bluuebunny/crossref_metadata_2025_split huggingface dataset:
Subgrid modelling for two-dimensional turbulence using neural networks
Authors: Maulik R. , San O. , Rasheed A. , Vedula P. 
Published: November 2018

In this investigation, a data-driven turbulence closure framework is introduced and deployed for the subgrid modelling of Kraichnan turbulence. The novelty of the proposed method lies in the fact that snapshots from high-fidelity numerical data are used to inform artificial neural networks for predicting the turbulence source term through localized grid-resolved information. In particular, our proposed methodology successfully establishes a map between inputs given by stencils of the vorticity and the streamfunction along with information from two well-known eddy-viscosity kernels. Through this we predict the subgrid vorticity forcing in a temporally and spatially dynamic fashion. Our study is botha priorianda posterioriin nature. In the former, we present an extensive hyper-parameter optimization analysis in addition to learning quantification through probability-density-function-based validation of subgrid predictions. In the latter, we analyse the performance of our framework for flow evolution in a classical decaying two-dimensional turbulence test case in the presence of errors related to temporal and spatial discretization. Statistical assessments in the form of angle-averaged kinetic energy spectra demonstrate the promise of the proposed methodology for subgrid quantity inference. In addition, it is also observed that some measure ofa posteriorierror must be considered during optimal model selection for greater accuracy. The results in this article thus represent a promising development in the formalization of a framework for generation of heuristic-free turbulence closures from data.
BUILDINGS, LANDSCAPES AND REGIMES OF MATERIALITY
Authors: Whyte William 
Published: November 2018

ABSTRACTBeginning with a surprisingly exuberant response to the landscape recorded by a distinguished scholar, this paper explores the agency of things and places though time. It argues that the recent ‘material turn’ is part of a broader re-enchantment of the world: a re-enchantment that has parallels with a similar process at the turn of the nineteenth century. Tracing this history suggests that within the space of a single generation the material world can be enchanted or disenchanted, with things and places imbued with – or stripped of –agency. In other words, different periods possess what we might call different regimes of materiality. Any approach which assumes the existence of material agency throughout history, or which imports our assumptions into a period which did not share them, will necessarily fail. Before we look at the material world, therefore, we need to examine how the material world was looked at, how it was conceptualised and how it was experienced. We need to apprehend its regime of materiality.
Subjective Perceptions of the Teaching–Research Nexus and Occupational Stress at Universities
Authors: Daumiller Martin , Dresel Markus 
Published: November 2018

Abstract. The duality of research and teaching is fundamental for university systems; however, it is often experienced as stressful. A study with 819 university scholars indicated the importance of subjective perceptions of the teaching–research nexus. Such views could be differentiated in perceived integration (e. g., research is part of teaching) and perceived synergy (e. g., research enriches teaching). Structural equation modeling showed that only perceived synergy was associated with reduced occupational stress.
Estrogen receptor β upregulated by lncRNA-H19 to promote cancer stem-like properties in papillary thyroid carcinoma
Authors: Li Mei , Chai Hui-Fang , Peng Fei , Meng Yu-Ting , Zhang Li-Zhi , Zhang Lin , Zou Hong , Liang Qi-Lan , Li Man-Man , Mao Kai-Ge , Sun Dong-Xu , Tong Meng-Ying , Deng Zi-Qian , Hou Zhi-Jie , Zhao Yi , Li Jia , Wang Xiao-Chao , Lv Sha-Sha , Zhang Qing-Qing , Yu Xiao , Lam Eric W.-F. , Liu Quentin , Cui Xiao-Nan , Xu Jie 
Published: November 2018

AbstractEstrogen receptor β (ERβ) plays critical roles in thyroid cancer progression. However, its role in thyroid cancer stem cell maintenance remains elusive. Here, we report that ERβ is overexpressed in papillary thyroid cancer stem cells (PTCSCs), whereas ablation of ERβ decreases stemness-related factors expression, diminishes ALDH+ cell populations, and suppresses sphere formation ability and tumor growth. Screening estrogen-responsive lncRNAs in PTC spheroid cells, we find that lncRNA-H19 is highly expressed in PTCSCs and PTC tissue specimens, which is correlated with poor overall survival. Mechanistically, estradiol (E2) significantly promotes H19 transcription via ERβ and elevates H19 expression. Silencing of H19 inhibits E2-induced sphere formation ability. Furthermore, H19 acting as a competitive endogenous RNA sequesters miRNA-3126-5p to reciprocally release ERβ expression. ERβ depletion reverses H19-induced stem-like properties upon E2 treatment. Appropriately, ERβ is upregulated in PTC tissue specimens. Notably, aspirin attenuates E2-induced cancer stem-like traits through decreasing both H19 and ERβ expression. Collectively, our findings reveal that ERβ-H19 positive feedback loop has a compelling role in PTCSC maintenance under E2 treatment and provides a potential therapeutic targeting strategy for PTC.
Overexpression of the vascular brassinosteroid receptor BRL3 confers drought resistance without penalizing plant growth
Authors: Fàbregas Norma , Lozano-Elena Fidel , Blasco-Escámez David , Tohge Takayuki , Martínez-Andújar Cristina , Albacete Alfonso , Osorio Sonia , Bustamante Mariana , Riechmann José Luis , Nomura Takahito , Yokota Takao , Conesa Ana , Alfocea Francisco Pérez , Fernie Alisdair R. , Caño-Delgado Ana I. 
Published: November 2018

AbstractDrought represents a major threat to food security. Mechanistic data describing plant responses to drought have been studied extensively and genes conferring drought resistance have been introduced into crop plants. However, plants with enhanced drought resistance usually display lower growth, highlighting the need for strategies to uncouple drought resistance from growth. Here, we show that overexpression of BRL3, a vascular-enriched member of the brassinosteroid receptor family, can confer drought stress tolerance in Arabidopsis. Whereas loss-of-function mutations in the ubiquitously expressed BRI1 receptor leads to drought resistance at the expense of growth, overexpression of BRL3 receptor confers drought tolerance without penalizing overall growth. Systematic analyses reveal that upon drought stress, increased BRL3 triggers the accumulation of osmoprotectant metabolites including proline and sugars. Transcriptomic analysis suggests that this results from differential expression of genes in the vascular tissues. Altogether, this data suggests that manipulating BRL3 expression could be used to engineer drought tolerant crops.
A rice Serine/Threonine receptor-like kinase regulates arbuscular mycorrhizal symbiosis at the peri-arbuscular membrane
Authors: Roth Ronelle , Chiapello Marco , Montero Héctor , Gehrig Peter , Grossmann Jonas , O’Holleran Kevin , Hartken Denise , Walters Fergus , Yang Shu-Yi , Hillmer Stefan , Schumacher Karin , Bowden Sarah , Craze Melanie , Wallington Emma J. , Miyao Akio , Sawers Ruairidh , Martinoia Enrico , Paszkowski Uta 
Published: November 2018

AbstractIn terrestrial ecosystems most plant species live in mutualistic symbioses with nutrient-delivering arbuscular mycorrhizal (AM) fungi. Establishment of AM symbioses includes transient, intracellular formation of fungal feeding structures, the arbuscules. A plant-derived peri-arbuscular membrane (PAM) surrounds the arbuscules, mediating reciprocal nutrient exchange. Signaling at the PAM must be well coordinated to achieve this dynamic cellular intimacy. Here, we identify the PAM-specific Arbuscular Receptor-like Kinase 1 (ARK1) from maize and rice to condition sustained AM symbiosis. Mutation of rice ARK1 causes a significant reduction in vesicles, the fungal storage structures, and a concomitant reduction in overall root colonization by the AM fungus Rhizophagus irregularis. Arbuscules, although less frequent in the ark1 mutant, are morphologically normal. Co-cultivation with wild-type plants restores vesicle and spore formation, suggesting ARK1 function is required for the completion of the fungal life-cycle, thereby defining a functional stage, post arbuscule development.
An interpretable approach for social network formation among heterogeneous agents
Authors: Yuan Yuan , Alabdulkareem Ahmad , Pentland Alex ‘Sandy’ 
Published: November 2018

AbstractUnderstanding the mechanisms of network formation is central in social network analysis. Network formation has been studied in many research fields with their different focuses; for example, network embedding algorithms in machine learning literature consider broad heterogeneity among agents while the social sciences emphasize the interpretability of link formation mechanisms. Here we propose a social network formation model that integrates methods in multiple disciplines and retain both heterogeneity and interpretability. We represent each agent by an “endowment vector” that encapsulates their features and use game-theoretical methods to model the utility of link formation. After applying machine learning methods, we further analyze our model by examining micro- and macro- level properties of social networks as most agent-based models do. Our work contributes to the literature on network formation by combining the methods in game theory, agent-based modeling, machine learning, and computational sociology.
HLA-B57 micropolymorphism defines the sequence and conformational breadth of the immunopeptidome
Authors: Illing Patricia T. , Pymm Phillip , Croft Nathan P. , Hilton Hugo G. , Jojic Vladimir , Han Alex S. , Mendoza Juan L. , Mifsud Nicole A. , Dudek Nadine L. , McCluskey James , Parham Peter , Rossjohn Jamie , Vivian Julian P. , Purcell Anthony W. 
Published: November 2018

AbstractImmunophenotypic differences between closely related human leukocyte antigen (HLA) alleles have been associated with divergent clinical outcomes in infection, autoimmunity, transplantation and drug hypersensitivity. Here we explore the impact of micropolymorphism on peptide antigen presentation by three closely related HLA molecules, HLA-B*57:01, HLA-B*57:03 and HLA-B*58:01, that are differentially associated with the HIV elite controller phenotype and adverse drug reactions. For each allotype, we mine HLA ligand data sets derived from the same parental cell proteome to define qualitative differences in peptide presentation using classical peptide binding motifs and an unbiased statistical approach. The peptide repertoires show marked qualitative overlap, with 982 peptides presented by all allomorphs. However, differences in peptide abundance, HLA-peptide stability, and HLA-bound conformation demonstrate that HLA micropolymorphism impacts more than simply the range of peptide ligands. These differences provide grounds for distinct immune reactivity and insights into the capacity of micropolymorphism to diversify immune outcomes.
A structural mechanism for directing corepressor-selective inverse agonism of PPARγ
Authors: Brust Richard , Shang Jinsai , Fuhrmann Jakob , Mosure Sarah A. , Bass Jared , Cano Andrew , Heidari Zahra , Chrisman Ian M. , Nemetchek Michelle D. , Blayo Anne-Laure , Griffin Patrick R. , Kamenecka Theodore M. , Hughes Travis S. , Kojetin Douglas J. 
Published: November 2018

AbstractSmall chemical modifications can have significant effects on ligand efficacy and receptor activity, but the underlying structural mechanisms can be difficult to predict from static crystal structures alone. Here we show how a simple phenyl-to-pyridyl substitution between two common covalent orthosteric ligands targeting peroxisome proliferator-activated receptor (PPAR) gamma converts a transcriptionally neutral antagonist (GW9662) into a repressive inverse agonist (T0070907) relative to basal cellular activity. X-ray crystallography, molecular dynamics simulations, and mutagenesis coupled to activity assays reveal a water-mediated hydrogen bond network linking the T0070907 pyridyl group to Arg288 that is essential for corepressor-selective inverse agonism. NMR spectroscopy reveals that PPARγ exchanges between two long-lived conformations when bound to T0070907 but not GW9662, including a conformation that prepopulates a corepressor-bound state, priming PPARγ for high affinity corepressor binding. Our findings demonstrate that ligand engagement of Arg288 may provide routes for developing corepressor-selective repressive PPARγ ligands.
Syncytial germline architecture is actively maintained by contraction of an internal actomyosin corset
Authors: Priti Agarwal , Ong Hui Ting , Toyama Yusuke , Padmanabhan Anup , Dasgupta Sabyasachi , Krajnc Matej , Zaidel-Bar Ronen 
Published: November 2018

AbstractSyncytial architecture is an evolutionarily-conserved feature of the germline of many species and plays a crucial role in their fertility. However, the mechanism supporting syncytial organization is largely unknown. Here, we identify a corset-like actomyosin structure within the syncytial germline of Caenorhabditis elegans, surrounding the common rachis. Using laser microsurgery, we demonstrate that actomyosin contractility within this structure generates tension both in the plane of the rachis surface and perpendicular to it, opposing membrane tension. Genetic and pharmacological perturbations, as well as mathematical modeling, reveal a balance of forces within the gonad and show how changing the tension within the actomyosin corset impinges on syncytial germline structure, leading, in extreme cases, to sterility. Thus, our work highlights a unique tissue-level cytoskeletal structure, and explains the critical role of actomyosin contractility in the preservation of a functional germline.
Proteostasis by STUB1/HSP70 complex controls sensitivity to androgen receptor targeted therapy in advanced prostate cancer
Authors: Liu Chengfei , Lou Wei , Yang Joy C. , Liu Liangren , Armstrong Cameron M. , Lombard Alan P. , Zhao Ruining , Noel Onika D. V. , Tepper Clifford G. , Chen Hong-Wu , Dall’Era Marc , Evans Christopher P. , Gao Allen C. 
Published: November 2018

AbstractProtein homeostasis (proteostasis) is a potential mechanism that contributes to cancer cell survival and drug resistance. Constitutively active androgen receptor (AR) variants confer anti-androgen resistance in advanced prostate cancer. However, the role of proteostasis involved in next generation anti-androgen resistance and the mechanisms of AR variant regulation are poorly defined. Here we show that the ubiquitin-proteasome-system (UPS) is suppressed in enzalutamide/abiraterone resistant prostate cancer. AR/AR-V7 proteostasis requires the interaction of E3 ubiquitin ligase STUB1 and HSP70 complex. STUB1 disassociates AR/AR-V7 from HSP70, leading to AR/AR-V7 ubiquitination and degradation. Inhibition of HSP70 significantly inhibits prostate tumor growth and improves enzalutamide/abiraterone treatments through AR/AR-V7 suppression. Clinically, HSP70 expression is upregulated and correlated with AR/AR-V7 levels in high Gleason score prostate tumors. Our results reveal a novel mechanism of anti-androgen resistance via UPS alteration which could be targeted through inhibition of HSP70 to reduce AR-V7 expression and overcome resistance to AR-targeted therapies.
Real-time coherent diffraction inversion using deep generative networks
Authors: Cherukara Mathew J. , Nashed Youssef S. G. , Harder Ross J. 
Published: November 2018

AbstractPhase retrieval, or the process of recovering phase information in reciprocal space to reconstruct images from measured intensity alone, is the underlying basis to a variety of imaging applications including coherent diffraction imaging (CDI). Typical phase retrieval algorithms are iterative in nature, and hence, are time-consuming and computationally expensive, making real-time imaging a challenge. Furthermore, iterative phase retrieval algorithms struggle to converge to the correct solution especially in the presence of strong phase structures. In this work, we demonstrate the training and testing of CDI NN, a pair of deep deconvolutional networks trained to predict structure and phase in real space of a 2D object from its corresponding far-field diffraction intensities alone. Once trained, CDI NN can invert a diffraction pattern to an image within a few milliseconds of compute time on a standard desktop machine, opening the door to real-time imaging.
Spontaneous innovation of hook-bending and unbending in orangutans (Pongo abelii)
Authors: Laumer I. B. , Call J. , Bugnyar T. , Auersperg A. M. I. 
Published: November 2018

AbstractBetty the crow astonished the scientific world as she spontaneously crafted hook-tools from straight wire in order to lift a basket out of vertical tubes. Recently it was suggested that this species’ solution was strongly influenced by predispositions from behavioural routines from habitual hook-tool manufacture. Nevertheless, the task became a paradigm to investigate tool innovation. Considering that young humans had surprising difficulties with the task, it was yet unclear whether the innovation of a hooked tool would be feasible to primates that lacked habitual hook making. We thus tested five captive orangutans in a hook bending and unbending task. Orangutans are habitually tool-using primates that have been reported to use but not craft hooked tools for locomotion in the wild. Two orangutans spontaneously innovated hook tools and four unbent the wire from their first trial on. Pre-experience with ready-made hooks had some effect but did not lead to continuous success. Further subjects improved the hook-design feature when the task required the subjects to bent the hook at a steeper angle. Our results indicate that the ability to represent and manufacture tools according to a current need does not require stereotyped behavioural routines, but can indeed arise innovatively. Furthermore, the present study shows that the capacity for hook tool innovation is not limited to large brained birds within non-human animals.
Altered Placental Chorionic Arterial Biomechanical Properties During Intrauterine Growth Restriction
Authors: Saw Shier Nee , Tay Jess Jia Hwee , Poh Yu Wei , Yang Liying , Tan Wei Ching , Tan Lay Kok , Clark Alys , Biswas Arijit , Mattar Citra Nurfarah Zaini , Yap Choon Hwai 
Published: November 2018

AbstractIntrauterine growth restriction (IUGR) is a pregnancy complication due to placental dysfunction that prevents the fetus from obtaining enough oxygen and nutrients, leading to serious mortality and morbidity risks. There is no treatment for IUGR despite having a prevalence of 3% in developed countries, giving rise to an urgency to improve our understanding of the disease. Applying biomechanics investigation on IUGR placental tissues can give important new insights. We performed pressure-diameter mechanical testing of placental chorionic arteries and found that in severe IUGR cases (RI > 90th centile) but not in IUGR cases (RI < 90th centile), vascular distensibility was significantly increased from normal. Constitutive modeling demonstrated that a simplified Fung-type hyperelastic model was able to describe the mechanical properties well, and histology showed that severe IUGR had the lowest collagen to elastin ratio. To demonstrate that the increased distensibility in the severe IUGR group was related to their elevated umbilical resistance and pulsatility indices, we modelled the placental circulation using a Windkessel model, and demonstrated that vascular compliance (and not just vascular resistance) directly affected blood flow pulsatility, suggesting that it is an important parameter for the disease. Our study showed that biomechanics study on placenta could extend our understanding on placenta physiology.
Fundamental of swapping phenomena in naturally occurring gas hydrates
Authors: Palodkar Avinash V. , Jana Amiya K. 
Published: November 2018

AbstractAmount of natural gas contained in the gas hydrate accumulations is twice that of all fossil fuel reserves currently available worldwide. The conventional oil and gas recovery technologies are not really suitable to gas hydrates because of their serious repercussions on geo-mechanical stability and seabed ecosystem. To address this challenge, the concept of methane-carbon dioxide (CH4-CO2) swapping has appeared. It has the potential in achieving safe and efficient recovery of natural gas, and sequestration of CO2. By this way, the energy generation from gas hydrates can become carbon neutral. This swapping phenomenon has not yet been elucidated at fundamental level. This work proposes a theoretical formulation to understand the physical insight into the transient swapping between natural gas and CO2 occurred under deep seabed and in permafrost. Addressing several practical concerns makes the model formulation novel and generalized enough in explaining the swapping phenomena at diverse geological conditions.
Space lidar observations constrain longwave cloud feedback
Authors: Vaillant de Guélis Thibault , Chepfer Hélène , Guzman Rodrigo , Bonazzola Marine , Winker David M. , Noel Vincent 
Published: November 2018

AbstractSome of the most challenging questions in atmospheric science relate to how clouds will respond as the climate warms. On centennial scales, the response of clouds could either weaken or enhance the warming due to greenhouse gas emissions. Here we use space lidar observations to quantify changes in cloud altitude, cover, and opacity over the oceans between 2008 and 2014, together with a climate model with a lidar simulator to also simulate these changes in the present-day climate and in a future, warmer climate. We find that the longwave cloud altitude feedback, found to be robustly positive in simulations since the early climate models and backed up by physical explanations, is not the dominant longwave feedback term in the observations, although it is in the model we have used. These results suggest that the enhanced longwave warming due to clouds might be overestimated in climate models. These results highlight the importance of developing a long-term active sensor satellite record to reduce uncertainties in cloud feedbacks and prediction of future climate.
Dramatic cropland expansion in Myanmar following political reforms threatens biodiversity
Authors: Zhang Yuchen , Prescott Graham W. , Tay Rebecca E. , Dickens Borame L. , Webb Edward L. , Htun Saw , Tizard Robert J. , Rao Madhu , Carrasco Luis Roman 
Published: November 2018

AbstractEffective conservation planning needs to consider the threats of cropland expansion to biodiversity. We used Myanmar as a case study to devise a modeling framework to identify which Key Biodiversity Areas (KBAs) are most vulnerable to cropland expansion in a context of increasingly resolved armed conflict. We studied 13 major crops with the potential to expand into KBAs. We used mixed-effects models and an agricultural versus forest rent framework to model current land use and conversion of forests to cropland for each crop. We found that the current cropland distribution is explained by higher agricultural value, lower transportation costs and lower elevation. We also found that protected areas and socio-political instability are effective in slowing down deforestation with conflicts in Myanmar damaging farmland and displacing farmers elsewhere. Under plausible economic development and socio-political stability scenarios, the models forecast 48.5% of land to be converted. We identified export crops such as maize, and pigeon pea as key deforestation drivers. This cropland expansion would pose a major threat to Myanmar’s freshwater KBAs. We highlight the importance of considering rapid land-use transitions in the tropics to devise robust conservation plans.