bluuebunny/crossref_metadata_2025 huggingface dataset:
Technical Note: 3D localization of lung tumors on cone beam CT projections via a convolutional recurrent neural network
Authors: Wang Chuang , Hunt Margie , Zhang Lei , Rimner Andreas , Yorke Ellen , Lovelock Michael , Li Xiang , Li Tianfang , Mageras Gig , Zhang Pengpeng
Published: January 2020

Purpose

To design a convolutional recurrent neural network (CRNN) that calculates three‐dimensional (3D) positions of lung tumors from continuously acquired cone beam computed tomography (CBCT) projections, and facilitates the sorting and reconstruction of 4D‐CBCT images.

Method

Under an IRB‐approved clinical lung protocol, kilovoltage (kV) projections of the setup CBCT were collected in free‐breathing. Concurrently, an electromagnetic signal‐guided system recorded motion traces of three transponders implanted in or near the tumor. Convolutional recurrent neural network was designed to utilize a convolutional neural network (CNN) for extracting relevant features of the kV projections around the tumor, followed by a recurrent neural network for analyzing the temporal patterns of the moving features. Convolutional recurrent neural network was trained on the simultaneously collected kV projections and motion traces, subsequently utilized to calculate motion traces solely based on the continuous feed of kV projections. To enhance performance, CRNN was also facilitated by frequent calibrations (e.g., at 10° gantry rotation intervals) derived from cross‐correlation‐based registrations between kV projections and templates created from the planning 4DCT. Convolutional recurrent neural network was validated on a leave‐one‐out strategy using data from 11 lung patients, including 5500 kV images. The root‐mean‐square error between the CRNN and motion traces was calculated to evaluate the localization accuracy.

Result

Three‐dimensional displacement around the simulation position shown in the Calypso traces was 3.4 ± 1.7 mm. Using motion traces as ground truth, the 3D localization error of CRNN with calibrations was 1.3 ± 1.4 mm. CRNN had a success rate of 86 ± 8% in determining whether the motion was within a 3D displacement window of 2 mm. The latency was 20 ms when CRNN ran on a high‐performance computer cluster.

Conclusions

CRNN is able to provide accurate localization of lung tumors with aid from frequent recalibrations using the conventional cross‐correlation‐based registration approach, and has the potential to remove reliance on the implanted fiducials.
A Transfer‐Learning Approach for Accelerated MRI Using Deep Neural Networks
Authors: Dar Salman Ul Hassan , Özbey Muzaffer , Çatlı Ahmet Burak , Çukur Tolga
Published: January 2020

Purpose

Neural networks have received recent interest for reconstruction of undersampled MR acquisitions. Ideally, network performance should be optimized by drawing the training and testing data from the same domain. In practice, however, large datasets comprising hundreds of subjects scanned under a common protocol are rare. The goal of this study is to introduce a transfer‐learning approach to address the problem of data scarcity in training deep networks for accelerated MRI.

Methods

Neural networks were trained on thousands (upto 4 thousand) of samples from public datasets of either natural images or brain MR images. The networks were then fine‐tuned using only tens of brain MR images in a distinct testing domain. Domain‐transferred networks were compared to networks trained directly in the testing domain. Network performance was evaluated for varying acceleration factors (4‐10), number of training samples (0.5‐4k), and number of fine‐tuning samples (0‐100).

Results

The proposed approach achieves successful domain transfer between MR images acquired with different contrasts (T1‐ and T2‐weighted images) and between natural and MR images (ImageNet and T1‐ or T2‐weighted images). Networks obtained via transfer learning using only tens of images in the testing domain achieve nearly identical performance to networks trained directly in the testing domain using thousands (upto 4 thousand) of images.

Conclusion

The proposed approach might facilitate the use of neural networks for MRI reconstruction without the need for collection of extensive imaging datasets.
Mapping of fatty acid composition with free‐breathing MR spectroscopic imaging and compressed sensing
Authors: Rioux James A. , Hewlett Miriam , Davis Christa , Bowen Chris V. , Brewer Kimberly , Clarke Sharon E. , Beyea Steven D.
Published: January 2020

Nonalcoholic fatty liver disease (NAFLD) is a growing health problem, and a major challenge in NAFLD management is identifying which patients are at risk of progression to more serious disease. Simple measurements of liver fat content are not strong predictors of clinical outcome, but biomarkers related to fatty acid composition (ie, saturated vs. unsaturated fat) may be more effective. MR spectroscopic imaging (MRSI) methods allow spatially resolved, whole‐liver measurements of chemical composition but are traditionally limited by slow acquisition times. In this work we present an accelerated MRSI acquisition based on spin echo single point imaging (SE‐SPI), which, using appropriate sampling and compressed sensing reconstruction, allows free‐breathing acquisition in a mouse model of fatty liver disease. After validating the technique's performance in oil/water phantoms, we imaged mice that had received a normal diet or a methionine and choline deficient (MCD) diet, some of which also received supplemental injections of iron to mimic hepatic iron overload. SE‐SPI was more resistant to the line‐broadening effects of iron than single‐voxel spectroscopy measurements, and was consistently able to measure the amplitudes of low‐intensity spectral peaks that are important to characterizing fatty acid composition. In particular, in the mice receiving the MCD diet, SE‐SPI showed a significant decrease in a metric associated with unsaturated fat, which is consistent with the literature. This or other related metrics may therefore offer more a specific biomarker of liver health than fat content alone. This preclinical study is an important precursor to clinical testing of the proposed method.

MR‐based quantification of fatty acid composition may allow for improved characterization of non‐alcoholic fatty liver disease. A spectroscopic imaging method with appropriate sampling strategy allows whole‐liver mapping of fat composition metrics in a free‐breathing mouse model. Changes in metrics like the surrogate unsaturation index (UIs) are visible in mice receiving a diet which induces fat accumulation in the liver, as compared to a normal diet; such metrics may prove useful in future clinical studies of liver disease.
Eismonde von Jupiter und Saturn
Authors: Wagner Roland
Published: January 2020

Seit 40 Jahren erforschen Sonden die Eismonde im äußeren Sonnensystem. Die Vielfalt dieser Körper, die mögliche Existenz von verborgenen Ozeanen und ihr Kryovulkanismus machen sie zu äußerst spannenden Himmelskörpern. Teil 1 dieses Zweiteilers stellt die Eismonde von Jupiter und Saturn vor. Jeder dieser Eismonde zeigt sich geologisch als eigene Welt. Bei den Jupitertrabanten ist die Oberfläche von Europa im Vergleich zu Ganymed geologisch sehr jung. Magnetfeldmessungen der Galileo‐Mission lassen unter der festen Eiskruste auf einen tiefen Ozean mit salzhaltigem Wasser schließen. Ein solcher Ozean existiert ebenfalls auf Callisto in größerer Tiefe, mutmaßlich auch auf Ganymed. Ganymed besitzt als einziger Eismond einen eisenhaltigen Kern, dessen starkes Magnetfeld das eines Ozeans überdeckt. Der Saturnmond Enceladus zeichnet sich durch aktiven Kryovulkanismus aus, der durch Gezeitenkräfte angetrieben ist.
Molecular mechanisms of vancomycin resistance
Authors: Stogios Peter J. , Savchenko Alexei
Published: January 2020

Vancomycin and related glycopeptides are drugs of last resort for the treatment of severe infections caused by Gram‐positive bacteria such as Enterococcus species, Staphylococcus aureus, and Clostridium difficile. Vancomycin was long considered immune to resistance due to its bactericidal activity based on binding to the bacterial cell envelope rather than to a protein target as is the case for most antibiotics. However, two types of complex resistance mechanisms, each comprised of a multi‐enzyme pathway, emerged and are now widely disseminated in pathogenic species, thus threatening the clinical efficiency of vancomycin. Vancomycin forms an intricate network of hydrogen bonds with the d‐Ala‐d‐Ala region of Lipid II, interfering with the peptidoglycan layer maturation process. Resistance to vancomycin involves degradation of this natural precursor and its replacement with d‐Ala‐d‐lac or d‐Ala‐d‐Ser alternatives to which vancomycin has low affinity. Through extensive research over 30 years after the initial discovery of vancomycin resistance, remarkable progress has been made in molecular understanding of the enzymatic cascades responsible. Progress has been driven by structural studies of the key components of the resistance mechanisms which provided important molecular understanding such as, for example, the ability of this cascade to discriminate between vancomycin sensitive and resistant peptidoglycan precursors. Important structural insights have been also made into the molecular evolution of vancomycin resistance enzymes. Altogether this molecular data can accelerate inhibitor discovery and optimization efforts to reverse vancomycin resistance. Here, we overview our current understanding of this complex resistance mechanism with a focus on the structural and molecular aspects.
Superionic State in Alumina Produced by Nonthermal Melting
Authors: Voronkov Roman A. , Medvedev Nikita , Volkov Alexander E.
Published: January 2020

Density functional–based molecular dynamics reveals a transient superionic state in Al2O3 produced by nonthermal phase transition under extreme electronic excitation. At electronic temperatures above Te ≈ 2.75 eV, the oxygen sublattice exhibits fluid behavior, whereas the aluminum sublattice is in a solid state. This state exists up to Te ≈ 3.25 eV, where Al2O3 turns metallic–superionic; at Te ≈ 3.75 eV, the aluminum sublattice disorders. Quenching the superionic state under pressure >400 GPa freezes it into a metastable mixed amorphous–crystalline phase where the oxygen subsystem is disordered solid, whereas the aluminum one is ordered.
An enhanced MAC protocol based on the IEEE 802.11 for data relay satellite systems
Authors: Wang Xingyu , Zhao Shanghong , Li Yongjun , Zhu Zhuodan , Zheng Yongxing , Yu Chen
Published: January 2020

Data relay satellite (DRS) systems play an important role in space information networks. Characterized by highly dynamic topology and discontinuous communication links, it is suggested that the IEEE 802.11 protocol employed in such a network could be more flexible. However, such a terrestrial network protocol could not be applied to DRS systems directly, nor supports a fast response due to the long propagation delay and severe packet collision. To address this challenge, we proposed an enhanced media access control (MAC) protocol based on the IEEE 802.11 protocol providing multiaccess for low earth orbit (LEO) distributed constellations. In this paper, we investigated the access delay performance of the proposed protocol in our model. Then, we derived a contention window adaption by using an iteration algorithm that can dynamically adjust the values of the contention window depending on the number of user satellites in the communication coverage. Simulation results show that the average access delay does not exceed 20 seconds, which is significantly lower than the standard protocol. Moreover, the traffic threshold is increased to 0.6, and the maximum throughput has doubled compared with the standard protocol. It is proved that the enhanced MAC protocol shows a better performance in DRS systems.
Two‐factor authentication using biometric based quantum operations
Authors: Sharma Mohit Kr , Nene Manisha J
Published: January 2020

Two‐way authentication methods are utilized in every online user authentication transactions. Use of one time passwords (OTP) have proved to be more secure method, than one factor authentication when the two authentication schemes are carried out on different media. However, current use of OTP restricts authentication to the device itself rather than the user. The fraud cases with OTP based transactions have also increased due to growth of technology. Hence, there is a requirement of enhancing security of OTP based transactions. The study in this paper anchors on mathematically proven properties of quantum cryptography and utilizes the quantum entanglement property to generate quantum OTP (QOTP) for authenticating the user based on its biometrics. The proposed method takes into consideration various quantum computing capabilities of user, thus paving path for gradual upgradation of infrastructure. The work in the paper gives the outline of infrastructure required for implementing the proposed model and concludes by comparing security analysis of existing and proposed model against man‐in‐the‐middle attack (MITM) and user end vulnerabilities to bring forth the importance of QOTP. The practical implementation of the proposed model is envisaged as future research work due to evolving nature of quantum experiments.
Metastable vacua in large-N QCD3
Authors: Armoni Adi , Dumitrescu Thomas T. , Festuccia Guido , Komargodski Zohar
Published: January 2020

Abstract

We reexamine the vacuum structure of three-dimensional quantum chromodynamics (QCD3) with gauge group SU(N), N

f
fundamental quark flavors, and a level-k Chern-Simons term. This analysis can be reliably carried out in the large-N, fixed N

f

, k limit of the theory, up to certain assumptions that we spell out explicitly. At leading order in the large-N expansion we find N

f
+ 1 distinct, exactly degenerate vacuum superselection sectors with different patterns of flavor-symmetry breaking. The associated massless Nambu-Goldstone bosons are generically accompanied by topological Chern-Simons theories. This set of vacua explicitly realizes many candidate phases previously proposed for QCD3. At subleading order in the large-N expansion, the exact degeneracy between the different superselection sectors is lifted, leading to a multitude of metastable vacua. If we dial the quark masses, different metastable vacua can become the true vacuum of the theory, leading to a sequence of first-order phase transitions. We show that this intricate large-N dynamics can be captured by the previously proposed bosonic dual theories for QCD3, provided these bosonic duals are furnished with a suitable scalar potential. Interestingly, this potential must include terms beyond quartic order in the scalar fields.
Thermal CFTs in momentum space
Authors: Manenti Andrea
Published: January 2020

Abstract

We study some aspects of conformal field theories at finite temperature in momentum space. We provide a formula for the Fourier transform of a thermal conformal block and study its analytic properties. In particular we show that the Fourier transform vanishes when the conformal dimension and spin are those of a “double twist” operator ∆ = 2∆ϕ+ℓ+ 2n. By analytically continuing to Lorentzian signature we show that the spectral density at high spatial momenta has support on the spectrum condition |ω| > |k|. This leads to a series of sum rules. Finally, we explicitly match the thermal block expansion with the momentum space Green’s function at finite temperature in several examples.
Kerr-Newman from minimal coupling
Authors: Moynihan Nathan
Published: January 2020

Abstract

We show that at 1PN all four-dimensional black hole solutions in asymptotically flat spacetimes can be derived from leading singularities involving minimally coupled three-particle amplitudes. Furthermore, we show that the rotating solutions can be derived from their non-rotating counterparts by a spin-factor deformation of the relevant minimally coupled amplitudes. To show this, we compute the tree-level and one-loop leading singularities for a heavy charged source with generic spin s. We compute the metrics both with and without a spin factor and show that we get both the Kerr-Newman and Reissner- Nordström solutions respectively. We then go on to compute the impulse imparted to the probe particle in the infinite spin limit and show that the spin factor induces a complex deformation of the impact parameter, as was recently observed for Kerr black holes in [1]. We interpret these observations as being the on-shell avatar of the Janis-Newman algorithm for charged black holes.
Gluing gravitational blocks for AdS black holes
Authors: Hosseini Seyed Morteza , Hristov Kiril , Zaffaroni Alberto
Published: January 2020

Abstract

We provide a unifying entropy functional and an extremization principle for black holes and black strings in AdS4 × S
7 and AdS5 × S
5 with arbitrary rotation and generic electric and magnetic charges. This is done by gluing gravitational blocks, basic building blocks that are directly inspired by the holomorphic blocks appearing in the factorization of supersymmetric partition functions in three and four dimensions. We also provide an explicit realization of the attractor mechanism by identifying the values of the scalar fields at the horizon with the critical points of the entropy functional. We give examples based on dyonic rotating black holes with a twist in AdS4 × S
7, rotating black strings in AdS5 × S
5, dyonic Kerr-Newman black holes in AdS4 × S
7 and Kerr-Newman black holes in AdS5 × S
5. In particular, our entropy functional extends existing results by adding rotation to the twisted black holes in AdS4 and by adding flavor magnetic charges for the Kerr-Newman black holes in AdS4. We also discuss generalizations to higher-dimensional black objects.
Uplifting anti-D6-brane
Authors: Cribiori Niccolò , Kallosh Renata , Roupec Christoph , Wrase Timm
Published: January 2020

Abstract

A simple, KKLT-like construction of de Sitter vacua in type IIA string theory is presented in an STU model with guidance from string theory U-duality and with an up- lifting anti-D6-brane. In four dimensions the model is reduced to

$$ \mathcal{N} $$

N

= 1 supergravity with three chiral multiplets, namely S, T and U , as well as one nilpotent multiplet representing the anti-D6-brane. We briefly discuss also a generalization with seven moduli.
Assessing Google Street View Image Availability in Latin American Cities
Authors: Fry Dustin , Mooney Stephen J. , Rodríguez Daniel A. , Caiaffa Waleska T. , Lovasi Gina S.
Published: January 2020

Virtual audits using Google Street View are an increasingly popular method of assessing neighborhood environments for health and urban planning research. However, the validity of these studies may be threatened by issues of image availability, image age, and variance of image age, particularly in the Global South. This study identifies patterns of Street View image availability, image age, and image age variance across cities in Latin America and assesses relationships between these measures and measures of resident socioeconomic conditions. Image availability was assessed at 530,308 near-road points within the boundaries of 371 Latin American cities described by the SALURBAL (Salud Urbana en America Latina) project. At the subcity level, mixed-effect linear and logistic models were used to assess relationships between measures of socioeconomic conditions and image availability, average image age, and the standard deviation of image age. Street View imagery was available at 239,394 points (45.1%) of the total sampled, and rates of image availability varied widely between cities and countries. Subcity units with higher scores on measures of socioeconomic conditions had higher rates of image availability (OR = 1.11 per point increase of combined index, p < 0.001) and the imagery was newer on average (− 1.15 months per point increase of combined index, p < 0.001), but image capture date within these areas varied more (0.59-month increase in standard deviation of image age per point increase of combined index, p < 0.001). All three assessed threats to the validity of Street View virtual audit studies spatially covary with measures of socioeconomic conditions in Latin American cities. Researchers should be attentive to these issues when using Street View imagery.
Gas Sensing and Power Harvesting Polyvinylidene Fluoride Nanocomposites Containing Hybrid Nanotubes
Authors: Ponnamma Deepalekshmi , Sharma Ashok K. , Saharan Priya , Al-Maadeed Mariam Al Ali
Published: January 2020

Gas sensing properties at room temperature and energy harvesting performances are realized for the polyvinylidene fluoride (PVDF) nanocomposites containing titanium dioxide (TiO2) nanotubes grown in the presence of carbon nanotubes (CNT). While hydrothermal reaction is practiced for the development of TiO2/CNT hybrid nanotubes, spin coating is done for the nanocomposite films to be deposited on sensing electrodes. Influence of various filler concentrations and the synergistic combination of fillers on the sensing characteristics are studied by recording the response times and the stability of the results. Upon exposure to liquefied petroleum gas, the PVDF/TiO2-CNT (2.5 wt.%) gas sensor shows a sensing response of 0.45 s (400 ppm LPG), approximately nine times higher than the composite containing 2.5 wt.% of TiO2 or 2.5 wt.% CNT. The piezoelectric response of the samples is also recorded and correlated with the synergistic influence of the filler materials. The current study can stimulate a good trend in fabricating self-powered gas sensors from PVDF nanocomposites.
Patient-Specific Mandibular Reconstruction Plates Increase Accuracy and Long-Term Stability in Immediate Alloplastic Reconstruction of Segmental Mandibular Defects
Authors: Zeller A. N. , Neuhaus M. T. , Weissbach L. V. M. , Rana M. , Dhawan A. , Eckstein F. M. , Gellrich N. C. , Zimmerer R. M.
Published: January 2020

Objectives

The aim of the current study was to evaluate potential differences in the accuracy of mandibular reconstruction and long-term stability, with respect to different reconstructive procedures.

Methods

In total, 42 patients who had undergone primary segmental mandibular resection with immediate alloplastic reconstruction, with either manually pre-bent or patient-specific mandibular reconstruction plates (PSMRP), were included in this study. Mandibular dimensions, in terms of six clinically relevant distances (capitulum [most lateral points], capitulum [most medial points], incisura [most caudal points], mandibular foramina, coronoid process [most cranial points], dorsal tip of the mandible closest to the gonion point) determined from tomographic images, were compared prior to, and after surgery.

Results

Dimensional alterations were significantly more often found when conventionally bent titanium reconstruction plates were used. These occurred in the area of the coronoid process (p = 0.014). Plate fractures were significantly (p = 0.022) more often found within the manually pre-bent group than within the PSMRP group (17%/0%).

Conclusion

The results suggest that the use of PSMRP may prevent rotation of the proximal mandibular segment, thus avoiding functional impairment. In addition, the use of PSMRP may potentially enhance the long-term stability of alloplastic reconstructions.
Recent Advances in Tumor Microenvironment Hydrogen Peroxide-Responsive Materials for Cancer Photodynamic Therapy
Authors: Yang Nan , Xiao Wanyue , Song Xuejiao , Wang Wenjun , Dong Xiaochen
Published: January 2020

Photodynamic therapy (PDT), as one of the noninvasive clinical cancer phototherapies, suffers from the key drawback associated with hypoxia at the tumor microenvironment (TME), which plays an important role in protecting tumor cells from damage caused by common treatments. High concentration of hydrogen peroxide (H2O2), one of the hallmarks of TME, has been recognized as a double-edged sword, posing both challenges, and opportunities for cancer therapy. The promising perspectives, strategies, and approaches for enhanced tumor therapies, including PDT, have been developed based on the fast advances in H2O2-enabled theranostic nanomedicine. In this review, we outline the latest advances in H2O2-responsive materials, including organic and inorganic materials for enhanced PDT. Finally, the challenges and opportunities for further research on H2O2-responsive anticancer agents are envisioned.
Priming recognition memory test cues: No evidence for an attributional basis of recollection
Authors: Ionita Carmen F. , Talmi Deborah , Taylor Jason R.
Published: January 2020

We argue that while the proposed memory model by Bastin et al. can explain familiarity-based memory judgements through the interaction of a core representation system and an attribution system, recollection-based memory judgements are not based on non-mnemonic signals being attributed to memory.
Preterm birth and risk for language delays before school entry: A sibling-control study
Authors: Zambrana Imac Maria , Vollrath Margarete E. , Jacobsson Bo , Sengpiel Verena , Ystrom Eivind
Published: January 2020

We investigated whether children born preterm are at risk for language delay using a sibling-control design in the Norwegian Mother and Child Cohort Study (MoBa), conducted by the Norwegian Institute of Public Health. Participants included 26,769 siblings born between gestational weeks 23 and 42. Language delay was assessed when the children were 1.5, 3, and 5 years old. To adjust for familial risk factors, comparisons were conducted between preterm and full-term siblings. Pregnancy-specific risk factors were controlled for by means of observed variables. Findings showed that preterm children born before week 37 had increased risk for language delays at 1.5 years. At 3 and 5 years, only children born before week 34 had increased risk for language delay. Children born weeks 29–33 and before week 29 had increased risk for language delay at 1.5 years (RR = 4.51, 95% CI [3.45, 5.88]; RR = 10.32, 95% CI [6.7, 15.80]), 3 years (RR = 1.50, 95% CI [1.02, 2.21]; RR = 2.78, 95% CI [1.09, 7.07]), and 5 years (RR = 1.63, 95% CI [1.06, 2.51]; RR = 2.98, 95% CI [0.87, 10.26]), respectively. In conclusion, children born preterm are at risk for language delays, with familial confounders only explaining a moderate share of the association. This suggests a cause-effect relationship between early preterm birth and risk for language delay in preschool children.
Causes of Higher Climate Sensitivity in CMIP6 Models
Authors: Zelinka Mark D. , Myers Timothy A. , McCoy Daniel T. , Po‐Chedley Stephen , Caldwell Peter M. , Ceppi Paulo , Klein Stephen A. , Taylor Karl E.
Published: January 2020

Equilibrium climate sensitivity, the global surface temperature response to CO
doubling, has been persistently uncertain. Recent consensus places it likely within 1.5–4.5 K. Global climate models (GCMs), which attempt to represent all relevant physical processes, provide the most direct means of estimating climate sensitivity via CO
quadrupling experiments. Here we show that the closely related effective climate sensitivity has increased substantially in Coupled Model Intercomparison Project phase 6 (CMIP6), with values spanning 1.8–5.6 K across 27 GCMs and exceeding 4.5 K in 10 of them. This (statistically insignificant) increase is primarily due to stronger positive cloud feedbacks from decreasing extratropical low cloud coverage and albedo. Both of these are tied to the physical representation of clouds which in CMIP6 models lead to weaker responses of extratropical low cloud cover and water content to unforced variations in surface temperature. Establishing the plausibility of these higher sensitivity models is imperative given their implied societal ramifications.
Sea Level Rise in New Zealand: The Effect of Vertical Land Motion on Century‐Long Tide Gauge Records in a Tectonically Active Region
Authors: Denys Paul H. , Beavan R. John , Hannah John , Pearson Chris F. , Palmer Neville , Denham Mike , Hreinsdottir Sigrun
Published: January 2020

Historically tide gauge (TG) data have been used to estimate global sea level rise. Critical to the analysis of TG records is the assumption that the TG sites are stable and not affected by vertical land motion (VLM). We analyze century‐long TG records from New Zealand that have been affected by VLM due to both major and transient earthquake events at a regional level as well as local instabilities. Using combined GPS and precise leveling, we estimate relative VLM between the GPS and TG of up to 1 mm/year. Based on 15–20 years of GPS data, the effect of seismic activity and slow slip events has uplifted sites by up to 0.8 mm/year on average in Wellington and Dunedin. Updated estimates of long‐term relative sea level (RSL) at four New Zealand TGs, as well as an estimate of RSL at a new fifth TG (New Plymouth), are determined using data through 2013—an additional 13 years compared to the previous study. The VLM corrected RSL rates gives our best estimate absolute sea level of +1.45 ± 0.28 mm/year (1891−2013). It is important that absolute sea level derived from RSL rates include realistic estimates of VLM, especially at TG sites that are close to plate boundaries, located in seismically active regions, affected by glacial isostatic adjustment, land ice loss, or gas/oil/water extraction.
The Continually Stable Subduction, Iron‐Spin Transition, and the Formation of LLSVPs From Subducted Oceanic Crust
Authors: Huang Chuan , Leng Wei , Wu Zhongqing
Published: January 2020

Large low shear velocity provinces (LLSVPs) in the lower mantle beneath Africa and the Pacific Ocean have been widely accepted as compositionally distinct zones characterized by their large spatial scale, distinctive geometry (high topography and steep side boundaries), and long‐term stability. One possible explanation for the chemical origin of the LLSVPs is that they formed from subducted oceanic crust. However, some previous geodynamic models suggest that it is difficult for a sufficient quantity of recycled crust to accumulate in the deep mantle and form chemical structures matching those of LLSVPs. Here we show that the continually stable subduction can significantly enhance the gathering of recycled oceanic crust above the core‐mantle boundary. The resulting chemical structures in our model show high elevations and steep sides similar to those of the seismically observed LLSVPs when the effects of iron‐spin transition in ferropericlase are incorporated. These LLSVP‐like structures usually emerge 1–1.5 billion years (Gyr) after the model starts and remain recognizable at 3 Gyr. The total volume of these structures first increases to approximately double the current LLSVPs' volume and then gradually decreases over time. With a subduction pattern corresponding to extroversion supercontinent cycles, two antipodal chemical structures form similar to the current LLSVPs and survive longer than 1 Gyr.
Combined Effects of Pressure and Water Saturation on the Seismic Anisotropy in Artificial Porous Sandstone With Aligned Fractures
Authors: Han Tongcheng , Gurevich Boris , Fu Li‐Yun , Qi Qiaomu , Wei Jianxin , Chen Xingyu
Published: January 2020

Fractures are commonly existing in the subsurface rocks, and understanding the seismic anisotropy in fractured rocks is of great importance in a range of geophysical applications. However, although all the fractured rocks are suffering from geological stresses and most of them are experiencing partial water saturation, the combined effects of confining pressure and water saturation on the seismic anisotropy in fractured rocks remain poorly understood. To obtain such knowledge, we measured and compared the anisotropic velocities and corresponding seismic anisotropy in two artificial porous sandstone samples with and without aligned fractures, respectively, as functions of varying confining pressure and degree of water saturation. We showed that the existence of aligned fractures significantly reduced the five measured velocities but dramatically enhanced the seismic anisotropy in the fractured sample. We also showed that confining pressure and water saturation had an interdependent complex effect on the seismic anisotropy of the fractured sample. The seismic anisotropy of the dry sample showed the highest‐pressure sensitivity, and the saturation effect was most significant at low confining pressure. Integrated interpretation of the experimental data indicated that wave‐induced fluid flow due to pore‐scale and mesoscale fluid distribution in the rocks is responsible for most of the observed pressure and saturation‐dependent anisotropic behaviors in the rocks. The results have helped to gain new knowledge on the seismic anisotropy in partially saturated fractured rocks subject to varying pressures and suggest the requirement for advanced theoretical models to fully understand the acquired data.
Updated Long‐Term Trends in Mesopause Temperature, Airglow Emissions, and Noctilucent Clouds
Authors: Dalin P. , Perminov V. , Pertsev N. , Romejko V.
Published: January 2020

We have updated long‐term trends in mesopause temperature, airglow emission intensities, and noctilucent clouds (NLCs) based on ground‐based observations conducted in the Moscow region (Russia). Trends in mesopause temperature and airglow emissions have been derived for the period 2000–2018 (19 years), and long‐term trends in NLC characteristics have been obtained for 1968–2018 (51 years). Trends in airglow emissions have been estimated separately for winter and summer seasons. There are statistically significant negative trends in molecular oxygen O2 A(0‐1) and hydroxyl OH(6‐2) emission intensities in both winter and summer. Responses of the airglow intensities to solar activity have been found to be significantly positive, with winter ones being 1.5–2 times greater than summer ones. There is a rather strong and statistically significant cooling of the summer mesopause at a rate of −2.4±2.3 K/decade, whereas the winter mesopause demonstrates a small and statistically insignificant cooling of −0.4±2.2 K/decade. The response of the mesopause temperature to solar activity is positive and about 2 times greater in winter than in summer. We consider long‐term trends in the summer mesopause temperature and NLC for the same time period and same geographical region. Secular trends in NLC parameters have been found to be small and statistically insignificant as observed from midlatitudes. NLCs demonstrate statistically significant negative response to solar activity. Ozone forcing produces minor effects on both airglow and NLC characteristics. The observed small secular NLC trends contradict large modeled NLC trends recently obtained by Lübken et al. (2018, https://doi.org/10.1029/2018GL077719).
Observing and Simulating Spatial Variations of Forest Carbon Stocks in Complex Terrain
Authors: Smeglin Yuting H. , Davis Kenneth J. , Shi Yuning , Eissenstat David M. , Kaye Jason P. , Kaye Margot W.
Published: January 2020

The terrestrial carbon (C) cycle remains the least constrained component in the global C cycle, partly due to the difficulty of quantifying C sources and sinks in complex terrain. In this paper, we used observations at the Shale Hills Critical Zone Observatory and a biogeochemistry model, Biome‐BGC, to study the spatial distribution of C stocks and fluxes in a first‐order watershed. The model simulated the average C pools and fluxes in the watershed after constraining three model parameters with observations. The model was able to generate the observed spatial patterns of C pools in the watershed, with higher biomass and soil C in the valley and lower values on the ridgetop, though the model underestimated the ridgetop to valley differences. We examined the simulated effect of four environmental factors, soil moisture, soil temperature, nitrogen (N) availability and solar radiation, on the spatial distribution of C pools. Among these factors, soil water and N availability coupled together dominate the spatial distribution of aboveground biomass. Soil water was the most important factor controlling soil C. These results are highly sensitive to van Genuchten parameters, which describe the soil water retention curve. This study highlights the importance of the hydrologic system in describing within‐watershed structure in terrestrial C stocks.
Geochemistry of Small Canadian Arctic Rivers with Diverse Geological and Hydrological Settings
Authors: Brown Kristina A. , Williams William J. , Carmack Eddy C. , Fiske Greg , François Roger , McLennan Donald , Peucker‐Ehrenbrink Bernhard
Published: January 2020

A survey of 25 coastal‐draining rivers across the Canadian Arctic Archipelago (CAA) shows that these systems are distinct from the largest Arctic rivers that drain watersheds extending far south of the Arctic circle. Observations collected from 2014 to 2016 illustrate the influences of seasonal hydrology, bedrock geology, and landscape physiography on each river's inorganic geochemical characteristics. Summertime data show the impact of coincident gradients in lake cover and surficial geology on river geochemical signatures. In the north and central CAA, drainage basins are generally smaller, underlain by sedimentary bedrock, and their hydrology is driven by seasonal precipitation pulses that undergo little modification before they enter the coastal ocean. In the southern CAA, a high density of lakes stores water longer within the terrestrial system, permitting more modification of water isotope and geochemical characteristics. Annual time‐series observations from two CAA rivers reveal that their concentration‐discharge relationships differ compared with those of the largest Arctic rivers, suggesting that future projections of dissolved ion fluxes from CAA rivers to the Arctic Ocean may not be reliably made based on compositions of the largest Arctic rivers alone, and that rivers draining the CAA region will likely follow different trajectories of change under a warming climate. Understanding how these small, coastal‐draining river systems will respond to climate change is essential to fully evaluate the impact of changing freshwater inputs to the Arctic marine system.
Interleukin-1β is a potential therapeutic target for periodontitis: a narrative review
Authors: Cheng Ran , Wu Zhiwu , Li Mingming , Shao Meiying , Hu Tao
Published: January 2020

Interleukin(IL)-1β, a pro-inflammatory cytokine, was elevated and participates in periodontitis. Not only the link between IL-1β and periodontitis was proved by clinical evidence, but also the increased IL-1β triggers a series of inflammatory reactions and promotes bone resorption. Currently, IL-1β blockage has been therapeutic strategies for autoimmune and autoinflammatory diseases such as rheumatoid arthritis, cryopyrin-associated periodic syndromes, gout and type II diabetes mellitus. It is speculated that IL-1β be a potential therapeutic target for periodontitis. The review focuses on the production, mechanism, present treatments and future potential strategies for IL-1β in periodontitis.
Interfacial Fe5C2-Cu catalysts toward low-pressure syngas conversion to long-chain alcohols
Authors: Li Yinwen , Gao Wa , Peng Mi , Zhang Junbo , Sun Jialve , Xu Yao , Hong Song , Liu Xi , Liu Xingwu , Wei Min , Zhang Bingsen , Ma Ding
Published: January 2020

Long-chain alcohols synthesis (LAS, C5+OH) from syngas provides a promising route for the conversion of coal/biomass/natural gas into high-value chemicals. Cu-Fe binary catalysts, with the merits of cost effectiveness and high CO conversion, have attracted considerable attention. Here we report a nano-construct of a Fe5C2-Cu interfacial catalyst derived from Cu4Fe1Mg4-layered double hydroxide (Cu4Fe1Mg4-LDH) precursor, i.e., Fe5C2 clusters (~2 nm) are immobilized onto the surface of Cu nanoparticles (~25 nm). The interfacial catalyst exhibits a CO conversion of 53.2%, a selectivity of 14.8 mol% and a space time yield of 0.101 g gcat−1 h−1 for long-chain alcohols, with a surprisingly benign reaction pressure of 1 MPa. This catalytic performance, to the best of our knowledge, is comparable to the optimal level of Cu-Fe catalysts operated at much higher pressure (normally above 3 MPa).
2N+4-rule and an atlas of bulk optical resonances of zigzag graphene nanoribbons
Authors: Payod Renebeth B. , Grassano Davide , Santos Gil Nonato C. , Levshov Dmitry I. , Pulci Olivia , Saroka Vasil A.
Published: January 2020

Development of on-chip integrated carbon-based optoelectronic nanocircuits requires fast and non-invasive structural characterization of their building blocks. Recent advances in synthesis of single wall carbon nanotubes and graphene nanoribbons allow for their use as atomically precise building blocks. However, while cataloged experimental data are available for the structural characterization of carbon nanotubes, such an atlas is absent for graphene nanoribbons. Here we theoretically investigate the optical absorption resonances of armchair carbon nanotubes and zigzag graphene nanoribbons continuously spanning the tube (ribbon) transverse sizes from 0.5(0.4) nm to 8.1(12.8) nm. We show that the linear mapping is guaranteed between the tube and ribbon bulk resonance when the number of atoms in the tube unit cell is $$2N+4$$
2
N
+
4
, where $$N$$
N
is the number of atoms in the ribbon unit cell. Thus, an atlas of carbon nanotubes optical transitions can be mapped to an atlas of zigzag graphene nanoribbons.
Reversible displacive transformation in MnTe polymorphic semiconductor
Authors: Mori Shunsuke , Hatayama Shogo , Shuang Yi , Ando Daisuke , Sutou Yuji
Published: January 2020

Displacive transformation is a diffusionless transition through shearing and shuffling of atoms. Diffusionless displacive transition with modifications in physical properties can help manufacture fast semiconducting devices for applications such as data storage and switching. MnTe is known as a polymorphic compound. Here we show that a MnTe semiconductor film exhibits a reversible displacive transformation based on an atomic-plane shuffling mechanism, which results in large electrical and optical contrasts. We found that MnTe polycrystalline films show reversible resistive switching via fast Joule heating and enable nonvolatile memory with lower energy and faster operation compared with conventional phase-change materials showing diffusional amorphous-to-crystalline transition. We also found that the optical reflectance of MnTe films can be reversibly changed by laser heating. The present findings offer new insights into developing low power consumption and fast-operation electronic and photonic phase-change devices.
Conditional control of RNA-guided nucleic acid cleavage and gene editing
Authors: Wang Shao-Ru , Wu Ling-Yu , Huang Hai-Yan , Xiong Wei , Liu Jian , Wei Lai , Yin Ping , Tian Tian , Zhou Xiang
Published: January 2020

Prokaryotes use repetitive genomic elements termed CRISPR (clustered regularly interspaced short palindromic repeats) to destroy invading genetic molecules. Although CRISPR systems have been widely used in DNA and RNA technology, certain adverse effects do occur. For example, constitutively active CRISPR systems may lead to a certain risk of off-target effects. Here, we introduce post-synthetic masking and chemical activation of guide RNA (gRNA) to controlling CRISPR systems. An RNA structure profiling probe (2-azidomethylnicotinic acid imidazolide) is used. Moreover, we accomplish conditional control of gene editing in live cells. This proof-of-concept study demonstrates promising potential of chemical activation of gRNAs as a versatile tool for chemical biology.
YAP1 mediates survival of ALK-rearranged lung cancer cells treated with alectinib via pro-apoptotic protein regulation
Authors: Tsuji Takahiro , Ozasa Hiroaki , Aoki Wataru , Aburaya Shunsuke , Yamamoto Funazo Tomoko , Furugaki Koh , Yoshimura Yasushi , Yamazoe Masatoshi , Ajimizu Hitomi , Yasuda Yuto , Nomizo Takashi , Yoshida Hironori , Sakamori Yuichi , Wake Hiroaki , Ueda Mitsuyoshi , Kim Young Hak , Hirai Toyohiro
Published: January 2020

Despite the promising clinical efficacy of the second-generation anaplastic lymphoma kinase (ALK) inhibitor alectinib in patients with ALK-rearranged lung cancer, some tumor cells survive and eventually relapse, which may be an obstacle to achieving a cure. Limited information is currently available on the mechanisms underlying the initial survival of tumor cells against alectinib. Using patient-derived cell line models, we herein demonstrate that cancer cells survive a treatment with alectinib by activating Yes-associated protein 1 (YAP1), which mediates the expression of the anti-apoptosis factors Mcl-1 and Bcl-xL, and combinatorial inhibition against both YAP1 and ALK provides a longer tumor remission in ALK-rearranged xenografts when compared with alectinib monotherapy. These results suggest that the inhibition of YAP1 is a candidate for combinatorial therapy with ALK inhibitors to achieve complete remission in patients with ALK-rearranged lung cancer.
De novo generation of hit-like molecules from gene expression signatures using artificial intelligence
Authors: Méndez-Lucio Oscar , Baillif Benoit , Clevert Djork-Arné , Rouquié David , Wichard Joerg
Published: January 2020

Finding new molecules with a desired biological activity is an extremely difficult task. In this context, artificial intelligence and generative models have been used for molecular de novo design and compound optimization. Herein, we report a generative model that bridges systems biology and molecular design, conditioning a generative adversarial network with transcriptomic data. By doing so, we can automatically design molecules that have a high probability to induce a desired transcriptomic profile. As long as the gene expression signature of the desired state is provided, this model is able to design active-like molecules for desired targets without any previous target annotation of the training compounds. Molecules designed by this model are more similar to active compounds than the ones identified by similarity of gene expression signatures. Overall, this method represents an alternative approach to bridge chemistry and biology in the long and difficult road of drug discovery.
African cratonic lithosphere carved by mantle plumes
Authors: Celli Nicolas Luca , Lebedev Sergei , Schaeffer Andrew J. , Gaina Carmen
Published: January 2020

How cratons, the ancient cores of continents, evolved since their formation over 2.5 Ga ago is debated. Seismic tomography can map the thick lithosphere of cratons, but its resolution is low in sparsely sampled continents. Here we show, using waveform tomography with a large, newly available dataset, that cratonic lithosphere beneath Africa is more complex and fragmented than seen previously. Most known diamondiferous kimberlites, indicative of thick lithosphere at the time of eruption, are where the lithosphere is thin today, implying surprisingly widespread lithospheric erosion over the last 200 Ma. Large igneous provinces, attributed to deep-mantle plumes, were emplaced near all lithosphere-loss locations, concurrently with or preceding the loss. This suggests that the cratonic roots foundered once modified by mantle plumes. Our results imply that the total volume of cratonic lithosphere has decreased since its Archean formation, with the fate of each craton depending on its movements relative to plumes.