bluuebunny/crossref_metadata_2025_split huggingface dataset:
Towards syntax-aware token embeddings
Authors: Popa Diana Nicoleta , Perez Julien , Henderson James , Gaussier Eric 
Published: July 2020

AbstractDistributional semantic word representations are at the basis of most modern NLP systems. Their usefulness has been proven across various tasks, particularly as inputs to deep learning models. Beyond that, much work investigated fine-tuning the generic word embeddings to leverage linguistic knowledge from large lexical resources. Some work investigated context-dependent word token embeddings motivated by word sense disambiguation, using sequential context and large lexical resources. More recently, acknowledging the need for an in-context representation of words, some work leveraged information derived from language modelling and large amounts of data to induce contextualised representations. In this paper, we investigate Syntax-Aware word Token Embeddings (SATokE) as a way to explicitly encode specific information derived from the linguistic analysis of a sentence in vectors which are input to a deep learning model. We propose an efficient unsupervised learning algorithm based on tensor factorisation for computing these token embeddings given an arbitrary graph of linguistic structure. Applying this method to syntactic dependency structures, we investigate the usefulness of such token representations as part of deep learning models of text understanding. We encode a sentence either by learning embeddings for its tokens and the relations between them from scratch or by leveraging pre-trained relation embeddings to infer token representations. Given sufficient data, the former is slightly more accurate than the latter, yet both provide more informative token embeddings than standard word representations, even when the word representations have been learned on the same type of context from larger corpora (namely pre-trained dependency-based word embeddings). We use a large set of supervised tasks and two major deep learning families of models for sentence understanding to evaluate our proposal. We empirically demonstrate the superiority of the token representations compared to popular distributional representations of words for various sentence and sentence pair classification tasks.
Regional climate policy under deep uncertainty: robust control and distributional concerns
Authors: Brock William , Xepapadeas Anastasios 
Published: July 2020

AbstractWe study climate change policies using the novel pattern scaling approach of regional transient climate response in order to develop a regional economy–climate model under conditions of deep uncertainty. We associate welfare weights with regions and analyze cooperative outcomes derived by the social planner's solution at the regional scale. Recent literature indicates that damages are larger in low latitude (warmer) areas and are projected to become relatively even larger in low latitude areas than at temperate latitudes. Under deep uncertainty, robust control policies are more conservative regarding emissions and, when regional distributional weights are introduced, carbon taxes are lower in the relatively poorer region. Mild concerns for robustness are welfare improving for the poor region, while strong concerns have welfare cost for all regions. We show that increasing regional temperatures will increase resources devoted to learning, in order to reduce deep uncertainty.
Reformulation of sugar contents in Canadian prepackaged foods and beverages between 2013 and 2017 and resultant changes in nutritional composition of products with sugar reductions
Authors: Bernstein Jodi T , Christoforou Anthea K , Weippert Madyson , L’Abbé Mary R 
Published: July 2020

AbstractObjective:To quantify total sugar reformulation in Canadian prepackaged foods and beverages between 2013 and 2017 and identify changes in the nutritional composition of the foods and beverages reformulated to be lower in total sugar.Design:Longitudinal examination of foods and beverages present in both 2013 and 2017 collections of the University of Toronto’s Food Label Information Program database (n 6628 matched products). The proportion of products with changes in sugar levels was determined. Wilcoxon signed-rank test was used to examine changes in sugar levels overall for products lower or higher in sugar and changes in nutrient composition for products lower in sugar.Setting:Largest grocery retailers by market share in Canada.Participants:Canadian prepackaged foods and beverages.Results:The majority (76·6 %) of products had no change in total sugar content, 12·4 % were reformulated to be lower in sugar and 11·0 % were higher in sugar. A median sugar reduction of 19·0 % (1·6 g) was seen among products lower in sugar which was offset by a median 18·0 % (1·5 g) increase among products higher in sugar. Overall, median levels of energies and other nutrients stayed the same or decreased among products reformulated to be lower in sugar, the exception was for starch, which increased.Conclusions:Limited progress was made to reformulate foods and beverages to be lower in total sugar between 2013 and 2017. Results from this study identify areas in the food supply where attention may be needed to avoid unintended consequences of sugar-focused reformulation in terms of overall nutritional composition.
Multi-chronometer dating of the Souter Head complex: rapid exhumation terminates the Grampian Event of the Caledonian Orogeny
Authors: MARK Darren F. , RICE Clive M. , HOLE Malcolm , CONDON Dan 
Published: July 2020

ABSTRACTThe Souter Head sub-volcanic complex (Aberdeenshire, Scotland) intruded the high-grade metamorphic core of the Grampian Orogen at 469.1 ± 0.6 Ma (uranium-238–lead-206 (238U–206Pb) zircon). It follows closely peak metamorphism and deformation in the Grampian Terrane and tightly constrains the end of the Grampian Event of the Caledonian Orogeny. Temporally coincident U–Pb and argon/argon (40Ar/39Ar) data show the complex cooled quickly with temperatures decreasing from ca.800 °C to less than 200 °C within 1 Ma. Younger rhenium–osmium (Re–Os) ages are due to post-emplacement alteration of molybdenite to powellite. The U–Pb and Ar/Ar data combined with existing geochronological data show that D2/D3 deformation, peak metamorphism (Barrovian and Buchan style) and basic magmatism in NE Scotland were synchronous at ca.470 Ma and are associated with rapid uplift (5–10 km Ma−1) of the orogen, which, by ca.469 Ma, had removed the cover to the metamorphic pile. Rapid uplift resulted in decompressional melting and the generation of mafic and felsic magmatism. Shallow slab break-off (50–100 km) is invoked to explain the synchroneity of these events. This interpretation implies that peak metamorphism and D2/D3 ductile deformation were associated with extension. Similarities in the nature and timing of orogenic events in Connemara, western Ireland, with NE Scotland suggest that shallow slab break-off occurred in both localities.
Increased monocyte to HDL cholesterol ratio in vitamin B12	deficiency: Is it related to cardiometabolic risk?
Authors: Kayhan Sanem , Kirnap Nazli Gulsoy , Tastemur Mercan 
Published: July 2020

Abstract. Vitamin B12 deficiency may have indirect cardiovascular effects in addition to hematological and neuropsychiatric symptoms. It was shown that the monocyte count-to-high density lipoprotein cholesterol (HDL-C) ratio (MHR) is a novel cardiovascular marker. In this study, the aim was to evaluate whether MHR was high in patients with vitamin B12 deficiency and its relationship with cardiometabolic risk factors. The study included 128 patients diagnosed with vitamin B12 deficiency and 93 healthy controls. Patients with vitamin B12 deficiency had significantly higher systolic blood pressure (SBP), diastolic blood pressure (DBP), MHR, C-reactive protein (CRP) and uric acid levels compared with the controls (median 139 vs 115 mmHg, p < 0.001; 80 vs 70 mmHg, p < 0.001; 14.2 vs 9.5, p < 0.001; 10.2 vs 4 mg/dl p < 0.001; 6.68 vs 4.8 mg/dl, p < 0.001 respectively). The prevalence of left ventricular hypertrophy was higher in vitamin B12 deficiency group (43.8%) than the control group (8.6%) (p < 0.001). In vitamin B12 deficiency group, a positive correlation was detected between MHR and SBP, CRP and uric acid (p < 0.001 r:0.34, p < 0.001 r:0.30, p < 0.001 r:0.5, respectively) and a significant negative correlation was detected between MHR and T-CHOL, LDL, HDL and B12 (p < 0.001 r: −0.39, p < 0.001 r: −0.34, p < 0.001 r: −0.57, p < 0.04 r: −0.17, respectively). MHR was high in vitamin B12 deficiency group, and correlated with the cardiometabolic risk factors in this group, which were SBP, CRP, uric acid and HDL. In conclusion, MRH, which can be easily calculated in clinical practice, can be a useful marker to assess cardiovascular risk in patients with vitamin B12 deficiency.
Comment on “Geometry of the Deep Calabrian Subduction (Central Mediterranean Sea) From Wide‐Angle Seismic Data and 3‐D Gravity Modeling” by Dellong Et Al.
Authors: Argnani Andrea 
Published: July 2020

AbstractThe recent paper by Dellong et al. does not report properly the literature on the Malta Escarpment and its tectonic activity. Moreover, the published set of data allows an alternative interpretation of one of their refraction profiles, which implies that only incipient subduction is present south of the Messina Strait, without need for well‐developed lithospheric tear faults south of Mt. Etna.
Preclinical pharmacology of a lipophenol in a mouse model of light-induced retinopathy
Authors: Taveau Nicolas , Cubizolle Aurélie , Guillou Laurent , Pinquier Nicolas , Moine Espérance , Cia David , Kalatzis Vasiliki , Vercauteren Joseph , Durand Thierry , Crauste Céline , Brabet Philippe 
Published: July 2020

AbstractEnvironmental light has deleterious effects on the outer retina in human retinopathies, such as ABCA4-related Stargardt’s disease and dry age-related macular degeneration. These effects involve carbonyl and oxidative stress, which contribute to retinal cell death and vision loss. Here, we used an albino Abca4−/− mouse model, the outer retina of which shows susceptibility to acute photodamage, to test the protective efficacy of a new polyunsaturated fatty acid lipophenol derivative. Anatomical and functional analyses demonstrated that a single intravenous injection of isopropyl-phloroglucinol-DHA, termed IP-DHA, dose-dependently decreased light-induced photoreceptor degeneration and preserved visual sensitivity. This protective effect persisted for 3 months. IP-DHA did not affect the kinetics of the visual cycle in vivo or the activity of the RPE65 isomerase in vitro. Moreover, IP-DHA administered by oral gavage showed significant protection of photoreceptors against acute light damage. In conclusion, short-term tests in Abca4-deficient mice, following single-dose administration and light exposure, identify IP-DHA as a therapeutic agent for the prevention of retinal degeneration.
Quantitative comparison between the rhizosphere effect of Arabidopsis thaliana and co-occurring plant species with a longer life history
Authors: Schneijderberg Martinus , Cheng Xu , Franken Carolien , de Hollander Mattias , van Velzen Robin , Schmitz Lucas , Heinen Robin , Geurts Rene , van der Putten Wim H , Bezemer T Martijn , Bisseling Ton 
Published: July 2020

Abstract
As a model for genetic studies, Arabidopsis thaliana (Arabidopsis) offers great potential to unravel plant genome-related mechanisms that shape the root microbiome. However, the fugitive life history of this species might have evolved at the expense of investing in capacity to steer an extensive rhizosphere effect. To determine whether the rhizosphere effect of Arabidopsis is different from other plant species that have a less fugitive life history, we compared the root microbiome of Arabidopsis to eight other, later succession plant species from the same habitat. The study included molecular analysis of soil, rhizosphere, and endorhizosphere microbiome both from the field and from a laboratory experiment. Molecular analysis revealed that the rhizosphere effect (as quantified by the number of enriched and depleted bacterial taxa) was ~35% lower than the average of the other eight species. Nevertheless, there are numerous microbial taxa differentially abundant between soil and rhizosphere, and they represent for a large part the rhizosphere effects of the other plants. In the case of fungal taxa, the number of differentially abundant taxa in the Arabidopsis rhizosphere is 10% of the other species’ average. In the plant endorhizosphere, which is generally more selective, the rhizosphere effect of Arabidopsis is comparable to other species, both for bacterial and fungal taxa. Taken together, our data imply that the rhizosphere effect of the Arabidopsis is smaller in the rhizosphere, but equal in the endorhizosphere when compared to plant species with a less fugitive life history.
SPEN induces miR-4652-3p to target HIPK2 in nasopharyngeal carcinoma
Authors: Li Yang , Lv Yumin , Cheng Chao , Huang Yan , Yang Liu , He Jingjing , Tao Xingyu , Hu Yingying , Ma Yuting , Su Yun , Wu Liyang , Yu Guifang , Jiang Qingping , Liu Shu , Liu Xiong , Liu Zhen 
Published: July 2020

AbstractSPEN family transcriptional repressor (SPEN), also known as the SMART/HDAC1-associated repressor protein (SHARP), has been reported to modulate the malignant phenotypes of breast cancer, colon cancer, and ovarian cancer. However, its role and the detail molecular basis in nasopharyngeal carcinoma (NPC) remain elusive. In this study, the SPEN mRNA and protein expression was found to be increased in NPC cells and tissues compared with nonmalignant nasopharyngeal epithelial cells and tissues. Elevated SPEN protein expression was found to promote the pathogenesis of NPC and lead to poor prognosis. Knockdown of SPEN expression resulted in inactivation ofPI3K/AKT and c-JUN signaling, thereby suppressing NPC migration and invasion. In addition, miR-4652-3p was found to be a downstream inducer of SPEN by targeting the homeodomain interacting protein kinase 2 (HIPK2) gene, a potential tumor suppressor that reduces the activation of epithelial–mesenchymal transition (EMT) signaling, thereby reducing its expression and leading to increased NPC migration, invasion, and metastasis. In addition, SPEN was found to induce miR-4652-3p expression by activating PI3K/AKT/c-JUN signaling to target HIPK2. Our data provided a new molecular mechanism for SPEN as a metastasis promoter through activation of PI3K/AKT signaling, thereby stimulating the c-JUN/miR-4652-3p axis to target HIPK2 in NPC.
Theoretical dissection of superconductivity in two-dimensional honeycomb borophene oxide B2O crystal with a high stability
Authors: Yan Luo , Liu Peng-Fei , Li Hengtao , Tang Yong , He Junjie , Huang Xingyong , Wang Bao-Tian , Zhou Liujiang 
Published: July 2020

AbstractAtomically thin borophene has recently been synthesized experimentally, significantly enriching the boron chemistry and broadening the family of two-dimensional (2D) materials. Recently, oxides of 2D materials have been widely investigated for next-generation electronic devices. Based on the first-principles calculations, we predict the existence of the superconductivity in honeycomb borophene oxide (B2O), which possesses a high stability and could be potentially prepared by intrinsically incorporating oxygen into the recently synthesized borophene. The mechanical, electronic, phonon properties, as well as electron–phonon coupling of metallic B2O monolayer, have been systematically scrutinized. Within the framework of the Bardeen–Cooper–Schrieffer theory framework, the B2O monolayer exhibits an intrinsic superconducting feature with a superconducting transition temperature (Tc) of ~10.3 K, higher than many 2D borides (0.2–7.8 K). Further, strain can be utilized to tune the superconductivity with the optimal Tc of 14.7 K under a tensile strain of 1%. The superconducting trait mainly originates from the out-of-plane soft-mode vibrations of the system, which are significantly enhanced via the light O atoms’ incorporation compared to other 2D metal-boride superconductors. This strategy would open a door to design 2D superconducting structures via the participation of light elements. We believe our findings greatly bloom the 2D superconducting family and pave the way for future nanoelectronics.
Spray-coated paper supercapacitors
Authors: Say Mehmet Girayhan , Brooke Robert , Edberg Jesper , Grimoldi Andrea , Belaineh Dagmawi , Engquist Isak , Berggren Magnus 
Published: July 2020

AbstractThe increasing demands to further electrify and digitalize our society set demands for a green electrical energy storage technology that can be scaled between very small, and heavily distributed electrical energy sources, to very large volumes. Such technology must be compatible with fast-throughput, large-volume and low-cost fabrication processes, such as using printing and coating techniques. Here, we demonstrate a sequential production protocol to fabricate supercapacitors including electrodes based on cellulose nanofibrils (CNF) and the conducting polymer PEDOT:PSS. Thin and lightweight paper electrodes, carbon adhesion layers and the gel electrolyte are fabricated using spray coating, screen printing, and bar coating, respectively. These all solid-state supercapacitors are flexible, mechanically robust and exhibit a low equivalent series resistance (0.22 Ω), thus resulting in a high power density (∼104 W/kg) energy technology. The supercapacitors are combined and connected to a power management circuit to demonstrate a smart packaging application. This work shows that operational and embedded supercapacitors can be manufactured in a manner to allow for the integration with, for instance smart packaging solutions, thus enabling powered, active internet-of-things (IoT) devices in a highly distributed application.
The Born supremacy: quantum advantage and training of an Ising Born machine
Authors: Coyle Brian , Mills Daniel , Danos Vincent , Kashefi Elham 
Published: July 2020

AbstractThe search for an application of near-term quantum devices is widespread. Quantum machine learning is touted as a potential utilisation of such devices, particularly those out of reach of the simulation capabilities of classical computers. In this work, we study such an application in generative modelling, focussing on a class of quantum circuits known as Born machines. Specifically, we define a subset of this class based on Ising Hamiltonians and show that the circuits encountered during gradient-based training cannot be efficiently sampled from classically up to multiplicative error in the worst case. Our gradient-based training methods use cost functions known as the Sinkhorn divergence and the Stein discrepancy, which have not previously been used in the gradient-based training of quantum circuits, and we also introduce quantum kernels to generative modelling. We show that these methods outperform the previous standard method, which used maximum mean discrepancy (MMD) as a cost function, and achieve this with minimal overhead. Finally, we discuss the ability of the model to learn hard distributions and provide formal definitions for ‘quantum learning supremacy’. We also exemplify the work of this paper by using generative modelling to perform quantum circuit compilation.
The development of the dog heartworm is highly sensitive to sterols which activate the orthologue of the nuclear receptor DAF-12
Authors: Long Thavy , Alberich Mélanie , André François , Menez Cécile , Prichard Roger K. , Lespine Anne 
Published: July 2020

AbstractPrevention therapy against Dirofilaria immitis in companion animals is currently threatened by the emergence of isolates resistant to macrocyclic lactone anthelmintics. Understanding the control over developmental processes in D. immitis is important for elucidating new approaches to heartworm control. The nuclear receptor DAF-12 plays a role in the entry and exit of dauer stage in Caenorhabditis elegans and in the development of free-living infective third-stage larvae (iL3) of some Clade IV and V parasitic nematodes. We identified a DAF-12 ortholog in the clade III nematode D. immitis and found that it exhibited a much higher affinity for dafachronic acids than described with other nematode DAF-12 investigated so far. We also modelled the DimDAF-12 structure and characterized the residues involved with DA binding. Moreover, we showed that cholesterol derivatives impacted the molting process from the iL3 to the fourth-stage larvae. Since D. immitis is unable to synthesize cholesterol and only completes its development upon host infection, we hypothesize that host environment contributes to its further molting inside the host vertebrate. Our discovery contributes to a better understanding of the developmental checkpoints of D. immitis and offers new perspectives for the development of novel therapies against filarial infections.
Estimation versus measurement of the glomerular filtration rate for kidney function assessment in patients with cancer undergoing cisplatin-based chemotherapy
Authors: Klöckl Marie-Christin , Kasparek Anne-Katrin , Riedl Jakob M. , Moik Florian , Mollnar Stefanie , Stotz Michael , Szkandera Joanna , Terbuch Angelika , Gerger Armin , Niedrist Tobias , Pichler Martin , Bauernhofer Thomas , Schilcher Gernot , Zitta Sabine , Rosenkranz Alexander R. , Friedl Claudia , Stöger Herbert , Posch Florian 
Published: July 2020

AbstractGlomerular filtration rate (GFR) assessment is indicated before every administration of cisplatin. The optimal modality for this purpose [GFR measurement by urinary Creatinine Clearance (uCrCl) versus GFR estimation (eGFR) by the CKD-EPI formula versus both] is unclear. We investigated whether eGFR only is safe in this setting. Paired uCrCl and eGFR determinations from 470 cisplatin cycles from 121 patients were analyzed [median age: 55 years; most frequent tumor site: genitourinary (45%); palliative treatment: n = 41 (34%)]. Primary endpoint was the proportion of cycles with uCrCl < 50 ml/min/1.73m2 and eGFR ≥ 50 ml/min/1.73m2 (i.e. a “false negative” result when only determining eGFR). The primary endpoint occurred in 8 of 470 cisplatin cycles (1.7%, 95%CI 0.5–2.9). In all 8 events, uCrCl was lower than eGFR (mean uCrCl vs. eGFR: 43 versus 112 ml/min/1.73m2). The uCrCl was re-measured in all patients, and showed normal results in all but 1 patient. None of these events precluded the administration of cisplatin at the planned date, and no subsequent cases of acute nephrotoxicity occurred. Overall agreement between uCrCl and eGFR was low, with qualitative analysis suggesting frequent incompliance with 24-h urine collection. We conclude that an eGFR is sufficient for assessing kidney function in patients with cancer undergoing cisplatin therapy.
Interferometric and fluorescence analysis of shock wave effects on cell membrane
Authors: Ito Yusuke , Veysset David , Kooi Steven E. , Martynowych Dmitro , Nakagawa Keiichi , Nelson Keith A. 
Published: July 2020

AbstractShock waves generated by laser pulses have been gaining attention for biological and medical applications in which shock-induced cell membrane deformation influences cell permeation. However, the mechanisms through which the deformation of cell membranes affects permeability remain mostly unknown because of the difficulty of observing in real time the transient and dynamic behaviors of the shock waves and the cells. Here we present an all-optical measurement method that can quantitatively capture the pressure distribution of the propagating shock wave and simultaneously monitor the dynamic behavior of cell membranes. Using this method, we find that the profile of the shock wave dictates the cell membrane permeation. The results suggest a possible mechanism of membrane permeation where sharp pressure gradients create pores on the membrane. Our measurement will foster further understanding of the interaction of shock waves with cells, while the proposed mechanism advances biological and medical applications of shock waves.