bluuebunny/crossref_metadata_2025_split huggingface dataset:
Early Pleistocene Obliquity‐Scale pCO2 Variability at ~1.5 Million Years Ago
Authors: Dyez Kelsey A. , Hönisch Bärbel , Schmidt Gavin A. 
Published: November 2018

AbstractIn the early Pleistocene, global temperature cycles predominantly varied with ~41‐kyr (obliquity‐scale) periodicity. Atmospheric greenhouse gas concentrations likely played a role in these climate cycles; marine sediments provide an indirect geochemical means to estimate early Pleistocene CO2. Here we present a boron isotope‐based record of continuous high‐resolution surface ocean pH and inferred atmospheric CO2 changes. Our results show that, within a window of time in the early Pleistocene (1.38–1.54 Ma), pCO2 varied with obliquity, confirming that, analogous to late Pleistocene conditions, the carbon cycle and climate covaried at ~1.5 Ma. Pairing the reconstructed early Pleistocene pCO2 amplitude (92 ± 13 μatm) with a comparably smaller global surface temperature glacial/interglacial amplitude (3.0 ± 0.5 K) yields a surface temperature change to CO2 radiative forcing ratio of S[CO2]~0.75 (±0.5) °C−1·W−1·m−2, as compared to the late Pleistocene S[CO2] value of ~1.75 (±0.6) °C−1·W−1·m−2. This direct comparison of pCO2 and temperature implicitly incorporates the large ice sheet forcing as an internal feedback and is not directly applicable to future warming. We evaluate this result with a simple climate model and show that the presumably thinner, though extensive, northern hemisphere ice sheets would increase surface temperature sensitivity to radiative forcing. Thus, the mechanism to dampen actual temperature variability in the early Pleistocene more likely lies with Southern Ocean circulation dynamics or antiphase hemispheric forcing. We also compile this new carbon dioxide record with published Plio‐Pleistocene δ11B records using consistent boundary conditions and explore potential reasons for the discrepancy between Pliocene pCO2 based on different planktic foraminifera.
Using Lightning as a HF Signal Source to Produce Ionograms
Authors: Obenberger K. S. , Dowell J. D. , Malins J. , Parris R. T. , Pedersen T. R. , Taylor G. B. 
Published: November 2018

AbstractModern techniques for specifying the ionosphere include the use of ionosondes, which both transmit and receive sweep soundings in the high‐frequency (HF) band. We replicate this process by observing the broad band emission from lightning using the Long Wavelength Array, Sevilleta, radio telescope. We use this station to observe the powerful broadband radio bursts from the breakdown of air that occurs during lightning flashes. For nearby lightning we observe both the direct line of sight and the delayed ionospheric reflection. By correlating the amplitude time series from the direct line of sight to that of the ionospheric reflection, we can accurately measure the group delay as a function of frequency. By separating into right‐hand circular and left‐hand circular, we can derive both the O mode and X mode ionograms. This novel technique allows for accurate ionograms to be made even in restricted frequency bands and provides a means to probe density profiles at multiple locations of the ionosphere on short time scales with a single receiver station.
The DST Group High‐Fidelity, Multichannel Oblique Incidence Ionosonde
Authors: Ayliffe Jim K. , Durbridge Lyndon J. , Frazer Gordon J. , Gardiner‐Garden Robert S. , Heitmann Andrew J. , Praschifka Justin , Quinn Adrian D. , Scarman Gavin C. , Turley Mike D. E. 
Published: November 2018

AbstractDefence Science and Technology Group has developed a complete oblique incidence ionosonde system to enhance ionospheric monitoring capabilities in support of the Jindalee Operational Radar Network. The Digital Oblique Receiving System, and its counterpart, the Digital Oblique Transmitting System, feature a direct‐digital, multichannel chirp‐sounder design that allows flexible collection of high‐resolution ionograms across many simultaneous paths, without compromising dynamic range. This paper outlines the hardware and software components of the Digital Oblique Receiving System/Digital Oblique Transmitting System, including the onboard signal processing that removes radio frequency interference and fits a parameterized electron density profile to the ionogram. Additional control and data management tools that have enabled the system to be effectively transitioned into routine operations are also described. The typical performance is illustrated through a selection of sample ionograms, highlighting the applications of Digital Oblique Receiving System/Digital Oblique Transmitting System to a wide variety of ionospheric studies, including those requiring Doppler and angle‐of‐arrival observations.
Combining Ground‐Penetrating Radar With Terrestrial LiDAR Scanning to Estimate the Spatial Distribution of Liquid Water Content in Seasonal Snowpacks
Authors: Webb R. W. , Jennings K. S. , Fend M. , Molotch N. P. 
Published: November 2018

AbstractMany communities and ecosystems around the world rely on mountain snowpacks to provide valuable water resources. An important consideration for water resources planning is runoff timing, which can be strongly influenced by the physical process of water storage within and release from seasonal snowpacks. The aim of this study is to present a novel method that combines light detection and ranging with ground‐penetrating radar to nondestructively estimate the spatial distribution of bulk liquid water content in a seasonal snowpack during spring snowmelt. We develop these methods in a manner to be applicable within a short time window, making it possible to spatially observe rapid changes that occur to this property at subdaily timescales. We applied these methods at two experimental plots in Colorado, showing the high variability of liquid water content in snow. Volumetric liquid water contents ranged from near zero to 19%vol within the scale of meters. We also show rapid changes in bulk liquid water content of up to 5%vol that occur over subdaily timescales. The presented methods have an average uncertainty in bulk liquid water content of 1.5%vol, making them applicable for future studies to estimate the complex spatio‐temporal dynamics of liquid water in snow.
Modeling Macroroughness Contribution to Fish Habitat Suitability Curves
Authors: Niayifar Amin , Oldroyd Holly J. , Lane Stuart N. , Perona Paolo 
Published: November 2018

AbstractImproved water management strategies necessitate a solid understanding of environmental impacts associated with various flow release policies. Habitat suitability models use hydrodynamic simulations to generate weighted usable area curves, which are useful in characterizing the ecological suitability of flow release rules. However, these models are not conveniently run to resolve the hydrodynamics at the smaller scales associated with macroroughness elements (e.g., individual stones), which produce wakes that contribute significantly to habitat suitability by serving as shelter zones where fishes can rest and feed. In this study, we propose a robust environmental indicator that considers the habitat generated by the wakes downstream of stones and can thus be used to assess the environmental efficiency of flow release rules for impounded streams. We develop an analytical solution to approximate the wake areas behind macroroughness elements, and the statistical distribution of wake areas is then found using the derived distribution approach. To illustrate the concept, we apply our theory to four exemplary river streams with dispersed stones having different statistical diameter size distributions, some of which allow for an analytical expression of the weighted usable area. We additionally investigate the impact of spatiotemporal changes in stone size distributions on the usable area and the consequent threshold flows. Finally, we include the proposed environmental indicator to solve a multiobjective reservoir optimization problem. This exemplifies its practical use and allows stakeholders to find the most favorable operational rules depending on the macroroughness characteristics of the impounded stream.
Relating Degradation of Pharmaceutical Active Ingredients in a Stream Network to Degradation in Water‐Sediment Simulation Tests
Authors: Honti Mark , Bischoff Fabian , Moser Andreas , Stamm Christian , Baranya Sándor , Fenner Kathrin 
Published: November 2018

AbstractMany pharmaceuticals inevitably end up in surface waters, exerting unwanted biological activity in nontarget organisms. This effect is confined by the compound's environmental persistence. Regulatory laboratory simulation tests are used in persistence assessment and exposure modeling. While doubt has been expressed about the usefulness of laboratory‐derived persistence indicators under field conditions, these remain the only inputs for chemical fate models due to difficulties of measuring persistence in situ, especially at large scales. To improve understanding about relationships between laboratory experiments and the environmental fate in streams, we developed a mathematical model of biodegradation in stream networks and combined it with in‐stream monitoring data to (i) test if persistence could be evaluated from field data, (ii) check if persistence extracted from laboratory tests applied in the field, and (iii) locate hot spots of biodegradation in a large river basin. The model describes partitioning, and particle settling and resuspension, and is structurally compatible with those applied for evaluating laboratory simulation tests. Application to the Rhine river basin suggests that biotransformation rate constants extracted from laboratory tests underestimate those in the field, yet the percentage of biotransformation in the Rhine basin is less than in the laboratory tests due effective biotransformation being limited to small‐ and medium‐sized streams. In conclusion, our data show that biotransformation rates can accurately be predicted if (i) monitoring is performed across a wide range in stream order and (ii) precise estimates for consumption and removal rates at wastewater treatment plants are known.
Quantifying the changes in genetic diversity within sequence-discrete bacterial populations across a spatial and temporal riverine gradient
Authors: Meziti Alexandra , Tsementzi Despina , Rodriguez-R Luis M , Hatt Janet K , Karayanni Hera , Kormas Konstantinos A , Konstantinidis Konstantinos T 
Published: November 2018

Abstract
Recent diversity studies have revealed that microbial communities of natural environments are dominated by species-like, sequence-discrete populations. However, how stable the sequence and gene-content diversity are within these populations and especially in highly dynamic lotic habitats remain unclear. Here we quantified the dynamics of intra-population diversity in samples spanning two years and five sites in the Kalamas River (Northwest Greece). A significant positive correlation was observed between higher intra-population sequence diversity and longer persistence over time, revealing that more diverse populations tended to represent more autochthonous (vs. allochthonous) community members. Assessment of intra-population gene-content changes caused by strain replacement or gene loss over time revealed different profiles with the majority of populations exhibiting gene-content changes close to 10% of the total genes, while one population exhibited ~21% change. The variable genes were enriched in hypothetical proteins and mobile elements, and thus, were probably functionally neutral or attributable to phage predation. A few notable exceptions to this pattern were also noted such as phototrophy-related proteins in summer vs. winter populations. Taken together, these results revealed that some freshwater genomes are remarkably dynamic, even across short time and spatial scales, and have implications for the bacterial species concept and microbial source tracking.
Predicting the naturalistic course of depression from a wide range of clinical, psychological, and biological data: a machine learning approach
Authors: Dinga Richard , Marquand Andre F. , Veltman Dick J. , Beekman Aartjan T. F. , Schoevers Robert A. , van Hemert Albert M. , Penninx Brenda W. J. H. , Schmaal Lianne 
Published: November 2018

AbstractMany variables have been linked to different course trajectories of depression. These findings, however, are based on group comparisons with unknown translational value. This study evaluated the prognostic value of a wide range of clinical, psychological, and biological characteristics for predicting the course of depression and aimed to identify the best set of predictors. Eight hundred four unipolar depressed patients (major depressive disorder or dysthymia) patients were assessed on a set involving 81 demographic, clinical, psychological, and biological measures and were clinically followed-up for 2 years. Subjects were grouped according to (i) the presence of a depression diagnosis at 2-year follow-up (yes n = 397, no n = 407), and (ii) three disease course trajectory groups (rapid remission, n = 356, gradual improvement n = 273, and chronic n = 175) identified by a latent class growth analysis. A penalized logistic regression, followed by tight control over type I error, was used to predict depression course and to evaluate the prognostic value of individual variables. Based on the inventory of depressive symptomatology (IDS), we could predict a rapid remission course of depression with an AUROC of 0.69 and 62% accuracy, and the presence of an MDD diagnosis at follow-up with an AUROC of 0.66 and 66% accuracy. Other clinical, psychological, or biological variables did not significantly improve the prediction. Among the large set of variables considered, only the IDS provided predictive value for course prediction on an individual level, although this analysis represents only one possible methodological approach. However, accuracy of course prediction was moderate at best and further improvement is required for these findings to be clinically useful.
Deferred autologous stem cell transplantation in systemic AL amyloidosis
Authors: Manwani Richa , Hegenbart Ute , Mahmood Shameem , Sachchithanantham Sajitha , Kyriakou Charalampia , Yong Kwee , Popat Rakesh , Rabin Neil , Whelan Carol , Dittrich Tobias , Kimmich Christoph , Hawkins Philip , Schönland Stefan , Wechalekar Ashutosh 
Published: November 2018

AbstractHigh-dose melphalan with autologous stem cell transplantation (ASCT) can induce durable haematological and organ responses in systemic AL amyloidosis (AL). Stringent selection criteria have improved safety of ASCT in AL but most patients are transplant-ineligible. We report our experience of deferred ASCT in AL patients who were transplant-ineligible at presentation but had improvements in organ function after induction chemotherapy, enabling them to undergo ASCT. Twenty-two AL patients underwent deferred ASCT from 2011 to 2017. All had serial organ function and clonal response assessment. Organ involvement and responses were defined by amyloidosis consensus criteria. All patients were transplant-ineligible at presentation, predominantly due to advanced cardiac involvement. All received bortezomib-based therapy, with 100% haematologic response (86% complete response (CR)/very good partial response (VGPR)), enabling reversal of ASCT exclusion criteria. Patients underwent deferred ASCT for haematologic progression (45%) or consolidation (55%). There was no transplant-related mortality. Haematologic responses post-ASCT: CR 50%, VGPR 27%, PR 18%, non-response 5%. In all, 85.7% achieved cardiac responses. Median overall survival (OS) was not reached. Median progression-free survival (PFS) was 54 months. This selected cohort achieved excellent haematologic responses, organ responses, PFS and OS with deferred ASCT. If larger studies confirm these findings, this may widen the applicability of ASCT in AL.
Fossilization transforms vertebrate hard tissue proteins into N-heterocyclic polymers
Authors: Wiemann Jasmina , Fabbri Matteo , Yang Tzu-Ruei , Stein Koen , Sander P. Martin , Norell Mark A. , Briggs Derek E. G. 
Published: November 2018

AbstractVertebrate hard tissues consist of mineral crystallites within a proteinaceous scaffold that normally degrades post-mortem. Here we show, however, that decalcification of Mesozoic hard tissues preserved in oxidative settings releases brownish stained extracellular matrix, cells, blood vessels, and nerve projections. Raman Microspectroscopy shows that these fossil soft tissues are a product of diagenetic transformation to Advanced Glycoxidation and Lipoxidation End Products, a class of N-heterocyclic polymers generated via oxidative crosslinking of proteinaceous scaffolds. Hard tissues in reducing environments, in contrast, lack soft tissue preservation. Comparison of fossil soft tissues with modern and experimentally matured samples reveals how proteinaceous tissues undergo diagenesis and explains biases in their preservation in the rock record. This provides a target, focused on oxidative depositional environments, for finding cellular-to-subcellular soft tissue morphology in fossils and validates its use in phylogenetic and other evolutionary studies.
Crystal structures of human ETB receptor provide mechanistic insight into receptor activation and partial activation
Authors: Shihoya Wataru , Izume Tamaki , Inoue Asuka , Yamashita Keitaro , Kadji Francois Marie Ngako , Hirata Kunio , Aoki Junken , Nishizawa Tomohiro , Nureki Osamu 
Published: November 2018

AbstractEndothelin receptors (ETA and ETB) are class A GPCRs activated by vasoactive peptide endothelins, and are involved in blood pressure regulation. ETB-selective signalling induces vasorelaxation, and thus selective ETB agonists are expected to be utilized for improved anti-tumour drug delivery and neuroprotection. Here, we report the crystal structures of human ETB receptor in complex with ETB-selective agonist, endothelin-3 and an ETB-selective endothelin analogue IRL1620. The structure of the endothelin-3-bound receptor reveals that the disruption of water-mediated interactions between W6.48 and D2.50 is critical for receptor activation, while these hydrogen-bonding interactions are partially preserved in the IRL1620-bound structure. Consistently, functional analysis reveals the partial agonistic effect of IRL1620. The current findings clarify the detailed molecular mechanism for the coupling between the orthosteric pocket and the G-protein binding, and the partial agonistic effect of IRL1620, thus paving the way for the design of improved agonistic drugs targeting ETB.
Crystallographic and spectroscopic assignment of the proton transfer pathway in [FeFe]-hydrogenases
Authors: Duan Jifu , Senger Moritz , Esselborn Julian , Engelbrecht Vera , Wittkamp Florian , Apfel Ulf-Peter , Hofmann Eckhard , Stripp Sven T. , Happe Thomas , Winkler Martin 
Published: November 2018

AbstractThe unmatched catalytic turnover rates of [FeFe]-hydrogenases require an exceptionally efficient proton-transfer (PT) pathway to shuttle protons as substrates or products between bulk water and catalytic center. For clostridial [FeFe]-hydrogenase CpI such a pathway has been proposed and analyzed, but mainly on a theoretical basis. Here, eleven enzyme variants of two different [FeFe]-hydrogenases (CpI and HydA1) with substitutions in the presumptive PT-pathway are examined kinetically, spectroscopically, and crystallographically to provide solid experimental proof for its role in hydrogen-turnover. Targeting key residues of the PT-pathway by site directed mutagenesis significantly alters the pH-activity profile of these variants and in presence of H2 their cofactor is trapped in an intermediate state indicative of precluded proton-transfer. Furthermore, crystal structures coherently explain the individual levels of residual activity, demonstrating e.g. how trapped H2O molecules rescue the interrupted PT-pathway. These features provide conclusive evidence that the targeted positions are indeed vital for catalytic proton-transfer.
Evidence of depolarization and ellipticity of high harmonics driven by ultrashort bichromatic circularly polarized fields
Authors: Barreau Lou , Veyrinas Kévin , Gruson Vincent , Weber Sébastien J. , Auguste Thierry , Hergott Jean-François , Lepetit Fabien , Carré Bertrand , Houver Jean-Christophe , Dowek Danielle , Salières Pascal 
Published: November 2018

AbstractHigh harmonics generated by counter-rotating laser fields at the fundamental and second harmonic frequencies have raised important interest as a table-top source of circularly polarized ultrashort extreme-ultraviolet light. However, this emission has not yet been fully characterized: in particular it was assumed to be fully polarized, leading to an uncertainty on the effective harmonic ellipticity. Here we show, through simulations, that ultrashort driving fields and ultrafast medium ionization lead to a breaking of the dynamical symmetry of the interaction, and consequently to deviations from perfectly circular and fully polarized harmonics, already at the single-atom level. We perform the complete experimental characterization of the polarization state of high harmonics generated along that scheme, giving direct access to the ellipticity absolute value and sign, as well as the degree of polarization of individual harmonic orders. This study allows defining optimal generation conditions of fully circularly polarized harmonics for advanced studies of ultrafast dichroisms.
Active intermixing of indirect and direct neurons builds the striatal mosaic
Authors: Tinterri Andrea , Menardy Fabien , Diana Marco A. , Lokmane Ludmilla , Keita Maryama , Coulpier Fanny , Lemoine Sophie , Mailhes Caroline , Mathieu Benjamin , Merchan-Sala Paloma , Campbell Kenneth , Gyory Ildiko , Grosschedl Rudolf , Popa Daniela , Garel Sonia 
Published: November 2018

AbstractThe striatum controls behaviors via the activity of direct and indirect pathway projection neurons (dSPN and iSPN) that are intermingled in all compartments. While such cellular mosaic ensures the balanced activity of the two pathways, its developmental origin and pattern remains largely unknown. Here, we show that both SPN populations are specified embryonically and intermix progressively through multidirectional iSPN migration. Using conditional mutant mice, we found that inactivation of the dSPN-specific transcription factor Ebf1 impairs selective dSPN properties, including axon pathfinding, while molecular and functional features of iSPN were preserved. Ebf1 mutation disrupted iSPN/dSPN intermixing, resulting in an uneven distribution. Such architectural defect was selective of the matrix compartment, highlighting that intermixing is a parallel process to compartment formation. Our study reveals while iSPN/dSPN specification is largely independent, their intermingling emerges from an active migration of iSPN, thereby providing a novel framework for the building of striatal architecture.
Discovery of rare cells from voluminous single cell expression data
Authors: Jindal Aashi , Gupta Prashant , Jayadeva  , Sengupta Debarka 
Published: November 2018

AbstractSingle cell messenger RNA sequencing (scRNA-seq) provides a window into transcriptional landscapes in complex tissues. The recent introduction of droplet based transcriptomics platforms has enabled the parallel screening of thousands of cells. Large-scale single cell transcriptomics is advantageous as it promises the discovery of a number of rare cell sub-populations. Existing algorithms to find rare cells scale unbearably slowly or terminate, as the sample size grows to the order of tens of thousands. We propose Finder of Rare Entities (FiRE), an algorithm that, in a matter of seconds, assigns a rareness score to every individual expression profile under study. We demonstrate how FiRE scores can help bioinformaticians focus the downstream analyses only on a fraction of expression profiles within ultra-large scRNA-seq data. When applied to a large scRNA-seq dataset of mouse brain cells, FiRE recovered a novel sub-type of the pars tuberalis lineage.