux frequencies of TH+neurons and also reduced calcium flux amplitudes in TH−neurons by ∼4-fold. Together, our results suggest that exposure to S100B pathologically alters spontaneous calcium activity in midbrain neurons via an extracellular mechanism involving L-type VGCCs expressed in DA neurons. These findings are relevant to understanding mechanisms underlying DA neuron loss during PD.Table of Contents ImageMain PointsExtracellular S100B increases Ca2+fluxes in dopaminergic neuronsL-type VGCCs in dopaminergic neurons are required for S100B-mediated increases in Ca2+fluxesChronic S100B alters Ca2+fluxes in dopaminergic and non-dopaminergic neurons
Myo-inositol Oxygenase Overexpression Rescues Vitamin C Deficient Arabidopsis (vtc) Mutants
Authors: Acosta-Gamboa Lucia M. , Nirman Nepal , Karina Medina-Jimenez , Campbell Zachary C. , Cunningham Shannon S. , Ae Lee Jung , Argelia Lorence 
Published: February 2021

AbstractBiosynthesis ofl-ascorbate (AsA) in plants is carried out by a complex metabolic network, which involvesd-mannose/l-galactose,d-galacturonate,l-gulose, andmyo-inositol as main precursors. Arabidopsis lines over-expressing enzymes in themyo-inositol pathway have elevated AsA, accumulate more biomass of both aerial and root tissues, and are tolerant to abiotic stresses as shown by manual and digital phenotyping. We crossedmyo-inositol oxygenase (MIOX4) over-expressers with two low-vitamin C mutants (vtc1-1 andvtc2-1) encoding enzymes involved ind-mannose/l-galactose route. The purpose of developing these crosses was to test MIOX4’s ability to restore the low AsA phenotype in mutants, and to assess the contribution of individual biosynthetic pathways to abiotic stress tolerance. We used a powerful high-throughput phenotyping platform for detailed phenotypic characterization of the Arabidopsis crosses with visible, fluorescence, near-infrared and infrared sensors. We combined digital phenotyping with photosynthetic parameters and soil water potential measurements. Our results show thatMIOX4is able to restore the AsA content of the mutants and the restored lines (vtc+MIOX4) show high AsA, enhanced growth rate, accumulate more biomass, and display healthier chlorophyll fluorescence and water content profiles compared to controls.HighlightsConstitutive expression of amyo-inositol oxygenase restored vitamin C deficient (vtcmutants). The restored lines have elevated ascorbate content and are tolerant to abiotic stresses. Under normal and abiotic stress conditions, the restored lines have enhanced biomass and increased water retention.
Comparative biofilm assays usingEnterococcus faecalisOG1RF identify new determinants of biofilm formation
Authors: Willett Julia L. E. , Dale Jennifer L. , Kwiatkowski Lucy M. , Powers Jennifer L. , Korir Michelle L. , Kohli Rhea , Barnes Aaron M. T. , Dunny Gary M. 
Published: February 2021

AbstractEnterococcus faecalisis a common commensal organism and a prolific nosocomial pathogen that causes biofilm-associated infections. NumerousE. faecalisOG1RF genes required for biofilm formation have been identified, but few studies have compared genetic determinants of biofilm formation and biofilm morphology across multiple conditions. Here, we cultured transposon (Tn) libraries in CDC biofilm reactors in two different media and used Tn sequencing (TnSeq) to identify core and accessory biofilm determinants, including many genes that are poorly characterized or annotated as hypothetical. Multiple secondary assays (96-well plates, submerged Aclar, and MultiRep biofilm reactors) were used to validate phenotypes of new biofilm determinants. We quantified biofilm cells and used fluorescence microscopy to visualize biofilms formed by 6 Tn mutants identified using TnSeq and found that disrupting these genes (OG1RF_10350,prsA,tig, OG1RF_10576, OG1RF_11288, and OG1RF_11456) leads to significant time- and medium-dependent changes in biofilm architecture. Structural predictions revealed potential roles in cell wall homeostasis for OG1RF_10350 and OG1RF_11288 and signaling for OG1RF_11456. Additionally, we identified growth medium-specific hallmarks of OG1RF biofilm morphology. This study demonstrates howE. faecalisbiofilm architecture is modulated by growth medium and experimental conditions, and identifies multiple new genetic determinants of biofilm formation.ImportanceE. faecalisis an opportunistic pathogen and a leading cause of hospital-acquired infections, in part due to its ability to form biofilms. A complete understanding of the genes required forE. faecalisbiofilm formation as well as specific features of biofilm morphology related to nutrient availability and growth conditions is crucial for understanding howE. faecalisbiofilm-associated infections develop and resist treatment in patients. We employed a comprehensive approach to analysis of biofilm determinants by combining TnSeq primary screens with secondary phenotypic validation using diverse biofilm assays. This enabled identification of numerous core (important under many conditions) and accessory (important under specific conditions) biofilm determinants inE. faecalisOG1RF. We found multiple genes whose disruption results in drastic changes to OG1RF biofilm morphology. These results expand our understanding of the genetic requirements for biofilm formation inE. faecalisthat affect the time course of biofilm development as well as the response to specific nutritional conditions.
Targeting an anchored phosphatase-deacetylase unit restores renal ciliary homeostasis
Authors: Gopalan Janani , Omar Mitch , Roy Ankita , Cruz Nelly M. , Falcone Jerome , Forbush Katherine , Himmelfarb Jonathan , Freedman Benjamin S. , Scott John D. 
Published: February 2021

AbstractPathophysiological defects in water homeostasis can lead to renal failure. Autosomal dominant polycystic kidney disease (ADPKD) is a common genetic disorder associated with abnormal cytoskeletal dynamics in the kidney collecting ducts and perturbed calcium and cAMP signaling in the ciliary compartment. We show that collecting ducts in mice lacking the A-Kinase anchoring protein AKAP220 exhibit enhanced development of primary cilia. Mechanistic studies reveal that AKAP220-associated protein phosphatase 1 (PP1) mediates this phenotype by promoting changes in the stability of histone deacetylase 6 (HDAC6) with concomitant defects in actin dynamics. This proceeds through a previously unrecognized adaptor function for PP1 as all ciliogenesis and cytoskeletal phenotypes are recapitulated in mIMCD3 knock-in cells expressing a phosphatase-targeting defective AKAP220-ΔPP1 mutant. Pharmacological blocking of local HDAC6 activity alters cilia development and reduces cystogenesis in kidney-on-chip and organoid models of ADPKD. These findings identify the AKAP220-PPI-HDAC6 pathway as a key effector in primary cilia development.
De novo assembly and annotation of a highly contiguous reference genome of the fathead minnow (Pimephales promelas) reveals an AT-rich repetitive genome with compact gene structure
Authors: Martinson John , Bencic David C. , Toth Gregory P. , Kostich Mitchell S. , Flick Robert W. , See Mary J. , Lattier David , Biales Adam D. , Huang Weichun 
Published: February 2021

ABSTRACTThe Fathead Minnow (FHM) is one of the most important and widely used model organisms in aquatic toxicology. The lack of a high-quality and well-annotated FHM reference genome, however, has severely hampered the efforts using modem ‘omics approaches with FHM for environmental toxicogenomics studies. We present here a de novo assembled and nearly complete reference of the fathead minnow genome. Compared to the current fragmented and sparsely annotated FHM genome assembly (FHM1), the new highly contiguous and well-annotated FHM reference genome (FHM2) represents a major improvement, having 95.1% of the complete BUSCOs (Benchmarking Universal Single-Copy Orthologs) and a scaffold N50 of 12.0 Mbps. The completeness of gene annotation for the FHM2 reference genome was demonstrated to be comparable to that of the zebrafish (ZF) GRCz11 reference genome. In addition, our comparative genomics analyses between FHM and ZF revealed highly conserved coding regions between two species while discovering much more compact gene structure in FHM than ZF. This study not only provides insights for assembling a highly repetitive AT-rich genome, but also delivers a critical genomic resource essential for toxicogenomics studies in environmental toxicology.
Larvae and adults exhibit contrasting patterns of immune gene expression and infection resistance in wild flour beetle populations
Authors: Tate Ann T. , Perry Abby , Jent Derrick G. 
Published: February 2021

AbstractIn nature, hosts face shifting patterns of parasite exposure and life history trade-offs as they develop from birth to old age. As a result, the net fitness benefit of immunological investment can change dramatically from one life stage to the next. Previous work has revealed a puzzling diversity of relative immune investment patterns among juvenile and adult stages, and it is not clear whether lessons learned from one particular population or species can be generalized to wild populations, after accounting for local adaptation and other variance-generating processes. In this study, we quantify larval and adult immune gene expression and resistance to bacterial infection in two flour beetle species (Tribolium castaneumandT. confusum) from two lab-adapted and five wild-derived populations. Our results provide a clear signal of higher infection-induced immunological investment and resistance in adults relative to larvae, despite variation among species in immune gene regulation. Better characterization of stage-specific investment in infection resistance in natural populations can inform our understanding of life history evolution and improve predictions of disease dynamics in the wild.
Visualization of SARS-CoV-2 Infection Scenes by ‘Zero-Shot’ Enhancements of Electron Microscopy Images
Authors: Drefs Jakob , Salwig Sebastian , Lücke Jörg 
Published: February 2021

AbstractElectron microscopy (EM) recordings of infected tissues serve to diagnose a disease, and they can contribute to our understanding of infection processes. Consequently, a large number of EM images of the interaction of SARS-CoV-2 viruses with cells have been made available by numerous labs. However, due to EM recording techniques at high resolution, images of infection scenes are very noisy and they appear two dimensional (‘flat’). Current research consequently aims (A) at methods that can remove noise, and (B) at techniques that allow for recovering a 3D impression of the virus or its parts. Here we discuss a novel method which can recover a spatial impression of a whole infection scene at high resolution. In contrast to previous approaches which aim at the reconstruction of single spike proteins or a single virus, the here used method can be applied to a single noisy EM image of an infection scene. As one example image, we show a high resolution image of SARS-CoV-2 viruses in Vero cell cultures (Fig. 1). The method we use is based on probabilistic machine learning algorithms which can operate in a ‘zero-shot’ setting, i.e., in a setting when just one noisy image (and no large and clean image corpus) is available. The probabilistic method we apply can estimate non-noisy images by inferring first order statistics (pixel means) across image patches using a previously learned probabilistic image representation. Estimating higher order statistics and appropriately chosen probabilistic models then allow for the generation of images that enhance details and give a spatial impression of a full nanoscopic scene.
Toroidal topology of population activity in grid cells
Authors: Gardner Richard J. , Hermansen Erik , Pachitariu Marius , Burak Yoram , Baas Nils A. , Dunn Benjamin A. , Moser May-Britt , Moser Edvard I. 
Published: February 2021

AbstractThe medial entorhinal cortex (MEC) is part of a neural system for mapping a subject’s position within a physical environment1,2. Grid cells, a key component of this system, fire in a characteristic hexagonal pattern of locations3, and are organized in modules4,5which collectively form a population code for the animal’s allocentric position1,6–8. The invariance of the correlation structure of this population code across environments9,10and behavioural states11,12, independently of specific sensory inputs, has pointed to intrinsic, recurrently connected continuous attractor networks (CANs) as a possible substrate of the grid pattern1,2,13–16. However, whether grid cell networks show continuous attractor dynamics, and how they interface with inputs from the environment, has remained elusive due to the small samples of cells obtained to date. Here we show, with simultaneous recordings from many hundreds of grid cells, and subsequent topological data analysis, that the joint activity of grid cells from an individual module resides on a toroidal manifold, as expected in a two-dimensional CAN. Positions on the torus correspond to the moving animal’s position in the environment. Individual cells are preferentially active at singular positions on the torus. Their positions are maintained, with minimal distortion, between environments and from wakefulness to sleep, as predicted by CAN models for grid cells but not by alternative feed-forward models where grid patterns are created from external inputs by Hebbian plasticity17–22. This demonstration of network dynamics on a toroidal manifold provides the first population-level visualization of CAN dynamics in grid cells.
Feasibility of X-ray beam nanofocusing with compound refractive lenses
Authors: Kohn V. G. , Folomeshkin M. S. 
Published: February 2021

A more general analytical theory of X-ray beam propagation through compound refractive lenses (CRLs) than the earlier study by Kohn [(2003). JETP, 97, 204–215] is presented. The problem of nanofocusing with CRLs is examined in detail. For a CRL with a relatively large aperture the focusing efficiency is limited by the radiation absorption in the lens material. The aperture does not affect the focusing process and it is replaced by the effective aperture. The X-ray transverse beam size at the focus is then by a factor of γ = β/δ times smaller than the transverse beam size just behind the CRL. Here, δ and β are the real and imaginary parts of the CRL material refractive index n = 1 − δ + iβ. In this instance, to improve focusing efficiency, it is advantageous to decrease the CRL aperture and increase the photon energy E. However, with increasing photon energy, the material absorption decreases, which results in the CRL aperture impact on the transverse beam size. The latter leads to the fact that with a proper CRL length the beam size is independent of both the aperture and photon energy but depends only on the CRL material electron density and is approximately equal to w

c
= λ/(8δ)1/2, where λ denotes the radiation wavelength, as predicted by Bergemann et al. [(2003). Phys. Rev. Lett, 91, 204801].
Side-bounce beamlines using single-reflection diamond monochromators at Cornell High Energy Synchrotron Source
Authors: Stoupin Stanislav , Krawczyk Thomas , Sagan David , Temnykh Alexander , Smieska Louisa , Woll Arthur , Ruff Jacob , Lyndaker Aaron , Pauling Alan , Croom Brendan P. , Trigg Edward B. 
Published: February 2021

The design and implementation of new beamlines featuring side-bounce (single-reflection) diamond monochromators at Cornell High Energy Synchrotron Source (CHESS) are described. Undulator radiation is monochromated using an interchangeable set of diamond crystal plates reflecting radiation in the horizontal (synchrotron) plane, where each crystal plate is set to one of the low-index Bragg reflections (111, 220, 311 and 400) in either Bragg or Laue reflection geometries. At the nominal Bragg angle of 18° these reflections deliver monochromated X-rays with photon energies of 9.7, 15.9, 18.65 and 22.5 keV, respectively. An X-ray mirror downstream of the diamond monochromator is used for rejection of higher radiation harmonics and for initial focusing of the monochromated beam. The characteristics of the X-ray beam entering the experimental station were measured experimentally and compared with the results of simulations. A reasonable agreement is demonstrated. It is shown that the use of selected high-dislocation-density `mosaic' diamond single-crystal plates produced using the chemical vapor deposition method yields a few-fold enhancement in the flux density of the monochromated beam in comparison with that delivered by perfect crystals under the same conditions. At present, the Functional Materials Beamline at CHESS, which is used for time-resolved in situ characterization of soft materials during processing, has been outfitted with the described setup.
1-2-3-4! Measuring the values of live music: methods, models and motivations
Authors: van der Hoeven Arno , Behr Adam , Hamilton Craig , Mulder Martijn , Rozbicka Patrycja 
Published: February 2021

PurposeThis paper sets out to compare different methodologies for measuring the value(s) of live popular music and to explore the different motivations amongst a range of organisations engaged in that work.Design/methodology/approachThe authors analyse how the values of live music are measured, who does it and why. Based on this analysis the authors present a model that visualises the myriad of organisations, methods, aims and objectives involved.FindingsThe authors identify three approaches to measuring the impact of live music (economic impact studies, mapping and censuses and social sciences and humanities) and three types of actors (industry, policy and academia). The analysis of these demonstrates that measuring live music is not a neutral activity, but itself constructs a vision on how live music ecologies functionPractical implicationsFor cultural organisations, demonstrating the outcomes of their work is important in acquiring various forms of support. The model presented in this paper helps them to select adequate methodologies and to reflect on the consequences of particular approaches to measuring live music activities.Originality/valueWhile the number of studies measuring live music's impact is growing, theoretical and methodological reflection on these activities is missing. The authors compare the different methodologies by discussing strengths and weaknesses. This results in a model that identifies gaps in existing studies and explores new directions for future live music research. It enhances understanding of how different ways of measuring live music affect policymaking and conceptions of what live music is and should be.