bluuebunny/crossref_metadata_2025_split huggingface dataset:
Equivalence of Discrete Fracture Network and Porous Media Models by Hydraulic Tomography
Authors: Dong Yanhui , Fu Yunmei , Yeh Tian‐Chyi Jim , Wang Yu‐Li , Zha Yuanyuan , Wang Liheng , Hao Yonghong 
Published: March 2019

AbstractHydraulic tomography (HT) has emerged as a potentially viable method for mapping fractures in geologic media as demonstrated by recent studies. However, most of the studies adopted equivalent porous media (EPM) models to generate and invert hydraulic interference test data for HT. While these models assign significant different hydraulic properties to fractures and matrix, they may not fully capture the discrete nature of the fractures in the rocks. As a result, HT performance may have been overrated. To explore this issue, this study employed a discrete fracture network (DFN) model to simulate hydraulic interference tests. HT with the EPM model was then applied to estimate the distributions of hydraulic conductivity (K) and specific storage (Ss) of the DFN. Afterward, the estimated fields were used to predict the observed heads from DFN models, not used in the HT analysis (i.e., validation). Additionally, this study defined the spatial representative elementary volume (REV) of the fracture connectivity probability for the entire DFN dominant. The study showed that if this spatial REV exists, the DFN is deemed equivalent to EPM and vice versa. The hydraulic properties estimated by HT with an EPM model can then predict head fields satisfactorily over the entire DFN domain with limited monitoring wells. For a sparse DFN without this spatial REV, a dense observation network is needed. Nevertheless, HT is able to capture the dominant fractures.
Fast Warming of the Surface Ocean Under a Climatological Scenario
Authors: Jamet Q. , Dewar W. K. , Wienders N. , Deremble B. 
Published: March 2019

AbstractWe examine various strategies for forcing ocean‐only models, including an atmospheric boundary layer model. This surface forcing allows air‐sea exchanges to affect atmospheric temperature and relative humidity, thus removing the assumption of an infinite atmospheric heat capacity associated with the prescription of these variables. When exposed to climatological winds, the simulated North Atlantic oceanic temperature warms considerably at the surface as compared to a model with full atmospheric variability. This warming is mainly explained by a weakened upper‐ocean vertical mixing in response to the weakly varying climatological winds. Specifying the atmospheric temperatures inhibits this warming but depends on the unrealistic large atmospheric heat capacity. We thus interpret the simulated warmer ocean as a more physically consistent ocean response. We conclude the use of an atmospheric boundary layer model provides many benefits for ocean only modeling, although a “normal” year strategy is required for maintaining high‐frequency winds.
Thank You to Our 2018 Peer Reviewers
Authors: East Amy E. , Buffington John , Coco Giovanni , Finnegan Noah J. , Hoitink Ton A. J. F. , Hubbard Bryn 
Published: March 2019

AbstractThe process of completing and communicating rigorous, high‐impact science depends heavily on obtaining quality peer review prior to publication. As AGU journals strive continually to publish excellent work, we recognize the demand that this places on reviewers' time, especially as most of us seem to receive ever‐increasing numbers of requests to review manuscripts. JGR‐Earth Surface typically strives to obtain three reviews per manuscript, to best ensure the quality of the science that we publish. We thank the members of the earth‐surface community who volunteered their time to complete these reviews for JGR‐Earth Surface in 2018: a total of 874 reviews provided by 650 scientists. We greatly appreciate your time, your thoughtful and constructive review comments, and especially your dedication to this all‐important part of producing high‐quality science.
Telomere length is associated with childhood trauma in patients with severe mental disorders
Authors: Aas Monica , Elvsåshagen Torbjørn , Westlye Lars T. , Kaufmann Tobias , Athanasiu Lavinia , Djurovic Srdjan , Melle Ingrid , van der Meer Dennis , Martin-Ruiz Carmen , Steen Nils Eiel , Agartz Ingrid , Andreassen Ole A. 
Published: March 2019

AbstractReduced telomere length (TL) and structural brain abnormalities have been reported in patients with schizophrenia (SZ) and bipolar disorder (BD). Childhood traumatic events are more frequent in SZ and BD than in healthy individuals (HC), and based on recent findings in healthy individuals could represent one important factor for TL and brain aberrations in patients. The study comprised 1024 individuals (SZ [n = 373]; BD [n = 249] and HC [n = 402]). TL was measured by quantitative polymerase chain reaction (qPCR), and childhood trauma was assessed using the Childhood Trauma Questionnaire (CTQ). Diagnosis was obtained by the Structured Clinical Interview (SCID) for the diagnostic and statistical manual of mental disorders-IV (DSM-IV). FreeSurfer was used to obtain regional and global brain volumes from T1-weighted magnetic resonance imaging (MRI) brain scans. All analyses were adjusted for current age and sex. Patients had on average shorter TL (F = 7.87, p = 0.005, Cohen’s d = 0.17) and reported more childhood trauma experiences than HC (χ2 = 148.9, p < 0.001). Patients with a history of childhood sexual, physical or emotional abuse had shorter TL relative to HC and to patients without a history of childhood abuse (F = 6.93, p = 0.006, Cohen’s d = 0.16). After adjusting for childhood abuse, no difference in TL was observed between patients and HC (p = 0.12). There was no statistically significant difference in reported childhood abuse exposure or TL between SZ and BD. Our analyses revealed no significant associations between TL and clinical characteristics or brain morphometry. We demonstrate shorter TL in SZ and BD compared with HC and showed that TL is sensitive to childhood trauma experiences. Further studies are needed to identify the biological mechanisms of this relationship.
A comprehensive, mechanistically detailed, and executable model of the cell division cycle in Saccharomyces cerevisiae
Authors: Münzner Ulrike , Klipp Edda , Krantz Marcus 
Published: March 2019

AbstractUnderstanding how cellular functions emerge from the underlying molecular mechanisms is a key challenge in biology. This will require computational models, whose predictive power is expected to increase with coverage and precision of formulation. Genome-scale models revolutionised the metabolic field and made the first whole-cell model possible. However, the lack of genome-scale models of signalling networks blocks the development of eukaryotic whole-cell models. Here, we present a comprehensive mechanistic model of the molecular network that controls the cell division cycle in Saccharomyces cerevisiae. We use rxncon, the reaction-contingency language, to neutralise the scalability issues preventing formulation, visualisation and simulation of signalling networks at the genome-scale. We use parameter-free modelling to validate the network and to predict genotype-to-phenotype relationships down to residue resolution. This mechanistic genome-scale model offers a new perspective on eukaryotic cell cycle control, and opens up for similar models—and eventually whole-cell models—of human cells.
Optimal features for auditory categorization
Authors: Liu Shi Tong , Montes-Lourido Pilar , Wang Xiaoqin , Sadagopan Srivatsun 
Published: March 2019

AbstractHumans and vocal animals use vocalizations to communicate with members of their species. A necessary function of auditory perception is to generalize across the high variability inherent in vocalization production and classify them into behaviorally distinct categories (‘words’ or ‘call types’). Here, we demonstrate that detecting mid-level features in calls achieves production-invariant classification. Starting from randomly chosen marmoset call features, we use a greedy search algorithm to determine the most informative and least redundant features necessary for call classification. High classification performance is achieved using only 10–20 features per call type. Predictions of tuning properties of putative feature-selective neurons accurately match some observed auditory cortical responses. This feature-based approach also succeeds for call categorization in other species, and for other complex classification tasks such as caller identification. Our results suggest that high-level neural representations of sounds are based on task-dependent features optimized for specific computational goals.
The exonuclease Xrn1 activates transcription and translation of mRNAs encoding membrane proteins
Authors: Blasco-Moreno Bernat , de Campos-Mata Leire , Böttcher René , García-Martínez José , Jungfleisch Jennifer , Nedialkova Danny D. , Chattopadhyay Shiladitya , Gas María-Eugenia , Oliva Baldomero , Pérez-Ortín José E. , Leidel Sebastian A. , Choder Mordechai , Díez Juana 
Published: March 2019

AbstractThe highly conserved 5’–3’ exonuclease Xrn1 regulates gene expression in eukaryotes by coupling nuclear DNA transcription to cytosolic mRNA decay. By integrating transcriptome-wide analyses of translation with biochemical and functional studies, we demonstrate an unanticipated regulatory role of Xrn1 in protein synthesis. Xrn1 promotes translation of a specific group of transcripts encoding membrane proteins. Xrn1-dependence for translation is linked to poor structural RNA contexts for translation initiation, is mediated by interactions with components of the translation initiation machinery and correlates with an Xrn1-dependence for mRNA localization at the endoplasmic reticulum, the translation compartment of membrane proteins. Importantly, for this group of mRNAs, Xrn1 stimulates transcription, mRNA translation and decay. Our results uncover a crosstalk between the three major stages of gene expression coordinated by Xrn1 to maintain appropriate levels of membrane proteins.
Ultra-strong long-chain polyamide elastomers with programmable supramolecular interactions and oriented crystalline microstructures
Authors: Song Lingzhi , Zhu Tianyu , Yuan Liang , Zhou Jiangjun , Zhang Yaqiong , Wang Zhongkai , Tang Chuanbing 
Published: March 2019

AbstractPolyamides are one of the most important polymers. Long-chain aliphatic polyamides could bridge the gap between traditional polyamides and polyethylenes. Here we report an approach to preparing sustainable ultra-strong elastomers from biomass-derived long-chain polyamides by thiol-ene addition copolymerization with diamide diene monomers. The pendant polar hydroxyl and non-polar butyrate groups between amides allow controlled programming of supramolecular hydrogen bonding and facile tuning of crystallization of polymer chains. The presence of thioether groups on the main chain can further induce metal–ligand coordination (cuprous-thioether). Unidirectional step-cycle tensile deformation has been applied to these polyamides and significantly enhances tensile strength to over 210 MPa while maintaining elasticity. Uniaxial deformation leads to a rearrangement and alignment of crystalline microstructures, which is responsible for the mechanical enhancement. These chromophore-free polyamides are observed with strong luminescence ascribed to the effect of aggregation-induced emission (AIE), originating from the formation of amide clusters with restricted molecular motions.
Slab morphology and deformation beneath Izu-Bonin
Authors: Zhang Haijiang , Wang Fan , Myhill Robert , Guo Hao 
Published: March 2019

AbstractSeismic tomography provides unique constraints on the morphology, the deformation, and (indirectly) the rheology of subducting slabs. We use teleseismic double-difference P-wave tomography to image with unprecedented clarity the structural complexity of the Izu-Bonin slab. We resolve a tear in the slab in the mantle transition zone (MTZ) between 26.5° N and 28° N. North of the tear, the slab is folded in the MTZ. Immediately above the fold hinge, a zone of reduced P-wavespeed may result from viscous dissipation within an incipient shear zone. To the south of the tear, the slab overturns and lies flat at the base of the MTZ. The ~680 km deep 2015 Bonin earthquake (Mw~7.9) is located at the northernmost edge of the overturning part of the slab. The localised tearing, shearing and buckling of the Izu-Bonin slab indicates that it remains highly viscous throughout the upper mantle and transition zone.
Cervicovaginal microbiota and local immune response modulate the risk of spontaneous preterm delivery
Authors: Elovitz Michal A. , Gajer Pawel , Riis Valerie , Brown Amy G. , Humphrys Michael S. , Holm Johanna B. , Ravel Jacques 
Published: March 2019

AbstractFailure to predict and understand the causes of preterm birth, the leading cause of neonatal morbidity and mortality, have limited effective interventions and therapeutics. From a cohort of 2000 pregnant women, we performed a nested case control study on 107 well-phenotyped cases of spontaneous preterm birth (sPTB) and 432 women delivering at term. Using innovative Bayesian modeling of cervicovaginal microbiota, seven bacterial taxa were significantly associated with increased risk of sPTB, with a stronger effect in African American women. However, higher vaginal levels of β-defensin-2 lowered the risk of sPTB associated with cervicovaginal microbiota in an ethnicity-dependent manner. Surprisingly, even in Lactobacillus spp. dominated cervicovaginal microbiota, low β-defensin-2 was associated with increased risk of sPTB. These findings hold promise for diagnostics to accurately identify women at risk for sPTB early in pregnancy. Therapeutic strategies could include immune modulators and microbiome-based therapeutics to reduce this significant health burden.
Polarization-state-resolved high-harmonic spectroscopy of solids
Authors: Klemke N. , Tancogne-Dejean N. , Rossi G. M. , Yang Y. , Scheiba F. , Mainz R. E. , Di Sciacca G. , Rubio A. , Kärtner F. X. , Mücke O. D. 
Published: March 2019

AbstractAttosecond metrology sensitive to sub-optical-cycle electronic and structural dynamics is opening up new avenues for ultrafast spectroscopy of condensed matter. Using intense lightwaves to precisely control the fast carrier dynamics in crystals holds great promise for next-generation petahertz electronics and devices. The carrier dynamics can produce high-order harmonics of the driving field extending up into the extreme-ultraviolet region. Here, we introduce polarization-state-resolved high-harmonic spectroscopy of solids, which provides deeper insights into both electronic and structural sub-cycle dynamics. Performing high-harmonic generation measurements from silicon and quartz, we demonstrate that the polarization states of the harmonics are not only determined by crystal symmetries, but can be dynamically controlled, as a consequence of the intertwined interband and intraband electronic dynamics. We exploit this symmetry-dynamics duality to efficiently generate coherent circularly polarized harmonics from elliptically polarized pulses. Our experimental results are supported by ab-initio simulations, providing evidence for the microscopic origin of the phenomenon.
Syngas to light olefins conversion with high olefin/paraffin ratio using ZnCrOx/AlPO-18 bifunctional catalysts
Authors: Su Junjie , Zhou Haibo , Liu Su , Wang Chuanming , Jiao Wenqian , Wang Yangdong , Liu Chang , Ye Yingchun , Zhang Lin , Zhao Yu , Liu Hongxing , Wang Dong , Yang Weimin , Xie Zaiku , He Mingyuan 
Published: March 2019

AbstractDirect synthesis of light olefins from syngas (STO) using a bifunctional catalyst composed of oxide and zeolite has attracted extensive attention in both academia and industry. It is highly desirable to develop robust catalysts that could enhance the CO conversion while simultaneously maintain high selectivity to C2-C4 olefins. Herein, we report a bifunctional catalyst consisting of ZnCr binary oxide (ZnCrOx) and low-Si AlPO-18 zeolite, showing both satisfying selectivity to C2-C4 olefins of 45.0% (86.7%, CO2free) and high olefin/paraffin ratio of 29.9 at the CO conversion of 25.2% under mild reaction conditions (4.0 MPa, 390 °C). By optimizing the reaction conditions, the CO conversion could be markedly increased to 49.3% with a slight drop in selectivity. CD3CN/CO-FTIR characterizations and theoretical calculations demonstrate that low-Si AlPO-18 zeolite has lower acid strength, and is therefore less reactive toward the hydride transfer in the STO reaction, leading to a higher olefin/paraffin ratio.
Spinal sagittal alignment and trapezoidal deformity in patients with degenerative cervical spondylolisthesis
Authors: Murata Kazuma , Endo Kenji , Suzuki Hidekazu , Matsuoka Yuji , Takamatsu Taichiro , Nishimura Hirosuke , Yamamoto Kengo 
Published: March 2019

AbstractDegenerative cervical spondylolisthesis (DCS) is a cervical deformity arising from regressive changes where trapezoidal deformity characterized by hypertrophic osteophytes of spinal elements is often observed. There is a paucity of literature about the spinal contour of DCS and trapezoidal vertebrae. We conducted this research to clarify the relationship between spinal sagittal alignment and trapezoidal deformity in DCS. Total seventy-nine patients with cervical spondylosis were enrolled. Twenty-four patients who exhibited cervical spondylolisthesis were classified into DCS group. Other patients were classified into a control group. Measurements of radiographic parameters and trapezoidal deformity were made. DCS was found mostly in C3-C4 and C4-C5 (16 and 10 cases, respectively). T1S and T1-T4 TK was larger in the DCS group than in the control (T1S: 29.9 ± 2.3° vs. 23.7 ± 1.5°, T1-T4 TK: 14.9 ± 2.1° vs. 9.0 ± 1.4°). C2-C7A was smaller in DCS (3.5 ± 3.6° vs. 11.9 ± 2.3°). Trapezoidal deformity was apparent in the vertebra below the slipped segment. Among sagittal parameters, T1S and T1-T4 TK were positively correlated with DCS (r = 0.523 and r = 0.438, respectively). For these correlations with DCS, both logistic and linear regression models predicted threshold values of approximately 30° for T1S and 15° for T1-T4 TK responsible for DCS. DCS was mostly found in the middle cervical region. Among sagittal parameters, enlarged T1S and T1-T4 TK, which were strongly correlated with amount of slippage, was considered affected to DCS. Cervical kyphosis and trapezoidal deformity also exhibited strong correlations with DCS, and were considered responsible for clinical instability.
Simultaneous production of two kinds of sounds in relation with sonic mechanism in the boxfish Ostracion meleagris and O. cubicus
Authors: Parmentier Eric , Solagna Laura , Bertucci Frédéric , Fine Michael L. , Nakae Masanori , Compère Philippe , Smeets Sarah , Raick Xavier , Lecchini David 
Published: March 2019

AbstractIn fishes, sonic abilities for communication purpose usually involve a single mechanism. We describe here the sonic mechanism and sounds in two species of boxfish, the spotted trunkfish Ostracion meleagris and the yellow boxfish Ostracion cubicus. The sonic mechanism utilizes a T-shaped swimbladder with a swimbladder fenestra and two separate sonic muscle pairs. Extrinsic vertical muscles attach to the vertebral column and the swimbladder. Perpendicularly and below these muscles, longitudinal intrinsic muscles cover the swimbladder fenestra. Sounds are exceptional since they are made of two distinct types produced in a sequence. In both species, humming sounds consist of long series (up to 45 s) of hundreds of regular low-amplitude pulses. Hums are often interspersed with irregular click sounds with an amplitude that is ten times greater in O. meleagris and forty times greater in O. cubicus. There is no relationship between fish size and many acoustic characteristics because muscle contraction rate dictates the fundamental frequency. We suggest that hums and clicks are produced by either separate muscles or by a combination of the two. The mechanism complexity supports an investment of boxfish in this communication channel and underline sounds as having important functions in their way of life.
Hierarchical Reconstruction of High-Resolution 3D Models of Large Chromosomes
Authors: Trieu Tuan , Oluwadare Oluwatosin , Cheng Jianlin 
Published: March 2019

AbstractEukaryotic chromosomes are often composed of components organized into multiple scales, such as nucleosomes, chromatin fibers, topologically associated domains (TAD), chromosome compartments, and chromosome territories. Therefore, reconstructing detailed 3D models of chromosomes in high resolution is useful for advancing genome research. However, the task of constructing quality high-resolution 3D models is still challenging with existing methods. Hence, we designed a hierarchical algorithm, called Hierarchical3DGenome, to reconstruct 3D chromosome models at high resolution (<=5 Kilobase (KB)). The algorithm first reconstructs high-resolution 3D models at TAD level. The TAD models are then assembled to form complete high-resolution chromosomal models. The assembly of TAD models is guided by a complete low-resolution chromosome model. The algorithm is successfully used to reconstruct 3D chromosome models at 5 KB resolution for the human B-cell (GM12878). These high-resolution models satisfy Hi-C chromosomal contacts well and are consistent with models built at lower (i.e. 1 MB) resolution, and with the data of fluorescent in situ hybridization experiments. The Java source code of Hierarchical3DGenome and its user manual are available here https://github.com/BDM-Lab/Hierarchical3DGenome.
Urtica dioica L. inhibits proliferation and enhances cisplatin cytotoxicity in NSCLC cells via Endoplasmic Reticulum-stress mediated apoptosis
Authors: D’Abrosca Brigida , Ciaramella Vincenza , Graziani Vittoria , Papaccio Federica , Della Corte Carminia Maria , Potenza Nicoletta , Fiorentino Antonio , Ciardiello Fortunato , Morgillo Floriana 
Published: March 2019

AbstractNon-small cell lung cancer (NSCLC) is the most common type of lung cancer and the ineffectiveness of the current therapies seriously limits the survival rate of NSCLC patients. In the search for new antitumor agents, nature has played a pivotal role providing a variety of molecules, which are likely to exert selective anti-tumour properties. Herein, we investigated the antiproliferative potential of Urtica dioica L. extract (UD) against NSCLC cell models with low sensitivity to cisplatin, a cytotoxic agent largely employed to cure NSCLCs. UD inhibited cell proliferation in the selected cells, while no toxic effects were observed in normal lung cells. Furthermore, the co-treatment of UD and cisplatin notably sensitised NSCLC cells to cisplatin. Mechanistically, we discovered that UD-promoted endoplasmic reticulum (ER) stress via activation of the growth arrest and DNA damage-inducible gene 153 (GADD153) triggering apoptosis. We also performed an extensive NMR analysis of UD, identifying rutin and oxylipins as the main secondary metabolites present in the mixture. Additionally, we discovered that an oxylipins’ enriched fraction contributes to the antiproliferative activity of the plant extract. In the future, this study may provide new chemical scaffolds for the design of anti-cancer agents that target NSCLCs with low sensitivity to cisplatinum.