bluuebunny/crossref_metadata_2025_split huggingface dataset:
Probing 10 μK stability and residual drifts in the cross-polarized dual-mode stabilization of single-crystal ultrahigh-Q optical resonators
Authors: Lim Jinkang , Liang Wei , Savchenkov Anatoliy A. , Matsko Andrey B. , Maleki Lute , Wong Chee Wei 
Published: January 2019

AbstractThe thermal stability of monolithic optical microresonators is essential for many mesoscopic photonic applications such as ultrastable laser oscillators, photonic microwave clocks, and precision navigation and sensing. Their fundamental performance is largely bounded by thermal instability. Sensitive thermal monitoring can be achieved by utilizing cross-polarized dual-mode beat frequency metrology, determined by the polarization-dependent thermorefractivity of a single-crystal microresonator, wherein the heterodyne radio-frequency beat pins down the optical mode volume temperature for precision stabilization. Here, we investigate the correlation between the dual-mode beat frequency and the resonator temperature with time and the associated spectral noise of the dual-mode beat frequency in a single-crystal ultrahigh-Q MgF2 resonator to illustrate that dual-mode frequency metrology can potentially be utilized for resonator temperature stabilization reaching the fundamental thermal noise limit in a realistic system. We show a resonator long-term temperature stability of 8.53 μK after stabilization and unveil various sources that hinder the stability from reaching sub-μK in the current system, an important step towards compact precision navigation, sensing, and frequency reference architectures.
Nitric oxide production and antioxidant function during viral infection of the coccolithophore Emiliania huxleyi
Authors: Schieler Brittany M , Soni Megha V , Brown Christopher M , Coolen Marco J L , Fredricks Helen , Van Mooy Benjamin A S , Hirsh Donald J , Bidle Kay D 
Published: January 2019

Abstract
Emiliania huxleyi is a globally important marine phytoplankton that is routinely infected by viruses. Understanding the controls on the growth and demise of E. huxleyi blooms is essential for predicting the biogeochemical fate of their organic carbon and nutrients. In this study, we show that the production of nitric oxide (NO), a gaseous, membrane-permeable free radical, is a hallmark of early-stage lytic infection in E. huxleyi by Coccolithoviruses, both in culture and in natural populations in the North Atlantic. Enhanced NO production was detected both intra- and extra-cellularly in laboratory cultures, and treatment of cells with an NO scavenger significantly reduced viral production. Pre-treatment of exponentially growing E. huxleyi cultures with the NO donor S-nitroso-N-acetylpenicillamine (SNAP) prior to challenge with hydrogen peroxide (H2O2) led to greater cell survival, suggesting that NO may have a cellular antioxidant function. Indeed, cell lysates generated from cultures treated with SNAP and undergoing infection displayed enhanced ability to detoxify H2O2. Lastly, we show that fluorescent indicators of cellular ROS, NO, and death, in combination with classic DNA- and lipid-based biomarkers of infection, can function as real-time diagnostic tools to identify and contextualize viral infection in natural E. huxleyi blooms.
Histone H3 binding to the PHD1 domain of histone demethylase KDM5A enables active site remodeling
Authors: Longbotham James E. , Chio Cynthia M. , Dharmarajan Venkatasubramanian , Trnka Michael J. , Torres Idelisse Ortiz , Goswami Devrishi , Ruiz Karen , Burlingame Alma L. , Griffin Patrick R. , Fujimori Danica Galonić 
Published: January 2019

AbstractHistone demethylase KDM5A removes methyl marks from lysine 4 of histone H3 and is often overexpressed in cancer. The in vitro demethylase activity of KDM5A is allosterically enhanced by binding of its product, unmodified H3 peptides, to its PHD1 reader domain. However, the molecular basis of this allosteric enhancement is unclear. Here we show that saturation of the PHD1 domain by the H3 N-terminal tail peptides stabilizes binding of the substrate to the catalytic domain and improves the catalytic efficiency of demethylation. When present in saturating concentrations, differently modified H3 N-terminal tail peptides have a similar effect on demethylation. However, they vary greatly in their affinity towards the PHD1 domain, suggesting that H3 modifications can tune KDM5A activity. Furthermore, hydrogen/deuterium exchange coupled with mass spectrometry (HDX-MS) experiments reveal conformational changes in the allosterically enhanced state. Our findings may enable future development of anti-cancer therapies targeting regions involved in allosteric regulation.
The influence of the stiffness of GelMA substrate on the outgrowth of PC12 cells
Authors: Wu Yibing , Xiang Yang , Fang Jiehua , Li Xiaokeng , Lin Zunwen , Dai Guangli , Yin Jun , Wei Peng , Zhang Deming 
Published: January 2019

Abstract
Recent studies have shown the importance of cell–substrate interaction on neurone outgrowth, where the Young’s modulus of the matrix plays a crucial role on the neurite length, migration, proliferation, and morphology of neurones. In the present study, PC12 cells were selected as the representative neurone to be cultured on hydrogel substrates with different stiffness to explore the effect of substrate stiffness on the neurone outgrowth. By adjusting the concentration of gelatin methacryloyl (GelMA), the hydrogel substrates with the variation of stiffnesses (indicated by Young’s modulus) from approximately 3–180 KPa were prepared. It is found that the stiffness of GelMA substrates influences neuronal outgrowth, including cell viability, adhesion, spreading, and average neurite length. Our results show a critical range of substrate’s Young’s modulus that support PC12 outgrowth, and modulate the cell characteristics and morphology. The present study provides an insight into the relationship between the stiffness of GelMA hydrogel substrates and PC12 cell outgrowth, and helps the design and optimization of tissue engineering scaffolds for nerve regeneration.
MicroRNAs and other non-coding RNAs in adipose tissue and obesity: emerging roles as biomarkers and therapeutic targets
Authors: Lorente-Cebrián Silvia , González-Muniesa Pedro , Milagro Fermín I. , Martínez J. Alfredo 
Published: January 2019

AbstractObesity is a metabolic condition usually accompanied by insulin resistance (IR), type 2 diabetes (T2D), and dyslipidaemia, which is characterised by excessive fat accumulation and related to white adipose tissue (WAT) dysfunction. Enlargement of WAT is associated with a transcriptional alteration of coding and non-coding RNAs (ncRNAs). For many years, big efforts have focused on understanding protein-coding RNAs and their involvement in the regulation of adipocyte physiology and subsequent role in obesity. However, diverse findings have suggested that a dysfunctional adipocyte phenotype in obesity might be also dependent on specific alterations in the expression pattern of ncRNAs, such as miRNAs. The aim of this review is to update current knowledge on the physiological roles of miRNAs and other ncRNAs in adipose tissue function and their potential impact on obesity. Therefore, we examined their regulatory role on specific WAT features: adipogenesis, adipokine secretion, inflammation, glucose metabolism, lipolysis, lipogenesis, hypoxia and WAT browning. MiRNAs can be released to body fluids and can be transported (free or inside microvesicles) to other organs, where they might trigger metabolic effects in distant tissues, thus opening new possibilities to a potential use of miRNAs as biomarkers for diagnosis, prognosis, and personalisation of obesity treatment. Understanding the role of miRNAs also opens the possibility of using these molecules on individualised dietary strategies for precision weight management. MiRNAs should be envisaged as a future therapeutic approach given that miRNA levels could be modulated by synthetic molecules (f.i. miRNA mimics and inhibitors) and/or specific nutrients or bioactive compounds.
The vermiform appendix: an immunological organ sustaining a microbiome inoculum
Authors: Vitetta Luis , Chen Jiezhong , Clarke Stephen 
Published: January 2019

Abstract
The hominoid vermiform appendix has been characterized as a diverticulum of the caecum and describes an entity at the juxtaposition of the colon in the confluence of tanias. The independent development of the lymphoid follicle centres of the appendix is progressed at birth in the presence of the intestinal commensal microbiome, an obligatory prompt for the diversification of intestinal and extra-intestinal mucosal immunological tissue. In the vermiform appendix, this activity is centred on further developing the inventory of primary antibodies and the maturation of T- and B-lymphocyte cells in the follicles within the lymphoid tissue. Furthermore, the columnar epithelia, enterocytes and goblet cells comprise the complement of cells that occupy the lamina propria and muscularis mucosae of the vermiform appendix’s mucosa, while macrophages and an abundance of immunoglobulin A and immunoglobulin G generating plasma cells seed the lamina propria. Intraepithelial immune cells consisting predominantly of specific CD8+ T regulatory lymphocytes occupy sites in the appendix analogous to those present in the intestinal epithelia of the caecal colon. The complement of bacterial genera concealed in the vermiform appendix is posited extant as a biofilm inoculum of the intestinal commensal microbiome. This facilitates re-inoculation of the proximal colon and to a lesser degree the terminal ilium post an intestinal perturbation such as occurs with daily lifestyle stressors, dietary choices and the short-term administration of antibiotics rather than an infectious fulminant colitis. A plausible appreciation results of the importance of multiple immunological aspects of a healthy vermiform appendix and the provision of a commensal biofilm to the gut that repairs a dysbiotic microbiome contributing to balancing intestinal pro- and anti-inflammatory activity for maintaining homeostasis in the gut. Since the composition of the gut microbiome can vary over the short-term and long-term, it is plausible that the appendix inoculum may be instrumental in maintaining the intestinal microbiome.
Direct electrochemical generation of supercooled sulfur microdroplets well below their melting temperature
Authors: Liu Nian , Zhou Guangmin , Yang Ankun , Yu Xiaoyun , Shi Feifei , Sun Jie , Zhang Jinsong , Liu Bofei , Wu Chun-Lan , Tao Xinyong , Sun Yongming , Cui Yi , Chu Steven 
Published: January 2019

Significance
Since the first discovery of supercooling in 1724, the study of supercooled matter has been mainly limited to varying temperature or pressure. Here we demonstrate an electrochemical approach to generate and observe supercooled sulfur. Our methodology combines dark-field microscopy, a transparent electrochemical cell, and a fast camera to visualize the process at single microdroplet with millisecond time resolution. This platform may open up opportunities for studying supercooled liquids as the droplets approach either homogeneous nucleation to the crystalline state or enter into the glass transition. Relevant to understanding lithium-sulfur battery chemistry, liquid sulfur is observed to form in the electrochemical cell and elucidates a long-debated reaction pathway for sulfur redox reaction in this environment.
Characterization of Virus-specific Immune Response During Varicella Zoster Virus Encephalitis in a Young Adult
Authors: Sullivan Nicole L , Eberhardt Christiane S , Wieland Andreas , Akondy Rama S , Yi Jumi , McElroy Anita K , Ahmed Rafi 
Published: January 2019

Abstract
An immunocompetent adult received corticosteroids for chest pain, which later was clinically found to be herpes zoster (HZ). She developed severe disease and rapid viral dissemination that elicited an exceptionally strong varicella zoster virus–specific B-cell and CD8 T-cell response. Clinicians should consider atypical HZ presentation prior to corticosteroid administration.
Continuous Leakage-Resilient Identity-Based Encryption with Tight Security
Authors: Zhou Yanwei , Yang Bo , Hou Hongxia , Zhang Lina , Wang Tao , Hu Mingxiao 
Published: January 2019

Abstract
In the actual applications, an adversary can break the security of cryptography scheme through various leakage attacks (e.g. side-channel attacks, cold-boot attacks, etc.), even the continuous leakage attacks. That is, a practical cryptography scheme must maintain its claimed security in the continuous leakage setting. However, the previous constructions on the leakage-resilient identity-based encryption (IBE) scheme could tolerate a leakage that is bounded, and cannot resist the continuous leakage attacks. In order to further achieve the better security, a novel method to build the continuous leakage-resilient IBE scheme with tight security is presented in this paper, and the scheme’s security is proved, in the standard model, based on a stronger security assumption that depends on the number of queries made by the adversary. In addition, our proposal has several advantages over previous such constructions, e.g. shorter public parameters, higher communication efficiency, tight security, etc.
Screening for poverty and intervening in a primary care setting: an acceptability and feasibility study
Authors: Pinto Andrew D , Bondy Madeleine , Rucchetto Anne , Ihnat John , Kaufman Adam 
Published: January 2019

Abstract

Background
A movement is emerging to encourage health providers and health organizations to take action on the social determinants of health. However, few evidence-based interventions exist. Digital tools have not been examined in depth.

Objective
To assess the acceptability and feasibility of integrating, within routine primary care, screening for poverty and an online tool that helps identify financial benefits.

Methods
The setting was a Community Health Centre serving a large number of low-income individuals in Toronto, Canada. Physicians were encouraged to use the tool at every possible encounter during a 1-month period. A link to the tool was easily accessible, and reminder emails were circulated regularly. This mixed-methods study used a combination of pre-intervention and post-intervention surveys, focus groups and interviews.

Results
Thirteen physicians participated (81.25% of all) and represented a range of genders and years in practice. Physicians reported a strong awareness of the importance of identifying poverty as a health concern, but low confidence in their ability to address poverty. The tool was used with 63 patients over a 1-month period. Although screening and intervening on poverty is logistically challenging in regular workflows, online tools could assist patients and health providers identify financial benefits quickly. Future interventions should include more robust follow-up.

Conclusions
Our study contributes to the evidence based on addressing the social determinants of health in clinical settings. Future approaches could involve routine screening, engaging other members of the team in intervening and following up, and better integration with the electronic health record.
Physics of planet trapping with applications to HL Tau
Authors: Cridland Alexander J , Pudritz Ralph E , Alessi Matthew 
Published: January 2019

ABSTRACT
We explore planet formation in the HL Tau disc and possible origins of the prominent gaps and rings observed by ALMA. We investigate whether dust gaps are caused by dynamically trapped planetary embryos at the ice lines of abundant volatiles. The global properties of the HL Tau disc (total mass and size) at its current age are used to constrain an evolving analytic disc model describing its temperature and density profiles. By performing a detailed analysis of the planet–disc interaction for a planet near the water ice line including a rigorous treatment of the dust opacity, we confirm that water is sufficiently abundant (1.5 × 10−4 molecules per H) to trap planets at its ice line due to an opacity transition. When the abundance of water is reduced by 50 ${{\ \rm per\ cent}}$ planet trapping disappears. We extend our analysis to other planet traps: the heat transition, dead zone edge, and the CO2 ice line and find similar trapping. The formation of planets via planetesimal accretion is computed for dynamically trapped embryos at the water ice line, dead zone, and heat transition. The end products orbit in the inner disc (R &lt; 3 au), unresolved by ALMA, with masses that range between sub-Earth to 5 Jupiter masses. While we find that the dust gaps correspond well with the radial positions of the CO2, CH4, and CO ice lines, the planetesimal accretion rates at these radii are too small to build large embryos within 1 Myr.
Bacillus clarussp. nov. is a newBacillus cereusgroup species isolated from soil
Authors: Acevedo Marysabel Méndez , Carroll Laura M. , Mukherjee Manjari , Mills Emma , Xiaoli Lingzi , Dudley Edward G. , Kovac Jasna 
Published: January 2019

AbstractBacillus cereusgroup orB. cereussensu lato (s.l.), is comprised of Gram-positive spore-forming, rod-like bacteria that are widespread in natural environments. Although the species in this group are known to be highly related in terms of phenotypic characteristics, they display different levels of pathogenicity. Biochemical assays are therefore considered to be insufficient for accurate taxonomic classification ofB. cereusgroup species. To facilitate accurate taxonomic classification and associated prediction of pathogenic potential, we have conducted comparative genomic analyses of publicly available genome assemblies ofB. cereusgroup isolates. Through that, we found that an isolate previously known asB. mycoidesATCC 21929 was sufficiently distant from valid and effective type strains to be considered a putative new species. We have conducted biochemical and bioinformatic characterization of strain ATCC 21929 that had been isolated from soil in Papua New Guinea. Strain ATCC 21929 most closely resemblesB. paramycoidesNH24A2T, producing ANIb and DDH values of 86.70% and 34.1%, respectively. Phenotypically, isolate ATCC 21929 does not possess cytochrome c oxidase activity, and is able to grow at a range of temperatures 15°C - 43°C and at a range of pH 6 - 9. With regards to fatty acid composition, this isolate has iso-C17:0 in highest abundance. We propose the strain ATCC 21929T(=PS00077AT= PS00077BT= PSU-0922T= BHPT) as a new species namedBacillus clarussp. nov. to facilitate accurate taxonomic classification ofB. cereusgroup isolates.
Glutamatergic and cholinergic metabotropic modulation induces plateau potentials in hippocampal OLM interneurons
Authors: Hagger-Vaughan Nicholas , Storm Johan F. 
Published: January 2019

AbstractOriens-lacunosum moleculare (OLM) cells are hippocampal inhibitory interneurons that have been implicated in regulation of information flow and synaptic plasticity in the CA1 circuit.Since anatomical evidence indicate that OLM cells express metabotopic cholinergic (mAChR) and glutamatergic (mGluR) receptors, such modulation of these cells may contribute to switching between functional modes of the hippocampus.Using a transgenic mouse line to identify the Chrna2-positive OLM cells, we investigated metabotropic neuromodulation of intrinsic properties of OLM cells.We found that both mAChR and mGluR activation increased the spontaneous action potential rate and caused the cells to exhibit long-lasting depolarizing plateau potentials following evoked spike trains.Both the mAChR- and mGluR-induced increased spontaneous firing rate and plateau potentials were dependent on intracellular calcium, and were eliminated by blocking Ca2+-dependent transient receptor potential (TRP) cation channels. At the receptor level, Group I mGluRs were found to be responsible for the glutamatergic modulation of the plateau potentials. There was also a pronounced synergy between the cholinergic and glutamatergic modulation of the plateau potentials.Our findings provide insights into how OLM cells are modulated by different neurotransmitters, and are likely to have functional implications on how OLM cells regulate hippocampal information processing during different brain states.
Dynamic causal modeling for calcium imaging data reveals differential effective connectivity for sensory processing in a barrel cortical column
Authors: Jung Kyesam , Kang Jiyoung , Chung Seungsoo , Park Hae-Jeong 
Published: January 2019

AbstractMulti-photon calcium imaging (CaI) is an important tool to assess activity among neural populations within a column in the sensory cortex. However, the complex asymmetrical interactions among neural populations, termed effective connectivity, cannot be directly assessed by measuring the activity of each neuron using CaI but calls for computational modeling. To estimate effective connectivity among neural populations, we proposed a dynamic causal model (DCM) for CaI by combining a convolution-based dynamic neural state model and a dynamic calcium ion concentration model for CaI signals. After conducting a simulation study to evaluate DCM for CaI, we applied it to an experimental CaI data measured at the layer 2/3 of a barrel cortical column that differentially responds to hit and error whisking trails in mice. We first identified neural populations and constructed computational models with intrinsic connectivity of neural populations within the layer 2/3 of the barrel cortex and extrinsic connectivity with latent external modes. Bayesian model inversion and comparison shows that a top-down model with latent inhibitory and excitatory external modes explains the observed CaI signals during hit and error trials better than any other model, with a single external mode or without any latent modes. The best model also showed differential intrinsic and extrinsic effective connectivity between hit and error trials (corresponding to the bottom-up and top-down processes) in the functional hierarchical architecture. Both simulation and experimental results suggest the usefulness of DCM for CaI in terms of exploration of the hierarchical interactions among neural populations observed in CaI.
Trapping a somatic endogenous retrovirus into a germline piRNA cluster immunizes the germline against further invasion
Authors: Duc Céline , Yoth Marianne , Mouniée Nolwenn , Jensen Silke , Vaury Chantal , Brasset Emilie 
Published: January 2019

AbstractBackgroundFor species survival, the germline must faithfully transmit the genetic information to the progeny. Transposable elements (TEs), which are major components of eukaryotic genomes, constitute a significant threat to genome stability due to their mobility. In the metazoan germline, their mobilization is limited by a class of small RNAs that are called PIWI-interacting RNAs (piRNAs) and are produced by dedicated genomic loci called piRNA clusters. Although the piRNA pathway is an adaptive genomic immunity system, it remains unclear how the germline is protected from transposon invasion. To address this question, we usedDrosophila melanogasterlines harboring a deletion withinflamenco,a major piRNA cluster that is specifically expressed in somatic follicular cells. This deletion leads to derepression of the retrotransposonZAMand to germline genome invasion.ResultsIn this mutant line that expressZAMin somatic follicular cells, we identifiedde novoproduction of sense and antisenseZAM-derived piRNAs that displayed a germinal molecular signature. These piRNAs originated from a newZAMinsertion into a germline dual-strand piRNA cluster and silencedZAMexpression specifically in germ cells. Finally, we found thatZAMtrapping in a germinal piRNA cluster is a frequent event that occurs early during the isolation of the mutant line.ConclusionsTransposons can hijack the host developmental process to propagate whenever their silencing is lost. Here, we show that the germline can protect itself by trapping invading somatic-specific TEs into germline piRNA clusters. This is the first demonstration of “auto-immunization” of the germline endangered by mobilization of a surrounding somatic TE.