bluuebunny/crossref_metadata_2025_split huggingface dataset:
Construction of a CRISPR‐based paired‐sgRNA library for chromosomal deletion of long non‐coding RNAs
Authors: Tao Minzhen , Mu Qiaochu , Zhang Yurui , Xie Zhen 
Published: March 2020

BackgroundDerived from an adaptive bacterial immune system, the clustered regularly interspaced palindromic repeats (CRISPR)/CRISPR‐associated 9 (Cas9) system has shown great potential in high‐throughput functional genomic screening, especially for protein‐coding genes. However, it is still challenging to apply the similar strategy to study non‐coding genomic elements such as long non‐coding RNAs (lncRNAs) or clusters of microRNAs, because short insertions or deletions may not be sufficient to generate loss‐of‐function phenotypes.MethodsHere, we presented a systematic strategy for designing a CRISPR‐based paired‐sgRNA library for high‐throughput screening in non‐coding regions. Due to the abundance of lncRNAs and their diverse regulatory roles in vivo, we repurposed microarray datasets to select 600 highly expressed lncRNAs in non‐small‐cell lung cancer and designed two schemes for lncRNA deletion with ~20 paired‐sgRNAs for each lncRNA. Through Golden‐Gate assembly, we generated a pooled CRISPR‐based library with a total of 12,878 sgRNA pairs.ResultsOver 80% of paired‐sgRNAs were recovered from final pooled library with a relatively even distribution. Cleavage efficiency of sgRNA pairs was validated through experiments of transient transfection and viral infection. Moreover, randomly selected paired‐sgRNAs showed that efficient deletion of genomic DNA could be achieved with a deletion size within the range of 500 to 3000 bp.ConclusionsIn summary, we have demonstrated a strategy to design and construct a pooled paired‐sgRNA library to generate genomic deletion in the lncRNA regions, validated their deletion efficiency and explored the relationship of deletion efficiency with respect to deletion size. This method would be also suitable for investigation of other uncharacterized non‐coding genomic regions in mammalian cells in an efficient and cost‐effective manner.
ZokorDB: tissue specific regulatory network annotation for non‐coding elements of plateau zokor
Authors: Xin Jingxue , Hao Junjun , Chen Lang , Zhang Tao , Li Lei , Chen Luonan , Zhao Wenmin , Lu Xuemei , Shi Peng , Wang Yong 
Published: March 2020

BackgroundPlateau zokor inhabits in sealed burrows from 2,000 to 4,200 meters at Qinghai‐Tibet Plateau. This extreme living environment makes it a great model to study animal adaptation to hypoxia, low temperature, and high carbon dioxide concentration.MethodsWe provide an integrated resource, ZokorDB, for tissue specific regulatory network annotation for zokor. ZokorDB is based on a high‐quality draft genome of a plateau zokor at 3,300 m and its transcriptional profiles in brain, heart, liver, kidney, and lung. The conserved non‐coding elements of zokor are annotated by their nearest genes and upstream transcriptional factor motif binding sites.ResultsZokorDB provides a general draft gene regulatory network (GRN), i.e., potential transcription factor (TF) binds to non‐coding regulatory elements and regulates the expression of target genes (TG). Furthermore, we refined the GRN by incorporating matched RNA‐seq and DNase‐seq data from mouse ENCODE project and reconstructed five tissue‐specific regulatory networks.ConclusionsA web‐based, open‐access database is developed for easily searching, visualizing, and downloading the annotation and data. The pipeline of non‐coding region annotation for zokor will be useful for other non‐model species. ZokorDB is free available at the website (bigd.big.ac.cn/zokordb/).
A general approach to compensation for losses incurred due to public health interventions in the infectious disease context
Authors: Holm Søren 
Published: March 2020

AbstractThis paper develops a general approach to how society should compensate for losses that individuals incur due to public health interventions aimed at controlling the spread of infectious diseases. The paper falls in three parts. The first part provides an initial introduction to the issues and briefly outlines five different kinds of public health interventions that will be used as test cases. They are all directed at individuals and aimed at controlling the spread of infectious diseases (1) isolation, (2) quarantine, (3) recommended voluntary social distancing, (4) changes in health care provision for asymptomatic carriers of multi-resistant microorganisms, and (5) vaccination. The interventions will be briefly described including the various risks, burdens and harms individuals who are subject to these interventions may incur. The second part briefly surveys current compensation mechanisms as far as any exist and argue that even where they exist they are clearly insufficient and do not provide adequate compensation. The third part will then develop a general framework for compensation for losses incurred due to public health interventions in the infectious disease context. This is the major analytical and constructive part of the paper. It first analyses pragmatic and ethical arguments supporting the existence of an obligation on the part of the state to compensate for such losses, and then considers whether this obligation can be defeated by (1) resource considerations, or (2) issues relating to personal responsibility.
Modeling higher order adaptivity of a network by multilevel network reification
Authors: Treur Jan 
Published: March 2020

AbstractIn network models for real-world domains, often network adaptation has to be addressed by incorporating certain network adaptation principles. In some cases, also higher order adaptation occurs: the adaptation principles themselves also change over time. To model such multilevel adaptation processes, it is useful to have some generic architecture. Such an architecture should describe and distinguish the dynamics within the network (base level), but also the dynamics of the network itself by certain adaptation principles (first-order adaptation level), and also the adaptation of these adaptation principles (second-order adaptation level), and may be still more levels of higher order adaptation. This paper introduces a multilevel network architecture for this, based on the notion network reification. Reification of a network occurs when a base network is extended by adding explicit states representing the characteristics of the structure of the base network. It will be shown how this construction can be used to explicitly represent network adaptation principles within a network. When the reified network is itself also reified, also second-order adaptation principles can be explicitly represented. The multilevel network reification construction introduced here is illustrated for an adaptive adaptation principle from social science for bonding based on homophily and one for metaplasticity in Cognitive Neuroscience.
Cosmology with Phase 1 of the Square Kilometre Array Red Book 2018: Technical specifications and performance forecasts
Authors:   Square Kilometre Array Cosmology Science Working Group:, Bacon David J. , Battye Richard A. , Bull Philip , Camera Stefano , Ferreira Pedro G. , Harrison Ian , Parkinson David , Pourtsidou Alkistis , Santos Mário G. , Wolz Laura , Abdalla Filipe , Akrami Yashar , Alonso David , Andrianomena Sambatra , Ballardini Mario , Bernal José Luis , Bertacca Daniele , Bengaly Carlos A. P. , Bonaldi Anna , Bonvin Camille , Brown Michael L. , Chapman Emma , Chen Song , Chen Xuelei , Cunnington Steven , Davis Tamara M. , Dickinson Clive , Fonseca José , Grainge Keith , Harper Stuart , Jarvis Matt J. , Maartens Roy , Maddox Natasha , Padmanabhan Hamsa , Pritchard Jonathan R. , Raccanelli Alvise , Rivi Marzia , Roychowdhury Sambit , Sahlén Martin , Schwarz Dominik J. , Siewert Thilo M. , Viel Matteo , Villaescusa-Navarro Francisco , Xu Yidong , Yamauchi Daisuke , Zuntz Joe 
Published: March 2020

Abstract
We present a detailed overview of the cosmological surveys that we aim to carry out with Phase 1 of the Square Kilometre Array (SKA1) and the science that they will enable. We highlight three main surveys: a medium-deep continuum weak lensing and low-redshift spectroscopic HI galaxy survey over 5 000 deg2; a wide and deep continuum galaxy and HI intensity mapping (IM) survey over 20 000 deg2 from

$z = 0.35$

to 3; and a deep, high-redshift HI IM survey over 100 deg2 from

$z = 3$

to 6. Taken together, these surveys will achieve an array of important scientific goals: measuring the equation of state of dark energy out to

$z \sim 3$

with percent-level precision measurements of the cosmic expansion rate; constraining possible deviations from General Relativity on cosmological scales by measuring the growth rate of structure through multiple independent methods; mapping the structure of the Universe on the largest accessible scales, thus constraining fundamental properties such as isotropy, homogeneity, and non-Gaussianity; and measuring the HI density and bias out to

$z = 6$

. These surveys will also provide highly complementary clustering and weak lensing measurements that have independent systematic uncertainties to those of optical and near-infrared (NIR) surveys like Euclid, LSST, and WFIRST leading to a multitude of synergies that can improve constraints significantly beyond what optical or radio surveys can achieve on their own. This document, the 2018 Red Book, provides reference technical specifications, cosmological parameter forecasts, and an overview of relevant systematic effects for the three key surveys and will be regularly updated by the Cosmology Science Working Group in the run up to start of operations and the Key Science Programme of SKA1.
Modulation of the intestinal microbiota and the metabolites produced by the administration of ice cream and a dietary supplement containing the same probiotics
Authors: Rodrigues Vivian Cristina da Cruz , Duque Ana Luiza Rocha Faria , Fino Luciana de Carvalho , Simabuco Fernando Moreira , Sartoratto Adilson , Cabral Lucélia , Noronha Melline Fontes , Sivieri Katia , Antunes Adriane Elisabete Costa 
Published: March 2020

AbstractThe aim of the present work was to compare the capacity to modulate the intestinal microbiota and the production of metabolites after 14 d administration of a commercial dietary supplement and a manufactured ice cream, both containing the same quantity of inulin and the same viable counts of Lactobacillus acidophilus LA-5 and Bifidobacterium animalis BB-12, using the Simulator of the Human Intestinal Microbial Ecosystem (SHIME®) model. Samples of the colonic contents were evaluated microbiologically by real-time quantitative PCR (qRT-PCR) and next-generation sequencing and chemically by the production of SCFA (acetate, propionate and butyrate) and ammonium ions ($\text{NH}_4^ + $). Statistical analyses were carried out for all the variables using the two-way ANOVA followed by the Tukey multiple comparisons test (P < 0·05) for metabolite production, qRT-PCR and the bioinformatics analysis for microbiota diversity. Dietary supplement and ice cream were able to deliver the probiotic L. acidophilus and B. animalis to the simulated colon and modulate the microbiota, increasing beneficial micro-organisms such as Bifidobacterium spp., Bacteroides spp. and Faecalibacterium spp. for dietary supplement administration, and Lactobacillus spp. for ice cream supplementation. However, the ice cream matrix was probably more favourable for the maintenance of the metabolic activity of the probiotics in the SHIME® model, due to the larger amounts of acetate, propionate, butyrate and ammonium ions obtained after 14 d of supplementation. In conclusion, both ways of probiotic supplementation could be efficient, each with its own particularities.
The Psychology of Repression and Polarization
Authors: Nugent Elizabeth R. 
Published: March 2020

ABSTRACTHow does political polarization occur under repressive conditions? Drawing on psychological theories of social identity, the author posits that the nature of repression drives polarization. Repression alters group identities, changing the perceived distance between groups and ultimately shaping the level of affective and preference polarization between them through differentiation processes. The author tests the proposed causal relationship using mixed-method data and analysis.The results of a laboratory experiment reveal that exposure to a targeted repression prime results in greater in-group identification and polarization between groups, whereas exposure to a widespread prime results in decreased levels of these same measurements. The effect of the primes appears to be mediated through group identification. Case-study evidence of polarization between political opposition groups that were differently repressed in Egypt and Tunisia reinforces these results. The findings have implications for understanding how polarization, as conditioned by repression, may alter the likelihood of the cooperative behavior among opposition actors necessary for the success of democratic politics.
Toll-based reinforcement learning for efficient equilibria in route choice
Authors: Ramos Gabriel de O. , Da Silva Bruno C. , Rădulescu Roxana , Bazzan Ana L. C. , Nowé Ann 
Published: March 2020

Abstract
The problem of traffic congestion incurs numerous social and economical repercussions and has thus become a central issue in every major city in the world. For this work we look at the transportation domain from a multiagent system perspective, where every driver can be seen as an autonomous decision-making agent. We explore how learning approaches can help achieve an efficient outcome, even when agents interact in a competitive environment for sharing common resources. To this end, we consider the route choice problem, where self-interested drivers need to independently learn which routes minimise their expected travel costs. Such a selfish behaviour results in the so-called user equilibrium, which is inefficient from the system’s perspective. In order to mitigate the impact of selfishness, we present Toll-based Q-learning (TQ-learning, for short). TQ-learning employs the idea of marginal-cost tolling (MCT), where each driver is charged according to the cost it imposes on others. The use of MCT leads agents to behave in a socially desirable way such that the is attainable. In contrast to previous works, however, our tolling scheme is distributed (i.e., each agent can compute its own toll), is charged a posteriori (i.e., at the end of each trip), and is fairer (i.e., agents pay exactly their marginal costs). Additionally, we provide a general formulation of the toll values for univariate, homogeneous polynomial cost functions. We present a theoretical analysis of TQ-learning, proving that it converges to a system-efficient equilibrium (i.e., an equilibrium aligned to the system optimum) in the limit. Furthermore, we perform an extensive empirical evaluation on realistic road networks to support our theoretical findings, showing that TQ-learning indeed converges to the optimum, which translates into a reduction of the congestion levels by 9.1%, on average.
Mesozoic‐Cenozoic Regional Stress Field Evolution in Svalbard
Authors: Maher Harmon , Senger Kim , Braathen Alvar , Mulrooney Mark Joseph , Smyrak‐Sikora Aleksandra , Osmundsen Per Terje , Ogata Kei 
Published: March 2020

AbstractCooling fracture orientations in diabase sills associated with the Cretaceous High Arctic Large Igneous Province and syn‐sedimentary Triassic faults help constrain a model for Svalbard's (NE Barents Shelf) Mesozoic stress field evolution. Fracture data from Edgeøya and adjacent islands in SE Svalbard, from S Spitsbergen, and from literature were used to model preferred orientations and temporal relationships. Orthogonal, roughly E‐W and N‐S, joints and veins in sills from SE Svalbard are interpreted as cooling fractures influenced by the ambient stress field. Aligned preferred orientations within the Triassic host strata are associated with a regional Cretaceous jointing episode driven by sill emplacement and/or erosional unloading. The regional maximum horizontal stress (likely σ1) is inferred to have been parallel to a dominant ≈E‐W set. Spitsbergen's more complex joint patterns are associated with proximity to the Cenozoic West Spitsbergen Fold‐and‐Thrust Belt, but ≈E‐W and ≈N‐S orientations occur and are typically the earlier set. Syn‐sedimentary, ≈NW‐SE striking, Triassic normal faults in SE Svalbard aligned with the maximum horizontal stress indicate a Triassic to Cretaceous counterclockwise stress field shift, with additional counterclockwise shifting during Cenozoic dextral transpression between Svalbard and Greenland. Localized joint preferred orientations consistent with both decoupled and coupled transpression occur. Changes in the regional maximum horizontal stress and deformation regime may reflect timing of which plate margin was crucial in influencing Svalbard's plate interior stress field, starting with Triassic Uralian activity to the E, then Cretaceous Amerasian Basin development to the NW, culminating with Cenozoic dextral transpression and transtension to the SW.
Linking Agricultural GHG Emissions to Global Trade Network
Authors: Zhao Xueli , Wu Xiaofang , Guan ChengHe , Ma Rong , Nielsen Chris P. , Zhang Bo 
Published: March 2020

AbstractAs part of the climate policy to meet the 2 °C target, actions in all economic sectors, including agriculture, are required to mitigate global greenhouse gas emissions. While there has been an ever‐increasing focus on agricultural greenhouse gas (AGHG) emissions, limited attention has been paid to their economic drivers in the globalized world economy and related mitigation potentials. This paper makes a first attempt to trace AGHG emissions via global trade networks using a multiregional input‐output model and a complex network model. Over one third of global AGHG emissions in 2012 can be linked with products traded internationally, of which intermediate trade and final trade contribute 64.2% and 35.8%, respectively. Japan, the United States, Germany, the United Kingdom, and Hong Kong are the world's five largest net importers of embodied emissions, while Ethiopia, Australia, Pakistan, India, and Argentina are the five largest net exporters. Some hunger‐afflicted developing countries in Asia and Africa are important embodied emission exporters, due to their large‐scale exports of agricultural products. Trade‐related virtual AGHG emission transfers shape a highly heterogenous network, due to the coexistence of numerous peripheral economies and a few highly connected hub economies. The network clustering structure is revealed by the regional integration of several trading communities, while hub economies are collectors and distributors in the global trade network, with important implications for emission mitigation. Achieving AGHG emission reduction calls for a combination of supply‐ and demand‐side policies covering the global trade network.
Glacier Outflow Dissolved Organic Matter as a Window Into Seasonally Changing Carbon Sources: Leverett Glacier, Greenland
Authors: Kellerman A. M. , Hawkings J. R. , Wadham J. L. , Kohler T. J. , Stibal M. , Grater E. , Marshall M. , Hatton J. E. , Beaton A. , Spencer R. G. M. 
Published: March 2020

AbstractThe Greenland Ice Sheet is losing mass at a remarkable rate as a result of climatic warming. This mass loss coincides with the export of dissolved organic matter (DOM) in glacial meltwaters. However, little is known about how the source and composition of exported DOM changes over the melt season, which is key for understanding its fate in downstream ecosystems. Over the 2015 ablation season, we sampled the outflow of Leverett Glacier, a large land‐terminating glacier of the Greenland Ice Sheet. Dissolved organic carbon (DOC) concentrations and DOM fluorescence were analyzed to assess the evolution of DOM sources over the course of the melt season. DOC concentrations and red‐shifted fluorescence were highly associated (R2 > 0.95) and suggest terrestrial inputs from overridden soils dominated DOM early season inputs before progressive dilution with increasing discharge. During the outburst period, supraglacial drainage events disrupted the subglacial drainage system and introduced dominant protein‐like fluorescence signatures not observed in basal flow. These results suggest that subglacial hydrology and changing water sources influence exported DOC concentration and DOM composition, and these sources were differentiated using fluorescence characteristics. Red‐shifted fluorescence components were robust proxies for DOC concentration. Finally, the majority of DOM flux, which occurs during the outburst and postoutburst periods, was characterized by protein‐like fluorescence from supraglacial and potentially subglacial microbial sources. As protein‐like fluorescence is linked to the bioavailability of DOM, the observed changes likely reflect seasonal variations in the impact of glacial inputs on secondary production in downstream ecosystems due to shifting hydrologic regimes.
Robust and replicable measurement for prepulse inhibition of the acoustic startle response
Authors: Miller Eric A. , Kastner David B. , Grzybowski Michael N. , Dwinell Melinda R. , Geurts Aron M. , Frank Loren M. 
Published: March 2020

AbstractMeasuring animal behavior in the context of experimental manipulation is critical for modeling, and understanding neuropsychiatric disease. Prepulse inhibition of the acoustic startle response (PPI) is a behavioral phenomenon studied extensively for this purpose, but the results of PPI studies are often inconsistent. As a result, the utility of this phenomenon remains uncertain. Here, we deconstruct the phenomenon of PPI and confirm several limitations of the methodology traditionally utilized to describe PPI, including that the underlying startle response has a non-Gaussian distribution, and that the traditional PPI metric changes with different stimuli. We then develop a novel model that reveals PPI to be a combination of the previously appreciated scaling of the startle response, as well as a scaling of sound processing. Using our model, we find no evidence for differences in PPI in a rat model of Fragile-X Syndrome (FXS) compared with wild-type controls. These results in the rat provide a reliable methodology that could be used to clarify inconsistent PPI results in mice and humans. In contrast, we find robust differences between wild-type male and female rats. Our model allows us to understand the nature of these differences, and we find that both the startle-scaling and sound-scaling components of PPI are a function of the baseline startle response. Males and females differ specifically in the startle-scaling, but not the sound-scaling, component of PPI. These findings establish a robust experimental and analytical approach that has the potential to provide a consistent biomarker of brain function.