bluuebunny/crossref_metadata_2025 huggingface dataset:
Implementation of harmonically mapped averaging in LAMMPS, and effect of potential truncation on anharmonic properties
Authors: Purohit Apoorva , Schultz Andrew J. , Kofke David A.
Published: January 2020

Implementation of the harmonically mapped averaging (HMA) framework in the Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) is presented for on-the-fly computations of the energy, pressure, and heat capacity of crystalline systems during canonical molecular dynamics simulations. HMA has a low central processing unit and storage requirements and is straightforward to use. As a case study, the properties of the Lennard-Jones and embedded-atom model (parameterized for nickel) crystals are computed. The results demonstrate the higher efficiency of the new class compared to the inbuilt LAMMPS classes for calculating these properties. However, HMA loses its effectiveness in systems where diffusion occurs in the crystal, and an example is presented to allow this behavior to be recognized. In addition to its improved precision, HMA is less affected by small errors introduced by having a larger time step in molecular dynamics simulations. We also present an analysis of the effect of potential truncation on anharmonic properties, and show that artifacts of truncation on the HMA averages can be eliminated simply by shifting the potential energy to zero at the truncation radius. Full properties can be obtained by adding easily computed values for the lattice and harmonic properties using the untruncated potential.
A theoretical study of acoustically driven antennas
Authors: Hassanien Ahmed E. , Breen Michael , Li Ming-Huang , Gong Songbin
Published: January 2020

Acoustically driven antennas operating at resonant wavelengths up to 105 times smaller than electrical antennas offer great potential for portable, low power communication systems in the very low frequency and low frequency range. Acoustic antennas with real resonant impedances have been demonstrated to offer orders of magnitude better total efficiency compared to similar sized, subwavelength electrically small antennas exhibiting large reactances. While most acoustic antennas share favorable impedance characteristics offering significant matching efficiency advantages over electrically small antennas, radiation efficiency varies greatly based on the implementation of the acoustically driven antenna. This paper presents a theoretical analysis of the three primary methods for implementing acoustically driven radiating elements, investigating both radiation and matching efficiencies comprising the total antenna efficiency. Radiation from the linear movement of unipolar charge driven both piezoelectrically and capacitively, the piezoelectrically actuated rotation of fixed dipole charges, and from flipping dipoles inside strain driven piezoelectrics are all presented and analyzed in terms of their design parameters and fundamental challenges. The efficiency of each type of acoustic antenna is referenced to an equivalent electrical antenna to benchmark the performance to a more familiar framework. Of the analyzed antenna types, piezoelectric alternating dipole antennas exhibit the most promise, with efficiencies more than a million times greater than electrically small antennas expected as piezoelectric materials, and resonator designs are optimized for acoustic radiation.
Plenoptic x-ray microscopy
Authors: Sowa Katarzyna M. , Kujda Marcin P. , Korecki Paweł
Published: January 2020

Plenoptic cameras use arrays of microlenses to capture multiple views of the same scene in a single compound image. They enable refocusing on different planes and depth estimation. However, until now, all types of plenoptic computational imaging processes have been limited to visible light. We demonstrate an x-ray plenoptic microscope that uses a concentrating microcapillary array instead of a microlens array and can simultaneously acquire from one hundred to one thousand x-ray projections of imaged volumes that are located in the focal spot region of the microcapillary array. Hence, tomographic slices at various depths near the focal plane can be reconstructed in a way similar to tomosynthesis but from a single x-ray exposure. The microscope enables the depth-resolved imaging of small subvolumes in large samples and can be used for the imaging of weakly absorbing artificial and biological objects by means of propagation phase-contrast.
Real-time fluorescence measurement of spontaneous activity in a high-density hippocampal network cultivated on a plasmonic dish
Authors: Minoshima Wataru , Hosokawa Chie , Kudoh Suguru N. , Tawa Keiko
Published: January 2020

High-density cultured neuronal networks have been used to evaluate synchronized features of neuronal populations. Voltage-sensitive dye (VSD) imaging of a dissociated cultured neuronal network is a critical method for studying synchronized neuronal activity in single cells. However, the signals of VSD are generally too faint—that is, the signal-to-noise ratio (S/N) is too low—to detect neuronal activity. In our previous research, a silver (Ag) plasmonic chip enhanced the fluorescence intensity of VSD to detect spontaneous neural spikes on VSD imaging. However, no high-density network was cultivated on the Ag plasmonic chip, perhaps because of the chemical instability of the Ag surface. In this study, to overcome the instability of the chip, we used a chemically stable gold (Au) plasmonic dish, which was a plastic dish with a plasmonic chip pasted to the bottom, to observe neuronal activity in a high-density neuronal network. We expected that the S/N in real-time VSD imaging of the Au plasmonic chip would be improved compared to that of a conventional glass-bottomed dish, and we also expected to detect frequent neural spikes. The increase in the number of spikes when inhibitory neurotransmitter receptors were inhibited suggests that the spikes corresponded to neural activity. Therefore, real-time VSD imaging of an Au plasmonic dish was effective for measuring spontaneous network activity in a high-density neuronal network at the spatial resolution of a single cell.
Sensing anisotropic stresses with ferromagnetic nanowires
Authors: Forzani L. , Gennaro A. M. , Koropecki R. R. , Ramos C. A.
Published: January 2020

We have measured the temperature variation of the magnetic anisotropy of Ni nanowires (Ni NWs) embedded in freestanding porous anodized aluminum oxide membranes, using DC magnetometry and ferromagnetic resonance. Both techniques show a significant reduction of the uniaxial anisotropy with decreasing temperature. This decrease can be explained by magnetoelastic effects, as Ni NWs are subjected to stress due to the difference in thermal expansion coefficients between the nanocomposite materials. Matching our experimental findings with previously measured thermal strains along the Ni NW axis led us to estimate the perpendicular stress. Thus, we postulate the Ni NWs as nanometric differential stress sensors.
On a class of Hamiltonian Choquard-type elliptic systems
Authors: Maia B. B. V. , Miyagaki O. H.
Published: January 2020

This paper is concerned with the existence of solutions for a class of Hamiltonian Choquard-type elliptic systems in the plane with exponential critical growth. Typical features of this class of problems are a lack of compactness because of the unboundedness of the domain and that the critical growth and the energy functional associated with this class of systems are strongly indefinite, that is, the domain has a saddle-point geometry where both positive and negative subspaces of the quadratic form are infinite-dimensional. Moreover, the presence of the nonlocal term in the nonlinearity provides a series of difficulties in obtaining certain estimates.
Sensitivity analysis of Johnson-Cook material parameters on adiabatic shear in different directions
Authors: Xu Nianwei , Wang Hui , Men Xiuhua , Fu Xiuli
Published: January 2020

This study investigates the effects of strain, strain rates, and forming directions (RD-rolling direction, TD-transverse direction, and ND-normal direction) on adiabatic shear, via dynamic impact compression tests using the Split Hopkinson Pressure Bar (SHPB) apparatus. A modified Johnson-Cook (J-C) constitutive model is proposed, which used to analyse the influence of the constitutive parameters on the sensitivity of adiabatic shear, employing a finite element software. The different sensitivities of adiabatic shear under different directions are explained by combining microscopic analysis and results from mechanical responses. The results show that the sensitivity of adiabatic shear can be related to the time of stress collapse in the following trend: ND > TD > RD; the sensitivities of these constitutive parameters on adiabatic shear are calculated and compared.
DeepKinZero: zero-shot learning for predicting kinase–phosphosite associations involving understudied kinases
Authors: Deznabi Iman , Arabaci Busra , Koyutürk Mehmet , Tastan Oznur
Published: January 2020

Motivation

Protein phosphorylation is a key regulator of protein function in signal transduction pathways. Kinases are the enzymes that catalyze the phosphorylation of other proteins in a target-specific manner. The dysregulation of phosphorylation is associated with many diseases including cancer. Although the advances in phosphoproteomics enable the identification of phosphosites at the proteome level, most of the phosphoproteome is still in the dark: more than 95% of the reported human phosphosites have no known kinases. Determining which kinase is responsible for phosphorylating a site remains an experimental challenge. Existing computational methods require several examples of known targets of a kinase to make accurate kinase-specific predictions, yet for a large body of kinases, only a few or no target sites are reported.

Results

We present DeepKinZero, the first zero-shot learning approach to predict the kinase acting on a phosphosite for kinases with no known phosphosite information. DeepKinZero transfers knowledge from kinases with many known target phosphosites to those kinases with no known sites through a zero-shot learning model. The kinase-specific positional amino acid preferences are learned using a bidirectional recurrent neural network. We show that DeepKinZero achieves significant improvement in accuracy for kinases with no known phosphosites in comparison to the baseline model and other methods available. By expanding our knowledge on understudied kinases, DeepKinZero can help to chart the phosphoproteome atlas.

Availability and implementation

The source codes are available at https://github.com/Tastanlab/DeepKinZero.

Supplementary information

Supplementary data are available at Bioinformatics online.
US Hegemony and the Trans-Pacific Partnership: Consensus, Crisis, and Common Sense
Authors: Biegon Rubrick
Published: January 2020

This article provides a critical analysis of the agency of the United States in the Trans-Pacific Partnership (TPP). Building on neo-Gramscian theory, it contextualises the US decision to withdraw from the TPP as an expression of hegemonic crisis. Through an examination of the strategic and geoeconomic logics and objectives of the trade agreement in US foreign economic policy, it maintains that the TPP was intended primarily to expand the structural and consensual power of the United States in the international political economy. Partly an attempt to kick-start a stalled neoliberal agenda, the TPP was also an effort to respond to China’s growing influence in trade governance. The article argues that, despite the revival of the TPP in the form of the Comprehensive and Progressive Agreement for Trans-Pacific Partnership, the inability of elite networks in the United States to implement the original accord is illustrative of a crisis of hegemony driven largely by the collapse of the ‘common sense’ in favour of economic globalisation.
Artificial intelligence in the legal sector: pressures and challenges of transformation
Authors: Brooks Chay , Gherhes Cristian , Vorley Tim
Published: January 2020

Recent technological developments in automation and artificial intelligence (AI) promise to disrupt the very foundations of how legal work is practised and delivered. Yet how they challenge current business models, where they encounter resistance and how the benefits of AI can be realised remain unexplored. Drawing on interviews with professionals in the UK legal services sector, the article highlights how technological and market pressures combine to challenge the business models of legal services firms. However, the findings reveal important cultural and structural challenges that hamper transformation. The article extends the debate on technological disruption in legal services through a focus on business model innovation as a tool that can support firms in the sector to reimagine legal services provision.
Capitate Glandular Trichomes Fail to Provide Significant Resistance to Banded Sunflower Moth (Lepidoptera: Tortricidae)
Authors: Prasifka Jarrad R , Hulke Brent S
Published: January 2020

Extracts from capitate glandular trichomes (CGT) of wild and cultivated sunflowers, Helianthus spp., have repellent or toxic effects on sunflower specialists and generalist herbivores less closely associated with sunflower. Though CGT have been primarily examined for their potential to provide partial resistance to the sunflower moth, Homoeosoma electellum Hulst (Lepidoptera: Pyralidae), a floret- and seed-feeding pest, the banded sunflower moth (Cochylis hospes Walsingham [Lepidoptera: Tortricidae]) is a similar species more common in the primary sunflower-producing states of North Dakota and South Dakota. Replicated field trials using partially inbred lines with low or high CGT densities were used to evaluate possible reductions to seed damage by C. hospes larvae in 2016–2017. Results failed to support the idea that CGT are a useful defense against larvae of C. hospes; the putative plant defense of high trichome density corresponded to slightly more, rather than less, insect damage. A test of a secondary explanation, that strength of sunflower hulls could help determine patterns of seed damage among tested lines, produced similarly negative results. Though timing of bloom differed between groups of most- and least-damaged lines, prior research and pheromone-trapping data suggest differences in plant maturity also cannot adequately explain the observed results. While the specific mechanisms remain unclear, significant differences in susceptibility to C. hospes exist for cultivated sunflower and limit losses from this primary insect pest.
Exposure of Foraging Bees (Hymenoptera) to Neonicotinoids in the U.S. Southern High Plains
Authors: Longing Scott D , Peterson Eric M , Jewett Christopher T , Rendon Bianca M , Discua Samuel A , Wooten Kimberly J , Subbiah Seenivasan , Smith Philip N , McIntyre Nancy E
Published: January 2020

Exposure to pesticides is a major threat to insect pollinators, potentially leading to negative effects that could compromise pollination services and biodiversity. The objectives of this study were to quantify neonicotinoid concentrations among different bee genera and to examine differences attributable to body size and surrounding land use. During the period of cotton planting (May–June), 282 wild bees were collected from habitat patches associated with cropland, grassland, and urban land cover and analyzed for three neonicotinoids (thiamethoxam, clothianidin, and imidacloprid). Twenty bees among eight genera contained one or more of the neonicotinoid compounds and detections occurred in all landscape types, yet with the most detections occurring in cropland-associated habitats. Apis Linnaeus (Hymenoptera: Apidae), Melissodes Latreille (Apidae), Perdita Smith (Andrenidae), and Lasioglossum Curtis (Halictidae) had multiple individuals with neonicotinoid detections. Two of the largest bees (Apis and Melissodes) had the greatest number of detections within genera, yet the relatively small-bodied genus Perdita had the three highest neonicotinoid concentrations reported. The number of detections within a genus and average generic body mass showed a marginally significant trend towards larger bees having a greater frequency of neonicotinoid detections. Overall, the relatively low percentage of detections across taxa suggests practices aimed at conserving grassland remnants in intensified agricultural regions could assist in mitigating exposure of wild bees to agrochemicals, while differences in bee traits and resource use could in part drive exposure. Further work is needed to address variable agrochemical exposures among pollinators, to support strategies for conservation and habitat restoration in affected landscapes.
Prediction models for atrial fibrillation applicable in the community: a systematic review and meta-analysis
Authors: Himmelreich Jelle C L , Veelers Lieke , Lucassen Wim A M , Schnabel Renate B , Rienstra Michiel , van Weert Henk C P M , Harskamp Ralf E
Published: January 2020

Aims

Atrial fibrillation (AF) is a common arrhythmia associated with an increased stroke risk. The use of multivariable prediction models could result in more efficient primary AF screening by selecting at-risk individuals. We aimed to determine which model may be best suitable for increasing efficiency of future primary AF screening efforts.

Methods and results

We performed a systematic review on multivariable models derived, validated, and/or augmented for AF prediction in community cohorts using Pubmed, Embase, and CINAHL (Cumulative Index to Nursing and Allied Health Literature) through 1 August 2019. We performed meta-analysis of model discrimination with the summary C-statistic as the primary expression of associations using a random effects model. In case of high heterogeneity, we calculated a 95% prediction interval. We used the CHARMS (Critical Appraisal and Data Extraction for Systematic Reviews of Prediction Modelling Studies) checklist for risk of bias assessment. We included 27 studies with a total of 2 978 659 unique participants among 20 cohorts with mean age ranging from 42 to 76 years. We identified 21 risk models used for incident AF risk in community cohorts. Three models showed significant summary discrimination despite high heterogeneity: CHARGE-AF (Cohorts for Heart and Aging Research in Genomic Epidemiology) [summary C-statistic 0.71; 95% confidence interval (95% CI) 0.66–0.76], FHS-AF (Framingham Heart Study risk score for AF) (summary C-statistic 0.70; 95% CI 0.64–0.76), and CHA2DS2-VASc (summary C-statistic 0.69; 95% CI 0.64–0.74). Of these, CHARGE-AF and FHS-AF had originally been derived for AF incidence prediction. Only CHARGE-AF, which comprises easily obtainable measurements and medical history elements, showed significant summary discrimination among cohorts that had applied a uniform (5-year) risk prediction window.

Conclusion

CHARGE-AF appeared most suitable for primary screening purposes in terms of performance and applicability in older community cohorts of predominantly European descent.
Pluralist Marriage Laws in a Former Colonial System: Cultural Authenticity or Hybridisation?
Authors: Bonthuys Elsje
Published: January 2020

Legal pluralism in former colonial territories, like South Africa, often involve the simultaneous existence of multiple marriage forms, distinguishing marital forms associated with former colonial systems from indigenous forms of marriage. These pluralist systems are not value-neutral but continue to favour marriages associated with colonial rules and processes. In addition, they create complicated distinctions between different forms of marriage which are thought to reflect the distinctive cultural or religious identities of those who marry according to these systems. This article argues for an alternative approach: the explicit recognition and encouragement of legal hybridisation as a strategy for disrupting colonial identities and hierarchies which recognises and values the historical and contemporary processes of hybridisation in the law and social practices. It uses the metaphors of the language politics around Afrikaans to describe a rigid form of pluralism based on claims of authentic identity on the one hand, and of isishweshwe, a colourful cotton fabric, which represents the resilience, vitality, and creative exchange which characterises hybridity and which promises to address gender and racial inequality inherent in the current model.
Cosmic rays escaping from Galactic starburst-driven superbubbles
Authors: Zhang Zhaowei , Murase Kohta , Mészáros Peter
Published: January 2020

We calculate spectra of escaping cosmic rays (CRs) accelerated at shocks produced by expanding Galactic superbubbles powered by multiple supernovae producing a continuous energy outflow in star-forming galaxies. We solve the generalized Kompaneets’ equations adapted to expansion in various external density profiles, including exponential and power-law shapes, and take into account that escaping CRs are dominated by those around their maximum energies. We find that the escaping CR spectrum largely depends on the specific density profiles and power source properties, and the results are compared to and constrained by the observed CR spectrum. As a generic demonstration, we apply the scheme to a superbubble occurring in the centre of the Milky Way, and find that under specific parameter sets the CRs produced in our model can explain the observed CR flux and spectrum around the second knee at 1017 eV.
The halo mass function in alternative dark matter models
Authors: Lovell M R
Published: January 2020

The claimed detection of large amounts of substructure in lensing flux anomalies, and in Milky Way stellar stream gap statistics, has led to a step change in constraints on simple warm dark matter models. In this study, we compute predictions for the halo mass function both for these simple models and for comprehensive particle physics models of sterile neutrinos and dark acoustic oscillations. We show that the mass function fit of Lovell et al. underestimates the number of haloes less massive than the half-mode mass, $M_\mathrm {hm}$, by a factor of 2, relative to the extended Press–Schechter (EPS) method. The alternative approach of applying EPS to the Viel et al. matter power spectrum fit instead suggests good agreement at $M_\mathrm {hm}$ relative to the comprehensive model matter power spectrum results, although the number of haloes with mass $\rm{\lt} M_\mathrm {hm}$ is still suppressed due to the absence of small-scale power in the fitting function. Overall, we find that the number of dark matter haloes with masses $\rm{\lt} 10^{8}{\, \rm M_\odot }$ predicted by competitive particle physics models is underestimated by a factor of ∼2 when applying popular fitting functions, although careful studies that follow the stripping and destruction of subhaloes will be required in order to draw robust conclusions.
SWI/SNF complex heterogeneity is related to polyphenotypic differentiation, prognosis, and immune response in rhabdoid tumors
Authors: Panwalkar Pooja , Pratt Drew , Chung Chan , Dang Derek , Le Paul , Martinez Daniel , Bayliss Jill M , Smith Kyle S , Adam Mike , Potter Steven , Northcott Paul A , Mascarenhas Leo , Shows Jared , Pawel Bruce , Margol Ashley , Huang Annie , Judkins Alexander R , Venneti Sriram
Published: January 2020

Background

Rhabdoid tumors (RTs) arise within (atypical teratoid/rhabdoid tumor [AT/RT]) or outside the brain (extra [e]CNS-RT) and are driven mainly by inactivation of the SWItch/sucrose nonfermentable (SWI/SNF) complex subunit SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1 (SMARCB1). A pathognomonic hallmark of RTs is heterogeneous multilineage differentiation, including anomalous neuronal differentiation in some eCNS-RTs. Because remodeling of the SWI/SNF complex regulates differentiation, we hypothesized that SWI/SNF Brahma-associated factors (BAF) and polybromo-associated BAF (PBAF) complex heterogeneity are related to both multilineage differentiation and clinical outcome.

Methods

We performed an integrated analysis of SWI/SNF complex alterations in the developing kidney and cerebellum (most common regions of RT origin) in comparison to eCNS-RT (n = 14) and AT/RT (n = 25) tumors. RT samples were interrogated using immunohistochemistry, DNA methylation, and gene expression analyses.

Results

The SWI/SNF BAF paralogs actin-like protein (ACTL)6A and ACTL6B were expressed in a mutually exclusive manner in the developing cerebellum and kidney. In contrast, a subset of eCNS-RTs lost mutual exclusivity and coexpressed both subunits. These tumors showed aberrant DNA methylation of genes that regulate neuronal and renal development and demonstrated immunohistochemical evidence of neuronal differentiation. In addition, low expression of the PBAF subunit polybromo-1 (PBRM1) identified a group of AT/RTs in younger children with better overall prognosis. PBRM1-low AT/RT and eCNS-RTs showed altered DNA methylation and gene expression in immune-related genes. PBRM1 knockdown resulted in lowering immunosuppressive cytokines, and PBRM1 levels in tumor samples showed an inverse relationship with cluster of differentiation (CD)8 cytotoxic T-cell infiltration.

Conclusions

Heterogeneity in SWI/SNF BAF (ACTL6A/ACTL6B) and PBAF (PBRM1) subunits is related to histogenesis, contributes to the immune microenvironment and prognosis in RTs, and may inform opportunities to develop immunotherapies.
RF-INDUCED TEMPERATURE INCREASE IN A STRATIFIED MODEL OF THE SKIN FOR PLANE-WAVE EXPOSURE AT 6–100 GHZ
Authors: Christ Andreas , Samaras Theodoros , Neufeld Esra , Kuster Niels
Published: January 2020

This study assesses the maximum temperature increase induced by exposure to electromagnetic fields between 6 and 100 GHz using a stratified model of the skin with four or five layers under plane wave incidence. The skin model distinguishes the stratum corneum (SC) and the viable epidermis as the outermost layers of the skin. The analysis identifies the tissue layer structures that minimize reflection and maximize the temperature increase induced by the electromagnetic field. The maximum observed temperature increase is 0.4°C for exposure at the present power density limit for the general population of 10 W m −2 . This result is more than twice as high as the findings reported in a previous study. The reasons for this difference are identified as impedance matching effects in the SC and less conservative thermal parameters. Modeling the skin as homogeneous dermis tissue can underestimate the induced temperature increase by more than a factor of three.
English “equity” and the civil law—a tale of two worlds
Authors: Lupoi Maurizio
Published: January 2020

This article explores how equity was begotten by canon and civil law and why it has no links with modern civil law.
Focus on Cell Biology of Virus-Plant and Virus-Vector Interactions
Authors: Wang Aiming , Burch-Smith Tessa M , Li Yi
Published: January 2020

A successful viral infection requires complex, compatible molecular interactions between the invading virus and the host. A better understanding of such interactions may assist in the development of novel approaches to control viral diseases for sustainable crop production. In the past decade, the cell biology of virus-host and virus-vector interactions has been one of the most exciting areas of research in the molecular plant-microbe field. This is partially attributed to the availability of powerful cell biology techniques, including imaging tools like confocal microscopy and electron microscopy and tomography. As a result, there has been an unprecedented increase in knowledge in the areas of the bi- and tripartite interactions of virus, host, and vector. We now have a much clearer picture of viral virulence mechanisms, virus-induced host defenses, viral counteracting strategies, and viral circulations in the insect vectors. This Focus Issue highlights molecular virus-plant and virus-vector interactions in the areas of cell biology and closely related disciplines and explores biotechnology-based antiviral strategies using knowledge generated from these research areas.

Additional content is available on the Focus on Cell Biology of Virus-Plant and Virus-Vector Interactions.

New Technologies for Studying Negative-Strand RNA Viruses in Plant and Arthropod Hosts

A Non-Conserved p33 Protein of Citrus Tristeza Virus Interacts with Multiple Viral Partners
Pre-operative transnasal endoscopy as a predictor of difficult airway
Authors: Gemma Marco , Buratti Luca , Di Santo Davide , Calvi Maria R. , Ravizza Alfredo , Bondi Stefano , Bussi Mario , Beretta Luigi
Published: January 2020

BACKGROUND

Consequences of failed endotracheal intubation can be catastrophic and predicting difficulty is therefore a critical issue. There is no consensus on the best way to predict difficulty.

OBJECTIVE

To evaluate the role of transnasal flexible endoscopic laryngoscopy (TFEL), a minimally invasive procedure, in the prediction of difficult intubation.

DESIGN

Prospective cohort study.

SETTING

San Raffaele Hospital, Milan, a tertiary university hospital.

PATIENTS

One hundred and sixty nine adults scheduled for elective ear, nose and throat surgery under general anaesthesia with pre-operative TFEL.

INTERVENTION

In addition to routine pre-operative evaluation by an anaesthesiologist, glottis exposure during TFEL was assessed with a scoring system similar to the modified Cormack–Lehane (MCL).

MAIN OUTCOME MEASURES

The extent to which TFEL improves the prediction of difficult direct laryngoscopy, measured with the MCL score, and of difficult intubation, measured with the intubation difficulty scale score.

RESULTS

When added to bedside evaluation, TFEL performed during tongue protrusion significantly (P = 0.005) improved the prediction of MCL. The area under the receiver operating characteristics curve was 0.75 [95% confidence interval (CI) 0.67 to 0.83] vs. 0.65 (95% CI 0.58 to 0.74). For the intubation difficulty scale (P = 0.049), the area under the receiver operating characteristics curve was 0.70 (95% CI 0.61 to 0.80) vs. 0.66 (95% CI 0.58 to 0.74).

CONCLUSION

TFEL is a useful tool in predicting difficult intubation, improving predictability of routine bedside evaluation.

TRIAL REGISTRATION

ClinicalTrials.gov identifier: NCT02671877.
An ultrasound assessment of gastric emptying following tea with milk in pregnancy
Authors: Irwin Ruairi , Gyawali Icchya , Kennedy Bernard , Garry Niamh , Milne Sarah , Tan Terry
Published: January 2020

BACKGROUND

Peri-operative fasting guidelines allow clear fluids including tea without milk to be consumed up to 2 h before surgery. Recent evidence has shown that a modest amount of milk consumed with clear fluids does not significantly slow gastric emptying.

OBJECTIVES

The aim of this study was to compare the gastric emptying of tea with milk versus water using ultrasonography in fasted pregnant patients.

DESIGN

A randomised controlled trial quantifying gastric emptying in two groups using ultrasonography by an operator blinded to the group allocation.

SETTING

Department of Anaesthesia and Peri-operative Medicine, Coombe Women and Infants University Hospital, Dublin. The study was conducted between October 2018 and June 2019.

PARTICIPANTS

Total 50 nonlabouring pregnant women, more than 36 weeks gestation.

INTERVENTIONS

After a standard overnight fast, women were randomised to either 250 ml of water or 250 ml of tea with milk. All patients underwent a gastric ultrasound assessment at regular intervals for 2 h after consumption of their drink.

MAIN OUTCOME MEASURE

The primary outcome was the difference in gastric antrum cross-sectional area (CSA) at 2 h.

RESULTS

A total of 50 women were recruited to the study. There was no significant difference in the median [IQR] gastric antrum CSA in either group at 2 h: 3.2 cm2 [2.3 to 3.7] vs. 3.1 cm2 [2.6 to 3.9]; P = 0.720. The gastric antrum CSA had returned to its baseline measurement in both groups by 90 min.

CONCLUSION

The change of gastric antrum CSA after 250 ml of tea with milk is similar to a corresponding volume of water in fasted pregnant patients. This study could help inform future peri-operative fasting guidelines regarding the use of a modest volume of milk with clear fluids.

TRIAL REGISTRY NUMBER

NCT 03694509 ClinicalTrials.gov.
Mechanisms of spectrotemporal modulation detection for normal- and hearing-impaired listeners
Authors: Ponsot Emmanuel , Varnet Léo , Wallaert Nicolas , Daoud Elza , Shamma Shihab A. , Lorenzi Christian , Neri Peter
Published: January 2020

Spectrotemporal modulations (STMs) offer a unified framework to probe suprathreshold auditory processing. Here, we introduce a novel methodological framework based on psychophysical reverse-correlation deployed in the modulation space to characterize how STMs are detected by the auditory system and how cochlear hearing loss impacts this processing. Our results show that young normal-hearing (NH) and older hearing-impaired (HI) individuals rely on a comparable non-linear processing architecture involving non-directional band-pass modulation filtering. We demonstrate that a temporal-modulation filter-bank model can capture the strategy of the NH group and that a broader tuning of cochlear filters is sufficient to explain the overall shift toward temporal modulations of the HI group. Yet, idiosyncratic behaviors exposed within each group highlight the contribution and the need to consider additional mechanisms. This integrated experimental-computational approach offers a principled way to assess supra-threshold auditory processing distortions of each individual.
The role of Fnr paralogs for controlling anaerobic metabolism in diazotrophPaenibacillus polymyxaWLY78
Authors: Shi Haowen , Li Yongbin , Hao Tianyi , Liu Xiaomeng , Zhao Xiyun , Chen Sanfeng
Published: January 2020

Fnr is a transcriptional regulator that controls the expression of a variety of genes in response to oxygen limitation in bacteria. Genome sequencing revealed four genes (fnr1,fnr3,fnr5andfnr7) coding for Fnr proteins inPaenibacillus polymyxaWLY78. Fnr1 and Fnr3 showed more similarity to each other than to Fnr5 and Fnr7. Also, Fnr1 and Fnr3 exhibited high similarity withBacillus cereusFnr andBacillus subtilisFnr in sequence and structures. Deletion analysis showed that the fourfnrgenes, especiallyfnr1andfnr3,have significant impacts on the growth and nitrogenase activity. Single deletion offnr1orfnr3led to 50% reduction in nitrogenase activity and double deletion offnr1andfnr3resulted to 90% reduction in activity. Both of the aerobically purified His-tagged Fnr1 and His-tagged Fnr3 inEscherichia colicould bind to the specific DNA promoter. Genome-wide transcription analysis showed that Fnr1 and Fnr3 indirectly activated expression ofnif(nitrogen fixation) genes and Fe transport genes under anaerobic condition. Fnr1 and Fnr3 inhibited expression of the genes involved in aerobic respiratory chain and activated expression of genes responsible for anaerobic electron acceptor genes.

IMPORTANCE

Paenibacillusis a genus of Gram-positive, facultative anaerobic and endospore-forming bacteria. The members of nitrogen-fixingPaenibacillushave great potential use as a bacterial fertilizer in agriculture. However, the functions offnrgene(s) in nitrogen fixation and other metabolisms inPaenibacillusspp. are not known. Here, we revealed that copy numbers vary largely among differentPaenibacillusspecies and strains. Deletion and complementation analysis demonstrated thatfnr1andfnr3have significant impacts on the growth and nitrogenase activity. Both of the aerobically purified His-tagged Fnr1 and His-tagged Fnr3 purified inEscherichia colicould bind to the specific DNA promoter asBacillus cereusFnr did. Fnr1 and Fnr3 indirectly activatednifexpression under anaerobic condition. Fnr1 and Fnr3 directly or indirectly activated or inhibited expression of many important genes involved in respiration, energy metabolism, Fe uptake and potentially specific electron transport for nitrogenase under anaerobic condition. This study not only reveals the roles offnrgenes in nitrogen fixation and anaerobic metabolism, but also provides insight into the evolution and regulatory mechanisms offnrinPaenibacillus.
Development of a soft cell confiner to decipher the impact of mechanical stimuli on cells
Authors: Prunet A. , Lefort S. , Delanoë-Ayari H. , Laperrousaz B. , Simon G. , Saci S. , Argoul F. , Guyot B. , Rieu J.-P. , Gobert S. , Maguer-Satta V. , Rivière C.
Published: January 2020

Emerging evidence suggests the importance of mechanical stimuli in normal and pathological situations for the control of many critical cellular functions. While the effect of matrix stiffness has been and is still extensively studied, few studies have focused on the role of mechanical stresses. The main limitation of such analyses is the lack of standardin vitroassays enabling extended mechanical stimulation compatible with dynamic biological and biophysical cell characterization. We have developed an agarose-based microsystem, the soft cell confiner, which enables the precise control of confinement for single or mixed cell populations. The rigidity of the confiner matches physiological conditions and enables passive medium renewal. It is compatible with time-lapse microscopy,in situimmunostaining, and standard molecular analyses, and can be used with both adherent and non-adherent cell lines. Cell proliferation of various cell lines (hematopoietic cells, MCF10A epithelial breast cells and HS27A stromal cells) was followed for several days up to confluence using video-microscopy and further documented by Western blot and immunostaining. Interestingly, even though the nuclear projected area was much larger upon confinement, with many highly deformed nuclei (non-circular shape), cell viability, assessed by live and dead cell staining, was unaffected for up to 8 days in the confiner. However, there was a decrease in cell proliferation upon confinement for all tested cell lines. The soft cell confiner is thus a valuable tool to decipher the effect of long-term confinement and deformation on the biology of cell populations. This tool will be instrumental in deciphering the impact of nuclear and cytoskeletal mechanosensitivity in normal and pathological conditions involving highly confined situations, such as those reported upon aging with fibrosis or during cancer.

Graphical abstract

A unique tool to analyze the role of long-term effect of mechanical confinement in normal and pathological conditions
miR-1290 stimulates proliferation of gastric cancer by targeting SP1 with overexpression of fucosyltransferase IV and α1, 3-fucosylated glycans
Authors: Aziz Faisal , Yulin Li , Yan Qiu
Published: January 2020

Fucosylation plays an important role in the development of carcinogenesis. miRNA-1290 emerged as crucial molecule to regulate cancer cell proliferation. This study evaluated the role of miRNA-1290 to development of gastric cancer by regulation of fucosyltransferase-IV, specific protein-1 (SP1) and α1,3-fucosylated glycans.We analyzed the role ofH. pyloriand miR-1290 in gastric cancer cells in induce fucosylation and cell proliferation, as well as SP1 and ubiquitin protein interaction. We found miR-1290 induced proliferation inH. pyloriCagA treated gastric cancer cells by stimulating FUT4/LeY fucosylation, as evidence by high expression of miR-1290 and phosphorylation of EGFR and MAPKs pathway in dose–dependent manner. In addition, miR-1290 inhibited SP1 protein with the regulation of ubiquitin-proteasomal system and leads to stimulate FUT4 and α1,3-fucosylated glycans level. We report the role of miRNA-1290 to stimulate FUT4 fucosylation and LeY through EGFR/MAPKs pathway by targeting SP1 in the development of gastric cancer.
Background reduction in STED-FCS using coherent-hybrid STED
Authors: Barbotin Aurélien , Urbančič Iztok , Galiani Silvia , Eggeling Christian , Booth Martin
Published: January 2020

Fluorescence correlation spectroscopy (FCS) is a valuable tool to study the molecular dynamics of living cells. When used together with a super-resolution stimulated emission depletion (STED) microscope, STED-FCS can measure diffusion processes at the nanoscale in living cells. In twodimensional (2D) systems like the cellular plasma membrane, a ring-shaped depletion focus is most commonly used to increase the lateral resolution, leading to more than 25-fold decrease in the observation volumee, reaching the relevant scale of supramolecular arrangements. However, STED-FCS faces severe limitations when measuring diffusion in three dimensions (3D), largely due to the spurious background contributions from undepleted areas of the excitation focus that reduce the signal quality and ultimately limit the resolution. In this paper, we investigate how different STED confinement modes can mitigate this issue. By simulations as well as experiments with fluorescent probes in solution and in cells, we demonstrate that the coherent-hybrid (CH) depletion pattern reduces background most efficiently and thus provides superior signal quality under comparable reduction of the observation volume. Featuring also the highest robustness to common optical aberrations, CH-STED can be considered the method of choice for reliable STED-FCS based investigations of 3D diffusion on the sub-diffraction scale.
Dual community assembly processes in dryland biocrust communities
Authors: Soliveres Santiago , Eldridge David J.
Published: January 2020

Biocrusts are critical components of drylands where they regulate a wide range of ecosystem functions, however, their response to the world‐wide phenomenon of shrub encroachment and to livestock grazing, the most extensive land use in drylands, is not well studied. Grazing by livestock and increases in shrub cover could influence biocrust communities directly via trampling or shading, or indirectly, by altering biotic interactions amongst biocrust taxa. The extent of these changes in biocrust cover, diversity and composition are poorly known.

We used linear models and structural equation modelling to examine the direct effects of grazing and shrubs on biocrust community composition and the indirect effects mediated by changes in species interactions.

Biocrust richness and cover increased with increasing shrub cover at the site level. This pattern occurred despite the negative response we found (lower cover and richness) under shrub patches versus open areas, which was consistent irrespective of the grazing level. Functional diversity and evenness were similar between shrubs and open at low grazing intensity, but at high grazing functional diversity was greater in the open. Competition between biocrust species was an important driver of their community assembly irrespective of shrub cover, grazing intensity or patch type. Structural equation models showed that the effects of grazing and shrub cover on functional evenness, functional diversity and richness were controlled by biotic interactions within the shrub microsites. In the open, however, these effects were either direct or mediated by changes in cover.

Biocrust cover, species richness and functional diversity increase with shrub cover at the site scale, despite the negative effects at the microsite level. We demonstrate here that drivers of community assembly differ markedly at small spatial scales. Though biocrust communities were directly driven by environmental filtering in the open, biotic interactions played a fundamental role in their assembly when growing beneath shrubs.

A free plain language summary can be found within the Supporting Information of this article.
Validation of degree‐day models for predicting the emergence of two fruit flies (Diptera: Tephritidae) in northeast Egypt
Authors: Bayoumy Mohamed H. , Michaud J. P. , Badr Faten A. A. , Ghanim Nabil M.
Published: January 2020

We estimated thermal developmental thresholds (T0) and degree‐day (DD) constants for the immature stages of two tephritid pests, Bactrocera zonata (Saunders) and Ceratitis capitata (Weidenmann). Males of both species were trapped in an Egyptian guava orchard during the fruiting seasons of 2016 and 2017 and trap catches were compared with peak flights predicted by the DD model based on local weather data. Ceratitis capitata had faster development than B. zonata at 20 and 25 °C, but their overall developmental rate was similar at 30 and 35 °C. The thermal threshold of development (T0) of B. zonata was higher than that of C. capitata, indicating greater sensitivity to cold. Although 35 °C yielded the fastest development of both species, survival was higher at 30 °C, with B. zonata experiencing a slight advantage, suggesting better tropical adaptation. Immature development of B. zonata and C. capitata was estimated to require 338 and 373 d, respectively, and 616 and 424 DD for a complete generation. Trap catches over both seasons showed good correspondence to peaks of fly activity predicted by the DD models; deviations from expectation ranged from 0 to 7 d for both fly species. Both species had four overlapping generations per season, with B. zonata abundance peaking in the first generation in both years, but only in 2016 for C. capitata. The models predict about eight and 12 generations per year in northeast Egypt for B. zonata and C. capitata, respectively. These models should be useful for timing pest control measures to coincide with periods of peak fly activity in fruit orchards.
LC–MS/MS‐based metabolomic analysis of caffeine‐degrading fungus Aspergillus sydowii during tea fermentation
Authors: Zhou Binxing , Ma Cunqiang , Ren Xiaoying , Xia Tao , Li Xiaohong
Published: January 2020

Natural microorganisms involved in solid‐state fermentation (SSF) of Pu‐erh tea have a significant impact on its chemical components. Aspergillus sydowii is a fungus with a high caffeine‐degrading capacity. In this work, A. sydowii was inoculated into sun‐dried green tea leaves for SSF. Metabolomic analysis was carried out by using UPLC–QTOF‐MS method, and caffeine and related demethylated products were determined by HPLC. The results showed that A. sydowii had a significant (P < 0.05) impact on amino acids, carbohydrates, flavonoids, and caffeine metabolism. Moreover, A. sydowii could promote the production of ketoprofen, baclofen, and tolbutamide. Along with caffeine degradation, theophylline, 3‐methylxanthine, 1,7‐dimethylxanthine, 1‐methylxanthine, and 7‐methylxanthine were increased significantly (P < 0.05) during inoculated fermentation, which showed that demethylation was the main pathway of caffeine degradation in A. sydowii secondary metabolism. The absolute quantification analysis showed that caffeine could be demethylated and converted to theophylline and 3‐methylxanthine. Particularly, about 93.24% of degraded caffeine was converted to theophylline, 27.92 mg/g of theophylline was produced after fermentation.

Practical Application

Aspergillus sydowii could cause caffeine degradation in Pu‐erh tea solid‐state fermentation and produce theophylline through the demethylation route. Using a starter strain to ferment tea leaves offers a more controllable, reproducible, and highly productive alternative for the biosynthesis of theophylline.