bluuebunny/crossref_metadata_2025_split huggingface dataset:
Global and Regional Assessments of Paleosecular Variation Activity Over the Past 100 ka
Authors: Panovska S. , Constable C. G. , Brown M. C. 
Published: April 2018

AbstractWe present a global compilation of paleomagnetic data spanning the past 100 ka. Sediment data comprise 61,687 declinations, 70,936 inclinations, and 69,596 relative paleointensities. Many sites are located in the northern Atlantic and western Pacific, with approximately twice as many data from the Northern Hemisphere as from the Southern Hemisphere. The 14,954 volcanic and archeomagnetic data are sparse, especially in the Southern Hemisphere. Directional and intensity information are aggregated under the paleosecular variation (PSV) index to assess occurrence of excursions over the past 100 ka. The Laschamp excursion (∼41 ka) is clearly defined across globally distributed sediment records with an average duration of 1,300 years. Regional stacks obtained using bootstrap resampling show a more pronounced Laschamp excursion in the Northern Hemisphere than in the Southern, and in the Atlantic Hemisphere compared with the Pacific. No anomalous indices occurred around the Mono Lake excursion or other periods in the bootstrap curves. This may result from low sedimentation rates, discrepancies in age scales, large age errors, and/or the lack of global character of any transitional events. These data and associated new uncertainty estimates for the sediment records provide a good foundation for global, time‐dependent, spherical harmonic field modeling for the past 100 ka.
Shear‐Wave Velocity Structure of Southern Africa's Lithosphere: Variations in the Thickness and Composition of Cratons and Their Effect on Topography
Authors: Ravenna Matteo , Lebedev Sergei , Fullea Javier , Adam Joanne M.‐C. 
Published: April 2018

AbstractSeismic‐wave velocities offer essential constraints on the temperature, thickness, and composition of the lithosphere of cratons. We invert broadband, Rayleigh‐wave phase and Love‐wave phase velocities measured across the Kaapvaal Craton and Limpopo Belt for depth distributions of shear‐wave velocity and radial anisotropy, from the upper‐crust down to deep upper mantle. Our probabilistic, Bayesian inversion addresses model nonuniqueness by means of direct parameter‐space sampling. An increase in Vs between the Moho and 100–150 km depths occurs across the region and can be explained by the gradual emergence of garnet below 80 km, due to the spinel peridotite‐garnet peridotite transformation and due to the exsolution of garnet from mantle orthopyroxene. Lateral variations in this Vs gradient can provide new information on lateral compositional variations. Cold cratonic lithosphere is manifest in very high shear velocities, up to 4.8 km/s. The depth extent of the shear‐velocity anomaly and the inferred lithospheric thickness increase from ∼200 km beneath the central and southwestern Kaapvaal to ∼300 km beneath the Limpopo Belt. Curiously, surface elevation decreases monotonically with the increasing lithospheric thickness. The relationship between the lithospheric thickness and topography depends on the lithospheric composition and, with the crustal structure taken into account, our results imply that the bottom part of the Limpopo lithosphere (200–300 km) is weakly‐to‐moderately depleted (Mg# 89.7–90.8). Our results also show that the central‐southwestern Kaapvaal lithosphere is thinner than it was (according to kimberlites) 100–200 m.y. ago. It may have been thinned by the same mantle plume that, initially, triggered the kimberlite eruptions.
Bridging Thermal Infrared Sensing and Physically‐Based Evapotranspiration Modeling: From Theoretical Implementation to Validation Across an Aridity Gradient in Australian Ecosystems
Authors: Mallick Kaniska , Toivonen Erika , Trebs Ivonne , Boegh Eva , Cleverly James , Eamus Derek , Koivusalo Harri , Drewry Darren , Arndt Stefan K. , Griebel Anne , Beringer Jason , Garcia Monica 
Published: April 2018

AbstractThermal infrared sensing of evapotranspiration (E) through surface energy balance (SEB) models is challenging due to uncertainties in determining the aerodynamic conductance (gA) and due to inequalities between radiometric (TR) and aerodynamic temperatures (T0). We evaluated a novel analytical model, the Surface Temperature Initiated Closure (STIC1.2), that physically integrates TR observations into a combined Penman‐Monteith Shuttleworth‐Wallace (PM‐SW) framework for directly estimating E, and overcoming the uncertainties associated with T0 and gA determination. An evaluation of STIC1.2 against high temporal frequency SEB flux measurements across an aridity gradient in Australia revealed a systematic error of 10–52% in E from mesic to arid ecosystem, and low systematic error in sensible heat fluxes (H) (12–25%) in all ecosystems. Uncertainty in TR versus moisture availability relationship, stationarity assumption in surface emissivity, and SEB closure corrections in E were predominantly responsible for systematic E errors in arid and semi‐arid ecosystems. A discrete correlation (r) of the model errors with observed soil moisture variance (r = 0.33–0.43), evaporative index (r = 0.77–0.90), and climatological dryness (r = 0.60–0.77) explained a strong association between ecohydrological extremes and TR in determining the error structure of STIC1.2 predicted fluxes. Being independent of any leaf‐scale biophysical parameterization, the model might be an important value addition in working group (WG2) of the Australian Energy and Water Exchange (OzEWEX) research initiative which focuses on observations to evaluate and compare biophysical models of energy and water cycle components.
An Analytical Stochastic Approach for Evaluating the Performance of Combined Sewer Overflow Tanks
Authors: Wang Jun , Guo Yiping 
Published: April 2018

AbstractStorm water detention tanks are widely used for the control of combined sewer overflows. Conventional continuous simulation and recently developed analytical probabilistic models have been used for analyzing the hydrologic operation of storm water detention tanks. These analyses are necessary in order to accurately estimate the runoff capture efficiency of a given control system or the required storage capacity for achieving a desired runoff capture efficiency. The analytical probabilistic models still have the shortcomings of making simplifying assumptions about the initial storage conditions of a detention tank. Developed in this study is a new stochastic analysis method which can provide similar results as provided by continuous simulations and overcome some of the shortcomings of the previously developed analytical probabilistic models. This stochastic analysis method uses closed‐form analytical equations to estimate the runoff capture efficiency and required storage capacity. Results from these analytical equations are validated by comparing with continuous simulation results and close agreements are observed. These analytical equations are therefore proposed as a computationally efficient alternative for analyzing the hydrologic performance of combined sewer overflow tanks.
Macrostrat: A Platform for Geological Data Integration and Deep‐Time Earth Crust Research
Authors: Peters Shanan E. , Husson Jon M. , Czaplewski John 
Published: April 2018

AbstractCharacterizing the lithology, age, and physical‐chemical properties of rocks and sediments in the Earth's upper crust is necessary to fully assess energy, water, and mineral resources and to address many fundamental questions. Although a large number of geological maps, regional geological syntheses, and sample‐based measurements have been produced, there is no openly available database that integrates rock record‐derived data, while also facilitating large‐scale, quantitative characterization of the volume, age, and material properties of the upper crust. Here we describe Macrostrat, a relational geospatial database and supporting cyberinfrastructure that is designed to enable quantitative spatial and geochronological analyses of the entire assemblage of surface and subsurface sedimentary, igneous, and metamorphic rocks. Macrostrat contains general, comprehensive summaries of the age and properties of 33,903 lithologically and chronologically defined geological units distributed across 1,474 regions in North and South America, the Caribbean, New Zealand, and the deep sea. Sample‐derived data, including fossil occurrences in the Paleobiology Database, more than 180,000 geochemical and outcrop‐derived measurements, and more than 2.3 million bedrock geologic map units from over 200 map sources, are linked to specific Macrostrat units and/or lithologies. Macrostrat has generated numerous quantitative results and its infrastructure is used as a data platform in several independently developed mobile applications. It is necessary to expand geographic coverage and to refine age models and material properties to arrive at a more precise characterization of the upper crust globally and test fundamental hypotheses about the long‐term evolution of Earth systems.
Temporal Markov Processes for Transport in Porous Media: Random Lattice Networks
Authors: Delgoshaie Amir H. , Jenny Patrick , Tchelepi Hamdi A. 
Published: April 2018

AbstractMonte Carlo (MC) simulations of transport in random porous networks indicate that for high variances of the lognormal permeability distribution, the transport of a passive tracer is non‐Fickian. Here we model this non‐Fickian dispersion in random porous networks using discrete temporal Markov models. We show that such temporal models capture the spreading behavior accurately. This is true despite the fact that the slow velocities are strongly correlated in time, and some studies have suggested that the persistence of low velocities would render the temporal Markovian model inapplicable. Compared to previously proposed temporal stochastic differential equations with case‐specific drift and diffusion terms, the models presented here require fewer modeling assumptions. Moreover, we show that discrete temporal Markov models can be used to represent dispersion in unstructured networks, which are widely used to model porous media. A new method is proposed to extend the state space of temporal Markov models to improve the model predictions in the presence of extremely low velocities in particle trajectories and extend the applicability of the model to higher temporal resolutions. Finally, it is shown that by combining multiple transitions, temporal models are more efficient for computing particle evolution compared to correlated CTRW with spatial increments that are equal to the lengths of the links in the network.
Chromatin conformation regulates the coordination between DNA replication and transcription
Authors: Almeida Ricardo , Fernández-Justel José Miguel , Santa-María Cristina , Cadoret Jean-Charles , Cano-Aroca Laura , Lombraña Rodrigo , Herranz Gonzalo , Agresti Alessandra , Gómez María 
Published: April 2018

AbstractChromatin is the template for the basic processes of replication and transcription, making the maintenance of chromosomal integrity critical for cell viability. To elucidate how dividing cells respond to alterations in chromatin structure, here we analyse the replication programme of primary cells with altered chromatin configuration caused by the genetic ablation of the HMGB1 gene, or three histone H1 genes. We find that loss of chromatin compaction in H1-depleted cells triggers the accumulation of stalled forks and DNA damage as a consequence of transcription–replication conflicts. In contrast, reductions in nucleosome occupancy due to the lack of HMGB1 cause faster fork progression without impacting the initiation landscape or fork stability. Thus, perturbations in chromatin integrity elicit a range of responses in the dynamics of DNA replication and transcription, with different consequences on replicative stress. These findings have broad implications for our understanding of how defects in chromatin structure contribute to genomic instability.
The IL-33-PIN1-IRAK-M axis is critical for type 2 immunity in IL-33-induced allergic airway inflammation
Authors: Nechama Morris , Kwon Jeahoo , Wei Shuo , Tun-Kyi Adrian , Welner Robert S. , Ben-Dov Iddo Z. , Arredouani Mohamed S. , Asara John M. , Chen Chun-Hau , Tsai Cheng-Yu , Nelson Kyle F. , Kobayashi Koichi S , Israel Elliot , Zhou Xiao Zhen , Nicholson Linda K. , Lu Kun Ping 
Published: April 2018

AbstractInterleukin 33 (IL-33) is among the earliest-released cytokines in response to allergens that orchestrate type 2 immunity. The prolyl cis-trans isomerase PIN1 is known to induce cytokines for eosinophil survival and activation by stabilizing cytokines mRNAs, but the function of PIN1 in upstream signaling pathways in asthma is unknown. Here we show that interleukin receptor associated kinase M (IRAK-M) is a PIN1 target critical for IL-33 signaling in allergic asthma. NMR analysis and docking simulations suggest that PIN1 might regulate IRAK-M conformation and function in IL-33 signaling. Upon IL-33-induced airway inflammation, PIN1 is activated for binding with and isomerization of IRAK-M, resulting in IRAK-M nuclear translocation and induction of selected proinflammatory genes in dendritic cells. Thus, the IL-33-PIN1-IRAK-M is an axis critical for dendritic cell activation, type 2 immunity and IL-33 induced airway inflammation.
A B-ARR-mediated cytokinin transcriptional network directs hormone cross-regulation and shoot development
Authors: Xie Mingtang , Chen Hongyu , Huang Ling , O’Neil Ryan C. , Shokhirev Maxim N. , Ecker Joseph R. 
Published: April 2018

AbstractCytokinin fulfills its diverse roles in planta through a series of transcriptional responses. We identify the in vivo DNA binding site profiles for three genetically redundant type-B ARABIDOPSIS RESPONSE REGULATORS (B-ARRs): ARR1, ARR10, and ARR12. The expression and genome-wide DNA binding locations of the three B-ARRs extensively overlap. Constructing a primary cytokinin response transcriptional network reveals a recurring theme of widespread cross-regulation between the components of the cytokinin pathway and other plant hormone pathways. The B-ARRs are found to have similar DNA binding motifs, though sequences flanking the core motif were degenerate. Cytokinin treatments amalgamate the three different B-ARRs motifs to identical DNA binding signatures (AGATHY, H(a/t/c), Y(t/c)) which suggests cytokinin may regulate binding activity of B-ARR family members. Furthermore, we find that WUSCHEL, a key gene required for apical meristem maintenance, is a cytokinin-dependent B-ARR target gene, demonstrating the importance of the cytokinin transcription factor network in shoot development.
Allostatic load as a predictor of grey matter volume and white matter integrity in old age: The Whitehall II MRI study
Authors: Zsoldos Enikő , Filippini Nicola , Mahmood Abda , Mackay Clare E. , Singh-Manoux Archana , Kivimäki Mika , Jenkinson Mark , Ebmeier Klaus P. 
Published: April 2018

AbstractThe allostatic load index quantifies the cumulative multisystem physiological response to chronic everyday stress, and includes cardiovascular, metabolic and inflammatory measures. Despite its central role in the stress response, research of the effect of allostatic load on the ageing brain has been limited. We investigated the relation of mid-life allostatic load index and multifactorial predictors of stroke (Framingham stroke risk) and diabetes (metabolic syndrome) with voxelwise structural grey and white matter brain integrity measures in the ageing Whitehall II cohort (N = 349, mean age = 69.6 (SD 5.2) years, N (male) = 281 (80.5%), mean follow-up before scan = 21.4 (SD 0.82) years). Higher levels of all three markers were significantly associated with lower grey matter density. Only higher Framingham stroke risk was significantly associated with lower white matter integrity (low fractional anisotropy and high mean diffusivity). Our findings provide some empirical support for the concept of allostatic load, linking the effect of everyday stress on the body with features of the ageing human brain.
The observed alteration in BCL2 expression following lithium treatment is influenced by the choice of normalization method
Authors: Odeya Damri , Galila Agam , Lilah Toker 
Published: April 2018

AbstractUpregulation of B-cell CLL/lymphoma (BCL)2 expression following lithium treatment is seemingly well established and has been related to the neuroprotective property of the drug. However, while demonstrated by some (but not all) studies based on low-throughput techniques (e.g. qPCR) this effect is not reflected in high-throughput studies, such as microarrays and RNAseq. This manuscript presents a systematic review of currently available reports of lithium’s effect on BCL2 expression. To our surprise, we found that the majority of the literature does not support the effect of lithium on BCL2 transcript or protein levels. Moreover, among the positive reports, several used therapeutically irrelevant lithium doses while others lack statistical power. We also noticed that numerous low-throughput studies normalized the signal using genes/proteins affected by lithium, imposing possible bias. Using wet bench experiments and reanalysis of publicly available microarray data, here we show that the reference gene chosen for normalization critically impacts the outcome of qPCR analyses of lithium’s effect on BCL2 expression. Our findings suggest that experimental results might be severely affected by the choice of normalizing genes, and emphasize the need to re-evaluate stability of these genes in the context of the specific experimental conditions.
Amniotic fluid C-reactive protein as a predictor of infection in caesarean section: a feasibility study
Authors: Marchocki Zbigniew , Vinturache Angela , Collins Kevin , O’ Reilly Paddy , O’Donoghue Keelin 
Published: April 2018

AbstractThis study evaluated the feasibility of maternal C-reactive protein (CRP) in amniotic fluid (AF) as a predictor of post-partum infection in women who undergo emergency or elective caesarean section (CS). AF bacterial culture and levels of hs-CRP in maternal serum and AF were evaluated in Day 0 and three days thereafter (Day 3) in 79 women undergoing CS. Univariate analyses assessed the clinical and demographic characteristics, whereas the ROC curves assessed the feasibility of hs-CRP as marker of inflammation in women who undergo CS. There was no difference in AF, Day 0, and Day 3 serum hs-CRP levels between women with sterile compared to those with bacterial growth in AF. Among women with positive AF cultures, AF and Day 0 serum hs-CRP levels were higher in women who underwent emergency compared to those who had elective CS (p = 0.04, and p = 0.02 respectively). hs-CRP in Day 0 and Day 3 serum but not in AF has a fair predictor value of infection in emergency CS only (AUC 0.767; 95% CI 0.606–0.928, and AUC 0.791; 95% CI 0.645–0.036, respectively). We conclude that AF hs-CRP is not feasible in assessing the risk of post-cesarean inflammation or infection.
Spatial patterning of the Notch ligand Dll4 controls endothelial sprouting in vitro
Authors: Tiemeijer L. A. , Frimat J-P. , Stassen O. M. J. A. , Bouten C. V. C. , Sahlgren C. M. 
Published: April 2018

AbstractAngiogenesis, the formation of new blood vessels, is a vital process for tissue growth and development. The Notch cell-cell signalling pathway plays an important role in endothelial cell specification during angiogenesis. Dll4 - Notch1 signalling directs endothelial cells into migrating tip or proliferating stalk cells. We used the directing properties of Dll4 to spatially control endothelial cell fate and the direction of endothelial sprouts. We created linear arrays of immobilized Dll4 using micro contact printing. HUVECs were seeded perpendicular to these Dll4 patterns using removable microfluidic channels. The Notch activating properties of surface immobilized Dll4 were confirmed by qPCR. After induction of sprouting, microscopic images of fluorescently labelled endothelial sprouts were analysed to determine the direction and the efficiency of controlled sprouting (Ecs). Directionality analysis of the sprouts showed the Dll4 pattern changes sprout direction from random to unidirectional. This was confirmed by the increase of Ecs from 54.5 ± 3.1% for the control, to an average of 84.7 ± 1.86% on the Dll4 patterned surfaces. Our data demonstrates a surface-based method to spatially pattern Dll4 to gain control over endothelial sprout location and direction. This suggests that spatial ligand patterning can be used to provide control over (neo) vascularization.
Tissue remodeling after ocular surface reconstruction with denuded amniotic membrane
Authors: Jie Jing , Yang Jie , He Hui , Zheng Jianlan , Wang Wenyan , Zhang Liying , Li Zhiyuan , Chen Jingyao , Vimalin Jeyalatha M. , Dong Nuo , Wu Huping , Liu Zuguo , Li Wei 
Published: April 2018

AbstractAmniotic membrane (AM) has been widely used as a temporary or permanent graft in the treatment of various ocular surface diseases. In this study, we compared the epithelial wound healing and tissue remodeling after ocular surface reconstruction with intact amniotic membrane (iAM) or denuded amniotic membrane (dAM). Partial limbal and bulbar conjunctival removal was performed on New Zealand rabbits followed by transplantation of cryo-preserved human iAM or dAM. In vivo observation showed that the epithelial ingrowth was faster on dAM compared to iAM after AM transplantation. Histological observation showed prominent epithelial stratification and increased goblet cell number on dAM after 2 weeks of follow up. Collagen VII degraded in dAM within 2 weeks, while remained in iAM even after 3 weeks. The number of macrophages and α-SMA positive cells in the stroma of remodelized conjunctiva in the dAM transplantation group was considerably less. In conclusion, dAM facilitates epithelial repopulation and goblet cell differentiation, further reduces inflammation and scar formation during conjunctival and corneal limbal reconstruction.
On-chip generation of microbubbles in photoacoustic contrast agents for dual modal ultrasound/photoacoustic in vivo animal imaging
Authors: Das Dhiman , Sivasubramanian Kathyayini , Yang Chun , Pramanik Manojit 
Published: April 2018

AbstractDual-modal photoacoustic (PA) and ultrasound (US) contrast agents are becoming increasingly popular in recent years. Here, a flow-focusing junction based microfluidic device is used for the generation of nitrogen microbubbles (<7 μm) in two photoacoustic contrast agents: methylene blue (MB) and black ink (BI). The microbubble diameter and production rate could be precisely controlled in both MB and BI solutions. Microbubbles were collected from the outlet of the microfluidic device and optical microscope was used to study the size distributions in both solutions. Next, the microbubbles in both solutions were injected into tubes for phantom imaging experiments. Signal to noise ratio (SNR) of both US, PA imaging experiments were calculated to be 51 dB, 58 dB in MB + microbubbles and 56 dB, 61 dB in BI + microbubbles, respectively. Finally, the microbubbles were injected into the urinary bladder of rats for in vivo animal imaging. The SNR in US imaging with MB + microbubbles and BI + microbubbles were 41 dB and 48 dB, respectively. Similarly, the SNR in PA imaging with the same solutions were 32 dB and 36 dB, respectively. The effect of size and concentration of microbubbles in both MB and BI solutions, on the US and PA signals, has been examined.