bluuebunny/crossref_metadata_2025_split huggingface dataset:
The 2005 Amazon Drought Legacy Effect Delayed the 2006 Wet Season Onset
Authors: Shi Mingjie , Liu Junjie , Worden John R. , Bloom A. Anthony , Wong Sun , Fu Rong 
Published: July 2019

AbstractWhile the long‐term drought effect on tropical forests has been observed in ground‐based and remote sensing measurements, the feedback of reduced forest biomass on subsequent rainfall is not well understood. We evaluate the impact of slow forest recovery after the 2005 Amazonian drought on local evapotranspiration (ET) and wet season onset (WSO) using remotely sensed precipitation, deuterium retrievals, reanalysis data, and a new ET product. A comparison to the 2009 rainy season, which exhibits similar large‐scale moisture flux convergence, shows that 2006 experienced a 25% ET reduction and 20 days of postponed WSO in the dry‐to‐wet transition. Our results imply that ET reduction due to drought‐driven legacy effect on the Amazon rainforest could be a crucial factor triggering WSO delay in the transitional season following drought events.
An Opposite Response of the Low‐Latitude Ionosphere at Asian and American Sectors During Storm Recovery Phases: Drivers From Below or Above
Authors: Xiong Chao , Lühr Hermann , Yamazaki Yosuke 
Published: July 2019

AbstractIn this study, we focus on the recovery phase of a geomagnetic storm that happened on 6–11 September 2017. The ground‐based total electron content data, as well as the F region in situ electron density, measured by the Swarm satellites show an interesting feature, revealing at low and equatorial latitudes on the dayside ionosphere prominent positive and negative responses at the Asian and American longitudinal sectors, respectively. The global distribution of thermospheric O/N2 ratio measured by global ultraviolet imager on board the Thermosphere, Ionosphere, Mesosphere Energetics and Dynamics satellite cannot well explain such longitudinally opposite response of the ionosphere. Comparison between the equatorial electrojet variations from stations at Huancayo in Peru and Davao in the Philippines suggests that the longitudinally opposite ionospheric response should be closely associated with the interplay of E region electrodynamics. By further applying nonmigrating tidal analysis to the ground‐based total electron content data, we find that the diurnal tidal components, D0 and DW2, as well as the semidiurnal component SW1, are clearly enhanced over prestorm days and persist into the early recovery phase, indicating the possibility of lower atmospheric forcing contributing to the longitudinally opposite response of the ionosphere on 9–11 September 2017.
Nearshore Lagrangian Connectivity: Submesoscale Influence and Resolution Sensitivity
Authors: Dauhajre Daniel P. , McWilliams James C. , Renault Lionel 
Published: July 2019

AbstractRealistic simulation of nearshore (from the shoreline to approximately 10‐km offshore) Lagrangian material transport is required for physical, biological, and ecological investigations of the coastal ocean. Recently, high‐resolution simulations of the coastal ocean have revealed a shelf populated with small‐scale, rapidly evolving currents that arise at resolutions
100 m. However, many historical and recent investigations of coastal connectivity utilize circulation models with ≈1‐km resolution. Here we show a resolution sensitivity to simulated Lagrangian transport and coastal connectivity with a hierarchy of Regional Oceanic Modeling System simulations of the Santa Barbara Channel at Δx= 1, 0.3, 0.1, and 0.036 km. At higher resolution (
100 m), rapid alongshore and vertical transport occurs in regions less than 1 km from the shoreline due to submesoscale shelf currents that open up new transport pathways on the shelf: submesoscale fronts and filaments, topographic wakes, and narrow alongshore jets. Shallow‐water fronts and filaments induce early time downwelling and subsequent dispersal at depth of surface material; this is not captured at coarser resolution (Δx= 1 km). Differences in three‐dimensional and two‐dimensional transport are explored in a higher‐resolution simulation: In general, three‐dimensional trajectories are more dispersive than two‐dimensional, due to a separation in their respective trajectories.
Energy Flux Observations in an Internal Tide Beam in the Eastern North Atlantic
Authors: Köhler Janna , Walter Maren , Mertens Christian , Stiehler Jan , Li Zhuhua , Zhao Zhongxiang , von Storch Jin‐Song , Rhein Monika 
Published: July 2019

AbstractLow‐mode internal waves propagate over large distances and provide energy for turbulent mixing when they break far from their generation sites. A realistic representation of the oceanic energy cycle in ocean and climate models requires a consistent implementation of their generation, propagation, and dissipation. Here we combine the long‐term mean energy flux from satellite altimetry with results from a 1/10° global ocean general circulation model that resolves the low modes of internal waves and in situ observations of stratification and horizontal currents to study energy flux and dissipation along a 1000 km internal tide beam in the eastern North Atlantic. Internal wave fluxes were estimated from twelve 36‐ to 48‐hr stations in along‐ and across‐beam direction to resolve both the inertial period and tidal cycle. The observed internal tide energy fluxes range from 5.9 kW m−1 near the generation sites to 0.5 kW m−1 at distant stations. Estimates of energy dissipation come from both finestructure and upper ocean microstructure profiles and range, vertically integrated, from 0.5 to 3.3 mW m−2 along the beam. Overall, the in situ observations confirm the internal tide pattern derived from satellite altimetry, but the in situ energy fluxes are more variable and decrease less monotonically along the beam. Internal tides in the model propagate over shorter distances compared to results from altimetry and in situ measurements, but more spatial details close the main generation sites are resolved.
Griffiths and Phelps Lightning Initiation Model, Revisited
Authors: Attanasio Alex , Krehbiel Paul R. , da Silva Caitano L. 
Published: July 2019

AbstractIn this paper we reconstruct Griffiths and Phelps' seminal model of streamer systems to test if it can reproduce the key observational features of fast positive breakdown. We first confirm that our implementation is accurate by reproducing the original results. The model describes how a system of positive streamers exhibits an initial exponential charge growth, as a function of position or time, which rapidly transitions into a quadratic steady state. The charge growth is accompanied by substantial electric field enhancement near the onset location, creating favorable conditions for lightning initiation. Due to the relatively low conductivity of streamers (effectively zero in this model), the electric field enhancement is created by the charge deposited in the first few meters of propagation, in the scale length where the charge growth transitions from exponential to quadratic. The quadratic growth of charge, combined with conical system expansion, makes the surface charge density of the moving front constant. The resulting electric field ahead of the streamer system remains nearly constant during its propagation, consistent with the observations of fast breakdown, which reveal a nearly constant propagation velocity, independently of discharge polarity. Minimal changes to the model allow for simulation of narrow bipolar events, reproducing very well their characteristic bipolar electric field change waveform. Despite its simplicity, the Griffiths and Phelps model provides valuable physical insights in the relationship between fast positive breakdown and lightning initiation.
Impact‐Induced Porosity and Microfracturing at the Chicxulub Impact Structure
Authors: Rae Auriol S. P. , Collins Gareth S. , Morgan Joanna V. , Salge Tobias , Christeson Gail L. , Leung Jody , Lofi Johanna , Gulick Sean P. S. , Poelchau Michael , Riller Ulrich , Gebhardt Catalina , Grieve Richard A. F. , Osinski Gordon R. ,   IODP‐ICDP Expedition 364 Scientists
Published: July 2019

AbstractPorosity and its distribution in impact craters has an important effect on the petrophysical properties of impactites: seismic wave speeds and reflectivity, rock permeability, strength, and density. These properties are important for the identification of potential craters and the understanding of the process and consequences of cratering. The Chicxulub impact structure, recently drilled by the joint International Ocean Discovery Program and International Continental scientific Drilling Program Expedition 364, provides a unique opportunity to compare direct observations of impactites with geophysical observations and models. Here, we combine small‐scale petrographic and petrophysical measurements with larger‐scale geophysical measurements and numerical simulations of the Chicxulub impact structure. Our aim is to assess the cause of unusually high porosities within the Chicxulub peak ring and the capability of numerical impact simulations to predict the gravity signature and the distribution and texture of porosity within craters. We show that high porosities within the Chicxulub peak ring are primarily caused by shock‐induced microfracturing. These fractures have preferred orientations, which can be predicted by considering the orientations of principal stresses during shock, and subsequent deformation during peak ring formation. Our results demonstrate that numerical impact simulations, implementing the Dynamic Collapse Model of peak ring formation, can accurately predict the distribution and orientation of impact‐induced microfractures in large craters, which plays an important role in the geophysical signature of impact structures.
Towards a Taxonomically Intelligent Phylogenetic Database
Authors: Page Roderic 
Published: July 2019

AbstractThis note outlines some of the key intellectual obstacles that stand in the way of creating a usable phylogenetic database. These challenges include the need to accommodate multiple taxonomic names and classifications, and the need for tools to query trees in biologically meaningful ways. Until these problems are addressed, and a taxonomically intelligent phylogenetic database created, much of our phylogenetic knowledge will languish in the pages of journals.
Treemap Versus BPA (Again): A Response to Dowling
Authors: Page Roderic , Charleston Michael 
Published: July 2019

AbstractTreeMap is a computer program for analysing host-parasite cospeciation. We respond to Dowling’s (Cladistics, 18: 416-435) recent comparison of TreeMap and Brooks Parsimony Analysis (BPA) by showing that Dowling’s comparison suffers from several mistakes and flaws. We discuss the problems with both BPA and TreeMap, and show that BPA incorrectly counts the true number coevolutionary events more often than TreeMap 1. We also discuss the two main limitations of TreeMap 1 correctly identified by Dowling, namely its inability to handle widespread parasites, and its coarse optimality criterion (the number of cospeciation events). We suggest a simple fix for widespread parasites. The newly released TreeMap 2 uses a more sensitive optimality criterion than TreeMap 1, addressing Dowling’s second concern.
Invariant mRNA content and mitotic protein breakdown as a solution to the Russian Doll problem of the mammalian cell cycle
Authors: Cooper Stephen , Shedden Kerby , Vu-Phan Dang 
Published: July 2019

AbstractIt is widely accepted that numerous genes are expressed in a cell-cycle dependent manner, with cycle-specific variations in mRNA content or peaks of protein content during the cell cycle. These proposed variations raise the problem of how varying cell cycle gene expression is regulated. This is the "infinite regression" problem or Russian Doll problem where postulating a cell-cycle specific control element merely pushes the explanation of cell-cycle variation back one step to the problem of how that control element itself appears and disappears at particular times during the cell cycle. We present evidence that cyclin mRNA content is invariant during the cell cycle and calculations reveal that mRNA variation does not account for observed protein variations during the cell cycle. The experimental evidence for protein breakdown only at the end of the cell cycle leads to a general model for cell-cycle control that avoids the Russian Doll problem.
Changes in Cholesterol Metabolism in Peripheral Cells of Alzheimer Disease Patients and Their Relatives
Authors: Pani Alessandra , La Colla Paolo , Abete Claudia , Mulas Claudia , Putzolu Marirosa , Norfo Claudia , Laconi Sergio , Borgia Anna , Zaru Christina , Palmas Manuela , Putzu Paolo , Mocali Alessandra , Paoletti Francesco , Dessi Sandra 
Published: July 2019

Abstract
Background.
Previous epidemiological and experimental studies indicated cholesterol as a central player in Alzheimer disease (AD). Here, we utilized skin fibroblasts and PBMC as possible ex vivo models for the study of dysfunctions of cholesterol homeostasis which may be related to AD development. Methods. We analyzed cholesterol homeostasis using colorimetric, thin layer chromatography (TLC), and histologic technique in ex vivo cultures of skin fibroblasts and PBMCs from patients with probable AD and their first-degree relatives. Additionally, healthy age-matched individuals served as controls. Findings. As compared to controls, skin fibroblasts and PBMCs from AD patients, displayed an evident alteration of cholesterol metabolism; namely an anomalous accumulation of cholesterol esters in their cytoplasm. No change in intracellular free cholesterol was observed. Cellular overloading of cholesterol esters was dramatically increased after specific growth stimulation of the different cell types. Cholesterol ester accumulation was negatively correlated to plasma levels of high density lipoprotein cholesterol (HDL-C) and positively correlated with severity of cognitive symptoms measured by Mini-Mental State Examination (MMSE). Inhibitors of cholesterol esterification, such as progesterone and SaH, as well as a potent inhibitor of cell proliferation, RAD, were able to prevent accumulation of cholesterol esters. Interpretation. Changes of cholesterol esters in the peripheral compartment may be indicative of a systemic alteration of intracellular cholesterol homeostasis, which in turn might create a cellular milieu favourable to the production of ß-amyloid in the brain. Pathways that control cholesterol esterification might represent promising targets for novel diagnostic and therapeutic AD approaches.
Beyond Spike Timing Theory – Thermodynamics of Neuronal Computation
Authors: Aur Dorian , Jog Mandar 
Published: July 2019

AbstractThis paper highlights ionic fluxes as information carriers in neurons. The theoretical framework regarding information transfer is presented as changes in the thermodynamic entropy that underlie specific computations determined by ionic flow. The removal or accumulation of information is analyzed in terms of ionic mass transfer related with changes in Shannon information entropy. Specifically, information transfer occurs during an action potential (AP) via the voltage gated ion channels in membranes and the same physical mechanism can be extended to various types of synapses. Since sequential APs from a selected neuron are not alike, then every spike may transfer slightly different amounts of information during their occurrence. The average efficiency in information transfer during APs is estimated using mutual information measures and Hodgkin-Huxley model. This general scheme of ions as carriers of information represents the required physical machinery for a dynamic information transfer that is missing in the current spike-timing description.
Cognitive dimensions of predator responses to imperfect mimicry?
Authors: Chittka Lars , Osorio Daniel 
Published: July 2019

AbstractMany palatable insects, for example hoverflies, deter predators by mimicking well-defended insects such as wasps. However, for human observers, these flies often seem to be little better than caricatures of wasps – their visual appearance and behaviour are easily distinguishable. This imperfect mimicry baffles evolutionary biologists, because one might expect natural selection to do a more thorough job. Here we discuss two types of cognitive processes that might explain why mimics distinguishable mimics might enjoy increased protection from predation. Speed accuracy tradeoffs in predator decision making might give imperfect mimics sufficient time to escape, and predators under time constraint might avoid time-consuming discriminations between well-defended models and inaccurate edible mimics, and instead adopt a “safety first” policy of avoiding insects with similar appearance. Categorization of prey types by predators could mean that wholly dissimilar mimics may be protected, provided they share some common property with noxious prey.
Optimising Blue Fluorescent Protein (BFP) for use as a mammalian reporter gene in parallel with Green Fluorescent Protein (GFP).
Authors: Joly Etienne 
Published: July 2019

AbstractTo obtain an optimised form of BFP for use as a reporter gene in mammalian cells, the brightest available GFP form, EGFP, was mutated at 5 different positions, yielding 8 different mutagenised forms of BFP. The intensity of the fluorescent signals attained in mammalian cells with all these various versions of BFP was analysed by flow cytometry of transiently transfected COS 7 cells. The best mutant obtained can be detected readily both by flow cytometry and fluorescence microscopy, even when expressed together with GFP. To explore whether cellular localization could enhance the fluorescence signals any further, plasmid constructs were made to target optimised versions of GFP and BFP to the nucleus, the endoplasmic reticulum (ER) and the cell surface. Expression in the nucleus or ER increased the fluorescence signal by ca. 50%, whereas cell surface expression resulted in a five-fold decrease compared to the ER and nuclear forms. Co-expression of GFP and BFP in the same cellular compartment did not result in any significant absorption of the blue fluorescence by GFP. Thus, targeting of GFP and BFP to various cellular compartments adds even further versatility to this convenient dual reporter-gene system.
Cartographic scale effect on channel slopes and stream power calculations
Authors: Lima Adalto Gonçalves 
Published: July 2019

AbstractThe channel slope is important in determining the stream power. In some research situations the slope is measured by topographical maps that, depending on the scale, can provide differentiated values. The objective of the research here reported was to delineate the implications of the inter-scales differences of channel slopes on the stream power calculation. Slopes of a small river, with a mixed bedrock–alluvial bed, located in a basaltic plateau in south Brazil, were examined. The measured slopes were compared at 1:50,000 and 1:10,000 scales. In the field, the bankfull geometry was surveyed in ten cross sections, for discharge calculation. The slopes measured by maps were used to determine the discharge, using the Gauckler–Manning equation, and to calculate the total and specific stream power. A tendency was verified for the 1:50,000 scale to overestimate the values in reaches of low slopes (<0.05), coinciding with mixed bedrock–alluvial reaches, while it underestimates in the reaches of larger slopes, i.e. knickzones. As larger is the absolute difference of slope between the analyzed scales, the larger is the stream power differential (%), and as smaller the slopes involved the larger will be that differential. In the analysed case, total and specific stream power differentials vary from 14.6 to 313.4%.
The study on estimation of time since death with proton magnetic resonance spectroscopy under different temperature
Authors: Yang Tiantong , Zhenwei Li , Yue Wu , Liang Liu , Na Zheng 
Published: July 2019

AbstractEstimation of the time of death (post-mortem interval, PMI) is occasionally a critical issue in adjudication of a criminal or civil action. But no objective and precise means has been derived for estimating PMI.One reason for this outcome may be the fact that most of these methods attempted to characterize PMI by a few or even just one specific parameter's variable in constant ambient temperature. It is crucial that we reduce or eliminate the effect of temperature variation in the estimation of PMI. Here we show the first results by using proton magnetic resonance spectroscopy (1H-MRS) technique to determine the order of degradation of certain substances, present in the brain tissue of a rabbit model, under different temperatures; our goal is to reduce or eliminate the temperature effect in the estimation of PMI.
Numbers, not value, motivate cooperation in humans and orangutans
Authors: Furlong Ellen , Opfer John 
Published: July 2019

AbstractCooperation among competitors-whether sharing the burden of wind resistance in the Tour de France, forming price-fixing cartels in economic markets, or adhering to arms-control agreements in international treaties-seldom spreads in proportion to the potential benefits. To gain insight into the minds of uncooperative agents, economists and social psychologists have used the prisoner's dilemma task to examine factors leading to cooperation among competitors. Two types of factors have emerged in these studies: the relative rewards of defecting versus cooperating and breakdowns in trust, forgiveness and communication. The generalizability of economic and social psychological factors, however, relies on the assumption that agents' comparisons of gains and losses (whether for themselves, others, or both) preserves ratio information over arbitrary units, such as dollars and cents, and real rewards, such as food. This assumption is inconsistent with psychophysical studies on how the brain represents quantitative information, which suggests that mental magnitudes increase logarithmically with actual value. Thus, discrimination of two numerical magnitudes improves as the numerical distance between them increases and decreases as the magnitudes increase. Here we show an important consequence of this representational system for economic decision making: in the prisoner's dilemma game, purely nominal increases in the numerical magnitude of payoffs (such as, converting dollar values to cents or whole grapes into grape-parts) has a large effect on cooperative behaviour. Moreover, a logarithmic scaling of the ratio of rewards for cooperation versus defection predicted 97% of variability in observed cooperation, whereas the objective ratio predicted 0% of variability. By linking the brain's system of representing the magnitude of rewards to motivations for cooperative behaviour, these findings suggest that the nature of numerical representations may also account for the subjective value function described by Bernoulli, in which the apparent value of monetary incentives increases logarithmically with actual value.
Sensory Transduction and Subjective Experience: Expression of eight genes in three senses suggests a radical model of consciousness
Authors: King Chris 
Published: July 2019

AbstractRecent research into whole genome mapping of the mouse brain has made possible direct investigation of the brain expression of unusual genes. A search of the Allen Brain Atlas database has provided genetic and neuro-anatomical evidence for widespread specific expression in the brain of eight genes specific to sensory transduction, in vision, hearing and touch. A novel biophysical model is proposed for the function of these proteins, in generating the internal model of experiential reality.