bluuebunny/crossref_metadata_2025_split huggingface dataset:
Towards Dynamical Seasonal Forecast of Extratropical Transition in the North Atlantic
Authors: Liu M. , Vecchi G. A. , Smith J. A. , Murakami H. , Gudgel R. , Yang X. 
Published: October 2018

AbstractExtratropical transition can extend the threat of tropical cyclones into the midlatitudes and modify it through expansion of rainfall and wind fields. Despite the scientific and socioeconomic interest, the seasonal forecast of extratropical transition has received little attention. The GFDL High‐Resolution Forecast‐Oriented Low Ocean Resolution (FLOR) model (HiFLOR) shows skill in seasonal forecasts of tropical cyclone frequency as well as major hurricanes. A July‐initialized 12‐member ensemble retrospective seasonal forecast experiment with HiFLOR in the North Atlantic is conducted, representing one of the very first attempts to predict the extratropical transition activity months in advance. HiFLOR exhibits retrospective skill in seasonal forecasts of basin‐wide and regional ET activity relative to best track and reanalysis data. In contrast, the skill of HiFLOR in predictions of non‐ET activity is limited. Future work targeted at improved predictions of non‐ET storms provides a path for enhanced TC activity forecasting.
Effect of ISO‐SSE Interaction on Accelerating the TS to Severe TS Development in the WNP Since the Late 1990s
Authors: Hong Chi‐Cherng , Tsou Chih‐Hua , Lee Ming‐Ying , Chang Chi‐Chun , Hsu Huang‐Hsiung , Chen Kuan‐Chieh 
Published: October 2018

AbstractThis study addressed the abrupt increase in the development speed of tropical storms (TSs) to severe TSs (≥ category 3, referred to as STSs) in the western North Pacific (WNP) during the late 1990s. Our investigation indicated that the TSs developed into STSs with a faster speed since the late 1990s. The eddy kinetic energy budget of synoptic‐scale eddy (SSE) indicated that the enhancement of energy conversion from intraseasonal oscillation (ISO) to SSE played a critical role in accelerating the TS‐to‐STS development. The increase of ISO‐SSE interaction was attributed to the mega La Niña–like mean state change. The anticyclone anomaly associated with mega La Niña and warm oceanic condition in the WNP substantially modified the mean TS genesis location (northwestward shift) and enhanced the ISO magnitude in the South China Sea and Philippine Sea, thereby amplifying the ISO‐SSE interaction in the WNP in the late 1990s.
Isotopic Composition of In Situ Soil NOx Emissions in Manure‐Fertilized Cropland
Authors: Miller David J. , Chai Jiajue , Guo Felix , Dell Curtis J. , Karsten Heather , Hastings Meredith G. 
Published: October 2018

AbstractSoil emissions represent ~25% of the global annual atmospheric budget of nitrogen oxides (NOx). The nitrogen isotopic composition of soil NOx emissions (δ15N‐NOx) is potentially useful to track soil emission contributions to NOx budgets, yet its in situ variations with fertilizer management and meteorology are unknown. We quantify in situ δ15N‐NOx distributions from liquid dairy manure‐fertilized cropland in State College, Pennsylvania at hourly resolution during spring 2016 and 2017. δ15N‐NOx (n = 37) ranged from −44.2 to −14.0‰ and was distinct between injected (−32.2 ± 12.1‰) and broadcast manure without tillage (−23.4 ± 2.1‰). δ15N‐NOx was not correlated with order of magnitude emission variations due to large changes in soil moisture. δ15N‐NOx differences between treatments were associated with nitrification and NO consumption contributions. Our results suggest that δ15N‐NOx can be a valuable observational tracer of soil emissions and varies with fertilizer management practices.
Understanding Rapid Adjustments to Diverse Forcing Agents
Authors: Smith C. J. , Kramer R. J. , Myhre G. , Forster P. M. , Soden B. J. , Andrews T. , Boucher O. , Faluvegi G. , Fläschner D. , Hodnebrog Ø. , Kasoar M. , Kharin V. , Kirkevåg A. , Lamarque J.‐F. , Mülmenstädt J. , Olivié D. , Richardson T. , Samset B. H. , Shindell D. , Stier P. , Takemura T. , Voulgarakis A. , Watson‐Parris D. 
Published: October 2018

AbstractRapid adjustments are responses to forcing agents that cause a perturbation to the top of atmosphere energy budget but are uncoupled to changes in surface warming. Different mechanisms are responsible for these adjustments for a variety of climate drivers. These remain to be quantified in detail. It is shown that rapid adjustments reduce the effective radiative forcing (ERF) of black carbon by half of the instantaneous forcing, but for CO2 forcing, rapid adjustments increase ERF. Competing tropospheric adjustments for CO2 forcing are individually significant but sum to zero, such that the ERF equals the stratospherically adjusted radiative forcing, but this is not true for other forcing agents. Additional experiments of increase in the solar constant and increase in CH4 are used to show that a key factor of the rapid adjustment for an individual climate driver is changes in temperature in the upper troposphere and lower stratosphere.
The Role of Near‐Fault Relief Elements in Creating and Maintaining a Strike‐Slip Landscape
Authors: Harbert S. A. , Duvall A. R. , Tucker G. E. 
Published: October 2018

AbstractStrike‐slip landscapes are often associated with a suite of characteristic geomorphic features that provide primary evidence for interpreting fault slip histories. Here we explore the role of shutter ridges, areas of relief advected laterally along faults, in generating two classic strike‐slip processes: progressive lateral offset of channels and stream capture. Landscape models and comparative analysis of the Marlborough Fault System, NZ, show that the length of channel offsets observable in a landscape is primarily controlled by the length of shutter ridges. In our simple landscape model, this scale is controlled by the drainage spacing, and therefore by the geometry of the mountain range. In a more complex landscape, this scale may be controlled by lithologic or structural contrasts. We also find that shutter ridge relief inhibits stream capture, especially at slow fault slip rates relative to hillslope erosion rates. In this case, lateral drainage advection enables streams to “outrun” capture.
The Uneven Nature of Daily Precipitation and Its Change
Authors: Pendergrass Angeline G. , Knutti Reto 
Published: October 2018

AbstractA few days with heavy rain contribute disproportionately to total precipitation, while many days with light drizzle contribute much less. What is not appreciated is just how asymmetric this distribution is in time, and the even more asymmetric nature of trends due to climate change. We diagnose the temporal asymmetry in models and observations. Half of annual precipitation falls in the wettest 12 days each year in the median across observing stations worldwide. Climate models project changes in precipitation that are more uneven than present‐day precipitation. In a scenario with high greenhouse‐gas emissions, one fifth of the projected increase in rain falls in the wettest 2 days of the year and 70% in the wettest 2 weeks. Adjusting modeled unevenness to match present‐day unevenness at stations, half of precipitation increase occurs in the wettest 6 days each year.
Paleolatitude of the Hawaiian Hot Spot Since 48 Ma: Evidence for a Mid‐Cenozoic True Polar Stillstand Followed by Late Cenozoic True Polar Wander Coincident With Northern Hemisphere Glaciation
Authors: Woodworth Daniel , Gordon Richard G. 
Published: October 2018

AbstractPaleospin axis locations since 48 Ma inferred from the distribution of equatorial sediment accumulation rates on the Pacific plate, together with paleomagnetic poles from magnetic anomaly skewness, indicate that the Hawaiian hot spot was nearly fixed in latitude from 48 to 12 Ma, but ≈3° north of its current latitude. From 48 to 12 Ma in the Pacific hot spot reference frame, which we take to be equivalent to the global hot spot reference frame, the spin axis was located near 87°N, 164°E, recording a stillstand in true polar wander. Global hot spots shifted coherently relative to the spin axis since ≈12 Ma, consistent with an episode of true polar wander, which may continue today. The motion of the spin axis away from the Hawaiian hot spot and toward Greenland since ≈12 Ma coincided with, and may have contributed to, the onset of northern hemisphere glaciation.
Relationship Between the Orientation of Maximum Permeability and Intermediate Principal Stress in Fractured Rocks
Authors: Lang Philipp S. , Paluszny Adriana , Nejati Morteza , Zimmerman Robert W. 
Published: October 2018

AbstractFlow and transport properties of fractured rock masses are a function of geometrical structures across many scales. These structures result from physical processes and states and are highly anisotropic in nature. Fracture surfaces often tend to be shifted with respect to each other, which is generally a result of stress‐induced displacements. This shift controls the fracture's transmissivity through the pore space that forms from the created mismatch between the surfaces. This transmissivity is anisotropic and greater in the direction perpendicular to the displacement. A contact mechanics‐based, first‐principle numerical approach is developed to investigate the effects that this shear‐induced transmissivity anisotropy has on the overall permeability of a fractured rock mass. Deformation of the rock and contact between fracture surfaces is computed in three dimensions at two scales. At the rock mass scale, fractures are treated as planar discontinuities along which displacements and tractions are resolved. Contact between the individual rough fracture surfaces is solved for each fracture at the small scale to find the stiffness and transmissivity that result from shear‐induced dilation and elastic compression. Results show that, given isotropic fracture networks, the direction of maximum permeability of a fractured rock mass tends to be aligned with the direction of the intermediate principal stress. This reflects the fact that fractures have the most pronounced slip in the plane of the maximum and minimum principal stresses, and for individual fractures transmissivity is most pronounced in the direction perpendicular to this slip.
Groundwater Is Key to Salmonid Persistence and Recruitment in Intermittent Mediterranean‐Climate Streams
Authors: Larsen Laurel G. , Woelfle‐Erskine Cleo 
Published: October 2018

AbstractJuvenile coho salmon thrive in intermittent streams of the Pacific Northwest yet are in danger of increased mortality from drought and rising temperatures. With warmer temperatures and more frequent climate extremes projected, the need to understand how intermittent stream hydrology and biogeochemistry impact juvenile salmonid habitat and behavior is imperative. Previous investigations indicated that dissolved oxygen limits the persistence of coho salmon in intermittent streams, leading to the hypothesis that groundwater inflow would ultimately control patterns of salmon recruitment and persistence. Here we tested that hypothesis in paired tributaries of Salmon Creek, Sonoma County, CA during California's extreme drought of 2011–2017. We used the fluorescent fingerprint of dissolved organic carbon, together with a parallel factor analysis, to estimate groundwater influence in individual stream pools, corroborating those estimates with stable isotope and radon analyses. Repeat snorkel surveys provided fish counts in those pools at the beginning and end of the period of surface‐water disconnection. Results suggested that coho salmon fry preferentially selected pools with a groundwater inflow signal and persisted in pools maintaining that signal through the dry season. This groundwater inflow signal was distinct from hyporheic influence, which exhibited little correlation with fish distribution. Groundwater within pools was young, and spot measurements suggested that it was relatively oxygenated. Proportional groundwater contributions to pools increased as drought deepened. Results suggest that maintaining relatively high groundwater levels in coastal aquifers may be imperative to the persistence of vulnerable salmonid populations in a changing climate.
Low-level expression of SAMHD1 in acute myeloid leukemia (AML) blasts correlates with improved outcome upon consolidation chemotherapy with high-dose cytarabine-based regimens
Authors: Rassidakis George Z. , Herold Nikolas , Myrberg Ida Hed , Tsesmetzis Nikolaos , Rudd Sean G. , Henter Jan-Inge , Schaller Torsten , Ng Siok-Bian , Chng Wee Joo , Yan Benedict , Ng Chin Hin , Ravandi Farhad , Andreeff Michael , Kantarjian Hagop M. , Medeiros L. Jeffrey , Xagoraris Ioanna , Khoury Joseph D. 
Published: October 2018

AbstractSterile alpha motif and histidine/aspartic acid domain containing protein 1 (SAMHD1) limits the efficacy of cytarabine (ara-C) used in AML by hydrolyzing its active metabolite ara-CTP and thus represents a promising therapeutic target. SAMHD1 has also been implicated in DNA damage repair that may impact DNA damage-inducing therapies such as anthracyclines, during induction therapy. To determine whether SAMHD1 limits ara-C efficacy during induction or consolidation therapy, SAMHD1 protein levels were assessed in two patient cohorts of de novo AML from The University of Texas MD Anderson Cancer Center (USA) and the National University Hospital (Singapore), respectively, using immunohistochemistry and tissue microarrays. SAMHD1 was expressed at a variable level by AML blasts but not in a broad range of normal hematopoietic cells in reactive bone marrows. A sizeable patient subset with low SAMHD1 expression (<25% of positive blasts) was identified, which was significantly associated with longer event-free (EFS) and overall (OS) survival in patients receiving high-dose cytarabine (HDAC) during consolidation. Therefore, evaluation of SAMHD1 expression level in AML blasts at diagnosis, may stratify patient groups for future clinical trials combining HDAC with novel SAMHD1 inhibitors as consolidation therapy.
A biomaterial with a channel-like pore architecture induces endochondral healing of bone defects
Authors: Petersen A. , Princ A. , Korus G. , Ellinghaus A. , Leemhuis H. , Herrera A. , Klaumünzer A. , Schreivogel S. , Woloszyk A. , Schmidt-Bleek K. , Geissler S. , Heschel I. , Duda G. N. 
Published: October 2018

AbstractBiomaterials developed to treat bone defects have classically focused on bone healing via direct, intramembranous ossification. In contrast, most bones in our body develop from a cartilage template via a second pathway called endochondral ossification. The unsolved clinical challenge to regenerate large bone defects has brought endochondral ossification into discussion as an alternative approach for bone healing. However, a biomaterial strategy for the regeneration of large bone defects via endochondral ossification is missing. Here we report on a biomaterial with a channel-like pore architecture to control cell recruitment and tissue patterning in the early phase of healing. In consequence of extracellular matrix alignment, CD146+ progenitor cell accumulation and restrained vascularization, a highly organized endochondral ossification process is induced in rats. Our findings demonstrate that a pure biomaterial approach has the potential to recapitulate a developmental bone growth process for bone healing. This might motivate future strategies for biomaterial-based tissue regeneration.
Biologically relevant laminin as chemically defined and fully human platform for human epidermal keratinocyte culture
Authors: Tjin Monica Suryana , Chua Alvin Wen Choong , Moreno-Moral Aida , Chong Li Yen , Tang Po Yin , Harmston Nathan Peter , Cai Zuhua , Petretto Enrico , Tan Bien Keem , Tryggvason Karl 
Published: October 2018

AbstractThe current expansion of autologous human keratinocytes to resurface severe wound defects still relies on murine feeder layer and calf serum in the cell culture system. Through our characterization efforts of the human skin basement membrane and murine feeder layer 3T3-J2, we identified two biologically relevant recombinant laminins—LN-511 and LN-421- as potential candidates to replace the murine feeder. Herein, we report a completely xeno-free and defined culture system utilizing these laminins which enables robust expansion of adult human skin keratinocytes. We demonstrate that our laminin system is comparable to the 3T3-J2 co-culture system in terms of basal markers’ profile, colony-forming efficiency and the ability to form normal stratified epidermal structure in both in vitro and in vivo models. These results show that the proposed system may not only provide safer keratinocyte use in the clinics, but also facilitate the broader use of other cultured human epithelial cells in regenerative medicine.
Improved methods for marking active neuron populations
Authors: Moeyaert Benjamien , Holt Graham , Madangopal Rajtarun , Perez-Alvarez Alberto , Fearey Brenna C. , Trojanowski Nicholas F. , Ledderose Julia , Zolnik Timothy A. , Das Aniruddha , Patel Davina , Brown Timothy A. , Sachdev Robert N. S. , Eickholt Britta J. , Larkum Matthew E. , Turrigiano Gina G. , Dana Hod , Gee Christine E. , Oertner Thomas G. , Hope Bruce T. , Schreiter Eric R. 
Published: October 2018

AbstractMarking functionally distinct neuronal ensembles with high spatiotemporal resolution is a key challenge in systems neuroscience. We recently introduced CaMPARI, an engineered fluorescent protein whose green-to-red photoconversion depends on simultaneous light exposure and elevated calcium, which enabled marking active neuronal populations with single-cell and subsecond resolution. However, CaMPARI (CaMPARI1) has several drawbacks, including background photoconversion in low calcium, slow kinetics and reduced fluorescence after chemical fixation. In this work, we develop CaMPARI2, an improved sensor with brighter green and red fluorescence, faster calcium unbinding kinetics and decreased photoconversion in low calcium conditions. We demonstrate the improved performance of CaMPARI2 in mammalian neurons and in vivo in larval zebrafish brain and mouse visual cortex. Additionally, we herein develop an immunohistochemical detection method for specific labeling of the photoconverted red form of CaMPARI. The anti-CaMPARI-red antibody provides strong labeling that is selective for photoconverted CaMPARI in activated neurons in rodent brain tissue.
Modelling Self-Organization in Complex Networks Via a Brain-Inspired Network Automata Theory Improves Link Reliability in Protein Interactomes
Authors: Cannistraci Carlo Vittorio 
Published: October 2018

AbstractProtein interactomes are epitomes of incomplete and noisy networks. Methods for assessing link-reliability using exclusively topology are valuable in network biology, and their investigation facilitates the general understanding of topological mechanisms and models to draw and correct complex network connectivity. Here, I revise and extend the local-community-paradigm (LCP). Initially detected in brain-network topological self-organization and afterward generalized to any complex network, the LCP is a theory to model local-topology-dependent link-growth in complex networks using network automata. Four novel LCP-models are compared versus baseline local-topology-models. It emerges that the reliability of an interaction between two proteins is higher: (i) if their common neighbours are isolated in a complex (local-community) that has low tendency to interact with other external proteins; (ii) if they have a low propensity to link with other proteins external to the local-community. These two rules are mathematically combined in C1*: a proposed mechanistic model that, in fact, outperforms the others. This theoretical study elucidates basic topological rules behind self-organization principia of protein interactomes and offers the conceptual basis to extend this theory to any class of complex networks. The link-reliability improvement, based on the mere topology, can impact many applied domains such as systems biology and network medicine.
EzColocalization: An ImageJ plugin for visualizing and measuring colocalization in cells and organisms
Authors: Stauffer Weston , Sheng Huanjie , Lim Han N. 
Published: October 2018

AbstractInsight into the function and regulation of biological molecules can often be obtained by determining which cell structures and other molecules they localize with (i.e. colocalization). Here we describe an open source plugin for ImageJ called EzColocalization to visualize and measure colocalization in microscopy images. EzColocalization is designed to be easy to use and customize for researchers with minimal experience in quantitative microscopy and computer programming. Features of EzColocalization include: (i) tools to select individual cells and organisms from images; (ii) filters to select specific types of cells and organisms based on physical parameters and signal intensity; (iii) heat maps and scatterplots to visualize the localization patterns of reporters; (iv) multiple metrics to measure colocalization for two or three reporters; (v) metric matrices to systematically measure colocalization at multiple combinations of signal intensity thresholds; and (vi) data tables that provide detailed information on each cell in a sample. These features make EzColocalization well-suited for experiments with low reporter signal, complex patterns of localization, and heterogeneous populations of cells and organisms.
Microperimetry and multimodal imaging in polypoidal choroidal vasculopathy
Authors: Acton Jennifer H. , Ogino Ken , Akagi Yumiko , Wild John M. , Yoshimura Nagahisa 
Published: October 2018

AbstractPolypoidal choroidal vasculopathy (PCV) is a degenerative macular disease. The study determined the topographical concordance in the areal extent of PCV, defined by indocyanine green angiography (ICGA), and the corresponding outcomes from spectral-domain optical coherence tomography (SD-OCT) and microperimetry, in 25 individuals (25 eyes) who had undergone 3 months of anti-vascular endothelial growth factor treatment. The differential light sensitivity within 10° eccentricity was evaluated by Pattern Deviation probability analysis. The concordances and proportional areal extents of the abnormality for ICGA, SD-OCT and microperimetry were compared. The concordance in the areal extent between all three modalities was 59%. The median concordance between ICGA and microperimetry was 60%; between ICGA and SD-OCT, 70%; and between SD-OCT and microperimetry, 72%. SD-OCT and microperimetry each identified a greater areal extent (>20%) compared to ICGA in 13 and 19 eyes, respectively. A greater areal extent (>20%) was present in 9 eyes for microperimetry compared to SD-OCT and in 5 eyes for SD-OCT compared to microperimetry. SD-OCT and microperimetry each identified a greater area of abnormality than ICGA which supports the clinical utility of SD-OCT. Strong concordance was present between SD-OCT and microperimetry; however, microperimetry identified additional areas of functional abnormality.