bluuebunny/crossref_metadata_2025 huggingface dataset:
The role of precursor decomposition in the formation of samarium doped ceria nanoparticles via solid-state microwave synthesis
Authors: Bregman Avi , Rimsza Jessica , Ringgold Marissa , Bell Nelson , Treadwell LaRico
Published: February 2021

The impact on the final morphology of ceria (CeO2) nanoparticles made from different precursors (commercial: cerium acetate/nitrate) and in house: cerium tri(methylsilyl)amide (Ce-TMSA)) via a microwave solid state reaction has been determined. In all instances, powder X-ray diffraction indicated that the cubic fluorite CeO2 phase (PDF# 04–004-9150, with the space group Fm-3 m) had formed. Scanning electron microscopy (SEM) images revealed spherical nanoparticles were produced from the Ce-TMSA precursor. The commercial acetate and nitrate precursors produced particles with irregular morphology. The roles of the precursor decomposition and binding energy in the synthesis of the nanocrystals with various morphologies, as well as a possible growth mechanism, were evaluated based on experimental and computational data. The formation of spherical shaped nanoparticles was determined to be due to the preferential single-step decomposition of the Ce-TMSA as well as the low activation energy to overcome decomposition. Due to the complicated decomposition of the commercial precursors and high activation energy the resulting particles adopted an irregular morphology. Highly uniform samarium doped ceria (SmxCe1-xO2-δ) nanospheres were also synthesized from Ce-TMSA and samarium tri(methylsilyl)amide (Sm-TMSA). The effects of reaction time and temperature, on the final morphology were observed through SEM. The rapid single-step decomposition of TMSA-based precursors as observed through thermogravimetric analysis (TGA) and confirmed through the calculation of potential energy surfaces and binding energies from density functional theory (DFT) calculations, indicated that nanoparticle formation follows LaMer’s classical nucleation theory.
Earthquake-induced clastic dyke and fluid inflow at the Miguel Burnier manganese-ore deposit, Quadrilátero Ferrífero of Minas Gerais, Brazil
Authors: DeFerreira Tiago Henrique , Cabral Alexandre Raphael , Rios Francisco Javier
Published: February 2021

A clastic dyke has been recognised within manganese (Mn)-rich Cenozoic sediments near a historical Mn-ore deposit in the Miguel Burnier district, Quadrilátero Ferrífero, in the southern São Francisco craton, Brazil. Here, we describe the clastic dyke, a subvertical fissure that is filled with friable arenaceous fragments, and characterise it as seismite. An overprint by stockwork-like Mn-oxide veinlets and Mn-oxide dissemination, mineralogically expressed as birnessite, lithiophorite and jianshuiite, and geochemically represented by metalliferous enrichments, particularly mercury (Hg), occurs in the clastic dyke and its immediate vicinity. Such an overprint also contains illite, which forms a mineral association with birnessite, lithiophorite and jianshuiite, and constrains the temperature of hydrothermal alteration to less than 300 °C. The recognition of seismite and its Hg enrichment indicate that the Cenozoic history of the Quadrilátero Ferrífero cratonic terrane has been affected by seismic episodes, which were not only conducive to local enrichment in Mn at Miguel Burnier, but also to the dam failure of the 5th of November 2015 (Agurto-Detzel et al. in Geophysical Research Letters 43: 4929–4936, 2016).
A novel tree seed algorithm for optimal reactive power planning and reconfiguration based STATCOM devices and PV sources
Authors: Belkacem Mahdad
Published: February 2021

Reactive power dispatch based on static synchronous compensator (STATCOM) and photovoltaic (PV) sources in coordination with reconfiguration strategy is vital task to ensure reliable operation of modern radial distribution (RD) systems. This paper introduces a novel tree seed algorithm (TSA) to improve the performance of modern RD power systems. A variant of TSA based on intelligent and flexible mechanism search is proposed to create an interactive equilibrium between exploration and exploitation during the search process to improve the global solution. Two objective functions, the total power loss and the margin reserve security are optimized under normal condition and critical load growth. To obtain reliable operation of the distribution system under critical situations, a reactive power dispatch based STATCOM devices is managed in coordination with the reconfiguration stage to find the best combination of sectionalizing switches and tie switches to be operated. The efficiency and particularity of the proposed distribution-planning strategy validated on two test systems, the radial 33 buses and the practical radial 250 buses (30 kV) of Sonelgaz Company located in Biskra in the south of Algeria. This radial electric network designed principally to deliver energy to several small and important agricultural consumers. Results obtained based on various test cases and scenarios using the proposed new planning strategy confirm the efficiency of the proposed planning strategy in terms of reduction of the total power loss, improvement voltage magnitude and enhancement of margin reserve.
Microbiological and Biochemical Properties in Eutric/Dystric Brunic Arenosols, Eutric/Endocalcaric Cambisols, and Haplic/Albic Luvisols Soils
Authors: Baćmaga Małgorzata , Wyszkowska Jadwiga , Borowik Agata , Kucharski Jan , Paprocki Łukasz
Published: February 2021

To understand the role of microorganisms in the functioning of forest ecosystems, the structure of bacterial communities and the enzymatic activity were determined in forest soils representing the following soil subtypes: Eutric/Dystric Brunic Arenosols (A), Eutric/Endocalcaric Cambisols (C), and Haplic/Albic Luvisols (L). Their microbiological and biochemical properties were compared based on bacterial counts and diversity, and activities of seven soil enzymes: dehydrogenases, catalase, urease, acid phosphatase, alkaline phosphatase, arylsulfatase, and β-glucosidase. Organotrophic bacteria and actinobacteria were the most abundant and featured the highest values of the EP (ecophysiological diversity index) in the Haplic/Albic Luvisol soil. In turn, the CD (colony development index) values of these bacterial groups were the highest in the Eutric/Endocalcaric Cambisols. The OTU number of bacteria allowed concluding that, at the class level, the Eutric/Dystric Brunic Arenosols and Haplic/Albic Luvisols were predominated by Alphaproteobacteria belonging to Proteobacteria, whereas the Eutric/Endocalcaric Cambisols by Actinobacteria. At the family rank, the Eutric/Dystric Brunic Arenosols were colonized in the highest numbers by Mycobacteriaceae, Rhodospirillaceae, Koribacteriaceae, and Acidobacteriaceae; the Eutric/Endocalcaric Cambisols by Nocardiaceae, Bradyrhizobiaceae, and Mycobacteriaceae, whereas Haplic/Albic Luvisols by Sinobacteriaceae and Rhodospirillaceae. Four bacterial genera, i.e., Rhodoplanes, Burkholderia belonging to Proteobacteria, Mycobacterium belonging to Actinobacteria, and Candidatus Solibacter belonging to Acidobacteria, were identified in all soils tested. The genetic diversity of bacteria was proved the highest in Eutric/Endocalcaric Cambisols. In turn, the highest enzymatic activity was found for Haplic/Albic Luvisols, while the lowest one for Eutric/Endocalcaric Cambisols. The present study results point out to significant differences between the soil types analyzed in terms of the diversity and structure of their bacterial communities and their enzymatic properties.
Moderate sewage sludge biochar application on alkaline soil for corn growth: a field study
Authors: Xie Shengyu , Yu Guangwei , Jiang Ruqing , Ma Jianli , Shang Xiaofu , Wang Gang , Wang Yin , Yang Yongan , Li Chunxing
Published: February 2021

In view of the risks induced by the inhibitory effects of applying impracticably large amounts of sewage sludge biochar (SSB) to the alkaline soil, this field study investigated the influence of moderate biochar amendments (0, 1500, 4500, and 9000 kg/hm2) on corn growth, alkaline soil properties, and the uptake of potentially toxic elements (PTEs). The results showed that applying more SSB would decrease the ammonium nitrogen concentration and increase the available phosphorus and potassium concentrations, which inhibited corn plant growth because of high background nutrient levels of the alkaline soil. When the alkaline soil was amended with 1500 kg/hm2 SSB, the dry weight of 100 niblets increased from 32.11 g in the control to 35.07 g. There was no significant variation in the total concentration of PTEs in the soil. The concentrations of Mn, Ni, Cu, and Zn in niblets decreased from 5.54, 0.83, 2.26, and 27.15 mg/kg in the control to 4.47, 0.62, 1.30, and 23.45 mg/kg, respectively. Accordingly, the health risk from corn consumption was significantly reduced. Furthermore, the combination of SSB and fertilizer improved corn growth and reduced the risk of consumption of PTEs. Therefore, considering the increase in corn fruit yield and the decrease in consumption risk, applying 1500 kg/hm2 of biochar to alkaline soils is a realistically achievable rate, which can broaden the utilization of SSB for remediation of different types of soil.
Using Reinforcement Learning for Generating Polynomial Models to Explain Complex Data
Authors: Ståhl Niclas , Mathiason Gunnar , Alcacoas Dellainey
Published: February 2021

Basic oxygen steel making is a complex chemical and physical industrial process that reduces a mix of pig iron and recycled scrap into low-carbon steel. Good understanding of the process and the ability to predict how it will evolve requires long operator experience, but this can be augmented with process target prediction systems. Such systems may use machine learning to learn a model of the process based on a long process history, and have an advantage in that they can make use of vastly more process parameters than operators can comprehend. While it has become less of a challenge to build such prediction systems using machine learning algorithms, actual production implementations are rare. The hidden reasoning of complex prediction model and lack of transparency prevents operator trust, even for models that show high accuracy predictions. To express model behaviour and thereby increasing transparency we develop a reinforcement learning (RL) based agent approach, which task is to generate short polynomials that can explain the model of the process from what it has learnt from process data. The RL agent is rewarded on how well it generates polynomials that can predict the process from a smaller subset of the process parameters. Agent training is done with the REINFORCE algorithm, which enables the sampling of multiple concurrently plausible polynomials. Having multiple polynomials, process developers can evaluate several alternative and plausible explanations, as observed in the historic process data. The presented approach gives both a trained generative model and a set of polynomials that can explain the process. The performance of the polynomials is as good as or better than more complex and less interpretable models. Further, the relative simplicity of the resulting polynomials allows good generalisation to fit new instances of data. The best of the resulting polynomials in our evaluation achieves a better$$R^2$$R2score on the test set in comparison to the other machine learning models evaluated.
Characterizations of continuous operators on $$C_b(X)$$ with the strict topology
Authors: Nowak Marian , Stochmal Juliusz
Published: February 2021

Let X be a completely regular Hausdorff space and $$C_b(X)$$

C
b

(
X
)

be the space of all bounded continuous functions on X, equipped with the strict topology $$\beta $$
β
. We study some important classes of $$(\beta ,\Vert \cdot \Vert _E)$$

(
β
,
‖
·

‖
E

)

-continuous linear operators from $$C_b(X)$$

C
b

(
X
)

to a Banach space $$(E,\Vert \cdot \Vert _E)$$

(
E
,
‖
·

‖
E

)

: $$\beta $$
β
-absolutely summing operators, compact operators and $$\beta $$
β
-nuclear operators. We characterize compact operators and $$\beta $$
β
-nuclear operators in terms of their representing measures. It is shown that dominated operators and $$\beta $$
β
-absolutely summing operators $$T:C_b(X)\rightarrow E$$

T
:

C
b

(
X
)

→
E

coincide and if, in particular, E has the Radon–Nikodym property, then $$\beta $$
β
-absolutely summing operators and $$\beta $$
β
-nuclear operators coincide. We generalize the classical theorems of Pietsch, Tong and Uhl concerning the relationships between absolutely summing, dominated, nuclear and compact operators on the Banach space C(X), where X is a compact Hausdorff space.
Pharmacological properties of baicalin on liver diseases: a narrative review
Authors: Yang Jin-yu , Li Min , Zhang Cheng-liang , Liu Dong
Published: February 2021

Baicalin is the main active component of Scutellaria baicalensis, widely used in traditional Chinese medicine thanks to its various pharmacological effects, such as anti-tumor, anti-inflammatory, and antibacterial properties, as well as cardiovascular, hepatic, and renal protective effect. Recently, the protective effects of baicalin on liver disease have received much more attention. Several studies showed that baicalin protects against several types of liver diseases including viral hepatitis, fatty liver disease, xenobiotic induced liver injury, cholestatic liver injury, and hepatocellular carcinoma, with a variety of pharmacological mechanisms. A comprehensive understanding of the mechanism of baicalin can provide a valuable reference for its clinical use, but up to now, no narrative review is available that summarizes the pharmacological effects of baicalin to clarify its potential use in the treatment of liver diseases. Therefore, this review summarizes the progress of baicalin research and the underlying mechanism in the treatment of various liver diseases, to promote further research and its clinical application.
Clinical and dermoscopic changes of acquired melanocytic nevi of patients treated with afamelanotide
Authors: Arisi Mariachiara , Rossi M. , Rovati C. , Tomasi C. , Mori L. , Laini L. , Calzavara-Pinton P. G.
Published: February 2021

Background

Afamelanotide (AFA) is a synthetic analogue of α-melanocyte-stimulating hormone that is approved for the treatment of patients affected by erythropoietic protoporphyria (EPP). AFA induces a “sun free” tanning and changes of acquired melanocytic nevi (AMN) that are generically described as “darkening”.

Objectives

To assess clinical and dermoscopic AMN changes during AFA treatment.

Methods

Adult EPP patients treated with two AFA implants 50 days apart were enrolled. They underwent a clinical and dermoscopic examination of all AMN at baseline (T0), and after 5 (T1) and 12 (T2) months from the first AFA implant. The general pattern, symmetry, number, and size of pigmented globules, morphology of the pigment network, and dermoscopic melanoma features were assessed.

Results

Fifteen patients were enrolled with 103 AMN. At T1 all reticular and 2-component AMN showed a focal network thickening that returned to baseline by T2. The increase of globules’ number was observed at T1 but not at T2. The difference in number was not influenced by patients’ age or phototype. Dermoscopic changes suggestive of malignancy were never seen. The development of new AMN was never registered.

Conclusions

AFA treatment induces reversible changes of AMN dermoscopic morphology without findings suggestive of malignant transformation and it does not stimulate the development of new AMN.
Management of Multiple Sources of Risk in Livestock Production
Authors: McKendree Melissa G.S. , Tonsor Glynn T. , Schulz Lee L.
Published: February 2021

Firm operators continually manage multiple sources of risk. In an application to cattle feedlot operations, our objective is to determine if producers view output price and animal health risks separately or jointly. We conduct a survey with a choice experiment placing operators in forward looking, decision-making scenarios, and capture information on past risk management approaches. Evidence regarding a relationship between animal health and output price risk mitigation is mixed and depends on the decision being made. Combined, these results provide new insight into how managers approach multiple risks when facing resource constraints.
Development of the mental health cultural adaptation and contextualization for implementation (mhCACI) procedure: a systematic framework to prepare evidence-based psychological interventions for scaling
Authors: Sangraula Manaswi , Kohrt Brandon A. , Ghimire Renasha , Shrestha Pragya , Luitel Nagendra P. , van’t Hof Edith , Dawson Katie , Jordans Mark J. D.
Published: February 2021

Background

Because of the high burden of untreated mental illness in humanitarian settings and low- and middle-income countries, scaling-up effective psychological interventions require a cultural adaptation process that is feasible and acceptable. Our adaptation process incorporates changes into both content and implementation strategies, with a focus on local understandings of distress and treatment mechanisms of action.

Methods

Building upon the ecological validity model, we developed a 10-step process, the mental health Cultural Adaptation and Contextualization for Implementation (mhCACI) procedure, and piloted this approach in Nepal for Group Problem Management Plus (PM+), a task-sharing intervention, proven effective for adults with psychological distress in low-resource settings. Detailed documentation tools were used to ensure rigor and transparency during the adaptation process.

Findings

The mhCACI is a 10-step process: (1) identify mechanisms of action, (2) conduct a literature desk review for the culture and context, (3) conduct a training-of-trainers, (4) translate intervention materials, (5) conduct an expert read-through of the materials, (6) qualitative assessment of intervention population and site, (7) conduct practice rounds, (8) conduct an adaptation workshop with experts and implementers, (9) pilot test the training, supervision, and implementation, and (10) review through process evaluation. For Group PM+, key adaptations were harmonizing the mechanisms of action with cultural models of ‘tension’; modification of recruitment procedures to assure fit; and development of a skills checklist.

Conclusion

A 10-step mhCACI process could feasibly be implemented in a humanitarian setting to rapidly prepare a psychological intervention for widespread implementation.
FUSION 2-CATEGORIES WITH NO LINE OPERATORS ARE GROUPLIKE
Authors: JOHNSON-FREYD THEO , YU MATTHEW
Published: February 2021

We show that if${\mathcal C}$is a fusion$2$-category in which the endomorphism category of the unit object isor, then the indecomposable objects of${\mathcal C}$form a finite group.
Fluid simulations of three-dimensional reconnection that capture the lower-hybrid drift instability
Authors: Allmann-Rahn F. , Lautenbach S. , Grauer R. , Sydora R. D.
Published: February 2021

Fluid models that approximate kinetic effects have received attention recently in the modelling of large-scale plasmas such as planetary magnetospheres. In three-dimensional reconnection, both reconnection itself and current sheet instabilities need to be represented appropriately. We show that a heat flux closure based on pressure gradients enables a 10-moment fluid model to capture key properties of the lower-hybrid drift instability (LHDI) within a reconnection simulation. Characteristics of the instability are examined with kinetic and fluid continuum models, and its role in the three-dimensional reconnection simulation is analysed. The saturation level of the electromagnetic LHDI is higher than expected, which leads to strong kinking of the current sheet. Therefore, the magnitude of the initial perturbation has significant impact on the resulting turbulence.
Getting RCEP across the Line
Authors: Elms Deborah K.
Published: February 2021

After eight years of effort, the 15 Asian members involved in the Regional Comprehensive Economic Partnership (RCEP) met in a virtual ceremony to sign the final document on Sunday, 15 November 2020. The final deal matches the original objective – to knit the region together and allow firms to build supply chains across the region to deliver goods, services, and investment to Asian markets more seamlessly. Getting this free trade agreement (FTA) to this point involved repeated missed deadlines, the loss of one important negotiating partner, and thousands of miles of travel for a rotating cast of officials, trade ministers, and leaders. RCEP began in late 2012 as an effort to unravel what has often been called the ‘spaghetti or noodle bowl’ of overlapping and inconsistent rules that can impede trade. While most of the countries in the region have extensive experience in trade and are outward oriented, trade in Asia has been bedeviled with challenges. This includes a range of both tariff and non-tariff obstacles that have made it more difficult than might be expected to trade, especially for final products, within the region.
The Dark Side of Human Values: How Values are Related to Bright and Dark Personality Traits
Authors: de Holanda Coelho Gabriel Lins , Hanel Paul H. P. , Monteiro Renan Pereira , Vilar Roosevelt , Gouveia Valdiney V.
Published: February 2021

In the present research, we replicate and extend previous findings on the relations between human values and bright\dark traits of personality, using the functional theory of human values (Gouveia, 2013). Specifically, we assessed which dark traits are associated with human values and whether the dark traits explained variance in values beyond the bright traits (Big Five). While prior research has investigated the relations between the three sets of constructs mainly in Western countries, we tested whether the findings hold in Brazil (N= 819). Although values are defined as positive constructs, several value subfunctions were positively correlated with the dark traits (e.g., excitement values with narcissism), while other relations were negative. Controlling for participants' age and gender, hierarchical regressions further revealed that dark traits explain variance in values beyond bright traits, although overall bright traits were more strongly associated with values than dark traits. Together, our findings replicate previous research. Implications for our understanding of the Dark Triad and cross-cultural research are discussed.
Statistical Relationship Between Interplanetary Magnetic Field Conditions and the Helicity Sign of Flux Transfer Event Flux Ropes
Authors: Kieokaew R. , Lavraud B. , Fargette N. , Marchaudon A. , Génot V. , Jacquey C. , Gershman D. , Giles B. , Torbert R. , Burch J.
Published: February 2021

Flux transfer events (FTEs) are transient phenomena produced by magnetic reconnection at the dayside magnetopause typically under southward interplanetary magnetic field (IMF) conditions. They are usually thought of as magnetic flux ropes with helical structures forming through patchy, unsteady or multiple X‐line reconnection. While the IMF often has a non‐zero BY component, its impacts on the FTE flux rope helicity remain unknown. We survey Magnetospheric Multiscale (MMS) observations of FTE flux ropes during years 2015–2017 and investigate the solar wind conditions prior to the events. By fitting a force‐free flux rope model, we select 84 events with good fits and obtain the helicity sign (i.e., handedness) of the flux ropes. We find that positive (negative) helicity flux ropes are mainly preceded by positive (negative) BY component. This finding is compatible with flux ropes formed through a multiple X‐lines mechanism.
Revisiting the Entrainment Relationship of Convective Plumes: A Perspective From Global Observations
Authors: Takahashi Hanii , Luo Zhengzhao Johnny , Stephens Graeme
Published: February 2021

Entrainment is an important process affecting convective transport and is a key parameter in convection modeling. For over half a century, an inverse relationship between entrainment rate (λ) and convective core size (R) has been used in modeling convective clouds. This short letter revisits the λ‐R relation using multiple years of CloudSat observations. Results show that the inverse relationship between λ and R is robust. However, they are not scaled by a simple constant. Global satellite observations provide some guidance for choosing the range of the scaling parameter. Further, our analysis shows that continental convective clouds tend to have smaller λ and larger R compared to oceanic convective clouds, suggesting that vertical mass transport by continental convection is more efficient. The satellite‐based study of the λ‐R relation has the potential to become a new diagnostic metric for assessing the representation of convection in weather and climate models.
MMS Observations of Broadband Electrostatic Waves in Electron Diffusion Region of Magnetotail Reconnection
Authors: Yu Xiancai , Lu Quanming , Wang Rongsheng , Huang Kai , Gao Xinliang , Wang Shui
Published: February 2021

In this study, the broadband electrostatic waves are observed in electron diffusion region (EDR). Detailed analysis has shown that the parallel electric field of these waves have a bipolar or continuous steepening waveform. The bipolar structures of the parallel electric field are usually accompanied by electron holes (EHs) in phase space. The parallel spatial scales of EHs are ∼3–5 ( is the Debye length), and the perpendicular spatial scales are larger than ∼18.6 . Therefore, the length ratios are larger than ∼3.7–6.2, which means that the EHs have oblate shapes. Associated with these plasma waves, electron beams propagating away from the X‐line have been observed. By performing a one‐dimensional (1‐D) electrostatic particle‐in‐cell simulation of the bump‐on‐tail instability, we reproduce two types of waveforms similar to those observed in the EDR during the different evolution stage of the instability, which implies that these electrostatic waves are generated by the bump‐on‐tail instabilities.
Wave Propagation in Infinituple‐Porosity Media
Authors: Zhang Lin , Ba Jing , Carcione José M.
Published: February 2021

The fractal texture (or fabric) of porous media, which supports fluid flow at different scales, is the main cause of wave anelasticity (dispersion and attenuation) on a wide range of frequencies. To model this phenomenon, we develop a theory of wave propagation in a fluid saturated infinituple‐porosity media containing inclusions at multiple scales, based on the differential effective medium (DEM) theory of solid composites and Biot‐Rayleigh theory for double‐porosity media. The dynamical equations are derived from first principles, that is, based on the strain (potential), kinetic, and dissipation energies, leading to generalized stiffness and density coefficients. The scale of the inclusions can be characterized by different distributions. The theory shows that the anelasticity depends on the size (radius) of the inclusions, parameter θ (exponential distribution), mean radius r0 and variance σr2 (Gaussian distribution) and the fractal dimension Df (self‐similar distribution). When Df = 2, θ = 1 and σr2 = 4, the three distributions give the same P‐wave velocities and attenuation, since each added inclusion phase has nearly the same volume fraction. For the modeling results, the range of anelasticity of Df = 2.99/θ = 1/σr2 = 4 is broader than that of Df < 2.99/θ < 1/σr2 < 4. To confirm the validity of the model, we compare the results with laboratory measurements on tight sandstone and carbonate samples in the range 1 Hz–1 kHz, Fox Hill sandstone (5 Hz–800 kHz) and field measurements of marine sediments (50 Hz–400 kHz). This comparison shows that the model successfully describes the observed anelasticity.
The Imminent Calving Retreat of Taku Glacier
Authors: McNeil Christopher , Amundson J. , O’Neel S. , Motyka R. , Sass L. , Truffer M. , Zechmann J. , Campbell S.
Published: February 2021

Long an anomaly among glaciers, advancing while most others shrank, Taku Glacier is starting to succumb to climate change, offering an unprecedented look at the onset of tidewater glacier retreat.
Dissection of intercellular communication using the transcriptome-based framework ICELLNET
Authors: Noël Floriane , Massenet-Regad Lucile , Carmi-Levy Irit , Cappuccio Antonio , Grandclaudon Maximilien , Trichot Coline , Kieffer Yann , Mechta-Grigoriou Fatima , Soumelis Vassili
Published: February 2021

Cell-to-cell communication can be inferred from ligand–receptor expression in cell transcriptomic datasets. However, important challenges remain: global integration of cell-to-cell communication; biological interpretation; and application to individual cell population transcriptomic profiles. We develop ICELLNET, a transcriptomic-based framework integrating: 1) an original expert-curated database of ligand–receptor interactions accounting for multiple subunits expression; 2) quantification of communication scores; 3) the possibility to connect a cell population of interest with 31 reference human cell types; and 4) three visualization modes to facilitate biological interpretation. We apply ICELLNET to three datasets generated through RNA-seq, single-cell RNA-seq, and microarray. ICELLNET reveals autocrine IL-10 control of human dendritic cell communication with up to 12 cell types. Four of them (T cells, keratinocytes, neutrophils, pDC) are further tested and experimentally validated. In summary, ICELLNET is a global, versatile, biologically validated, and easy-to-use framework to dissect cell communication from individual or multiple cell-based transcriptomic profiles.
Giant nonlinear optical activity in two-dimensional palladium diselenide
Authors: Yu Juan , Kuang Xiaofei , Li Junzi , Zhong Jiahong , Zeng Cheng , Cao Lingkai , Liu Zongwen , Zeng Zhouxiaosong , Luo Ziyu , He Tingchao , Pan Anlian , Liu Yanping
Published: February 2021

Nonlinear optical effects in layered two-dimensional transition metal chalcogenides have been extensively explored recently because of the promising prospect of the nonlinear optical effects for various optoelectronic applications. However, these materials possess sizable bandgaps ranging from visible to ultraviolet region, so the investigation of narrow-bandgap materials remains deficient. Here, we report our comprehensive study on the nonlinear optical processes in palladium diselenide (PdSe2) that has a near-infrared bandgap. Interestingly, this material exhibits a unique thickness-dependent second harmonic generation feature, which is in contrast to other transition metal chalcogenides. Furthermore, the two-photon absorption coefficients of 1–3 layer PdSe2 (β ~ 4.16 × 105, 2.58 × 105, and 1.51 × 105 cm GW−1) are larger by two and three orders of magnitude than that of the conventional two-dimensional materials, and giant modulation depths (αs ~ 32%, 27%, and 24%) were obtained in 1–3 layer PdSe2. Such unique nonlinear optical characteristics make PdSe2 a potential candidate for technological innovations in nonlinear optoelectronic devices.
Determinants of genome-wide distribution and evolution of uORFs in eukaryotes
Authors: Zhang Hong , Wang Yirong , Wu Xinkai , Tang Xiaolu , Wu Changcheng , Lu Jian
Published: February 2021

Upstream open reading frames (uORFs) play widespread regulatory functions in modulating mRNA translation in eukaryotes, but the principles underlying the genomic distribution and evolution of uORFs remain poorly understood. Here, we analyze ~17 million putative canonical uORFs in 478 eukaryotic species that span most of the extant taxa of eukaryotes. We demonstrate how positive and purifying selection, coupled with differences in effective population size (Ne), has shaped the contents of uORFs in eukaryotes. Besides, gene expression level is important in influencing uORF occurrences across genes in a species. Our analyses suggest that most uORFs might play regulatory roles rather than encode functional peptides. We also show that the Kozak sequence context of uORFs has evolved across eukaryotic clades, and that noncanonical uORFs tend to have weaker suppressive effects than canonical uORFs in translation regulation. This study provides insights into the driving forces underlying uORF evolution in eukaryotes.
A genetically stable Zika virus vaccine candidate protects mice against virus infection and vertical transmission
Authors: Adam Awadalkareem , Fontes-Garfias Camila R. , Sarathy Vanessa V. , Liu Yang , Luo Huanle , Davis Emily , Li Wenqian , Muruato Antonio E. , Wang Binbin , Ahatov Renat , Mahmoud Yoseph , Shan Chao , Osman Samantha R. , Widen Steven G. , Barrett Alan D. T. , Shi Pei-Yong , Wang Tian
Published: February 2021

Although live attenuated vaccines (LAVs) have been effective in the control of flavivirus infections, to date they have been excluded from Zika virus (ZIKV) vaccine trials due to safety concerns. We have previously reported two ZIKV mutants, each of which has a single substitution in either envelope (E) glycosylation or nonstructural (NS) 4B P36 and displays a modest reduction in mouse neurovirulence and neuroinvasiveness, respectively. Here, we generated a ZIKV mutant, ZE4B-36, which combines mutations in both E glycosylation and NS4B P36. The ZE4B-36 mutant is stable and attenuated in viral replication. Next-generation sequence analysis showed that the attenuating mutations in the E and NS4B proteins are retained during serial cell culture passages. The mutant exhibits a significant reduction in neuroinvasiveness and neurovirulence and low infectivity in mosquitoes. It induces robust ZIKV-specific memory B cell, antibody, and T cell-mediated immune responses in type I interferon receptor (IFNR) deficient mice. ZIKV-specific T cell immunity remains strong months post-vaccination in wild-type C57BL/6 (B6) mice. Vaccination with ZE4B-36 protects mice from ZIKV-induced diseases and vertical transmission. Our results suggest that combination mutations in E glycosylation and NS4B P36 contribute to a candidate LAV with significantly increased safety but retain strong immunogenicity for prevention and control of ZIKV infection.
Author Correction: Selection and validation of reference genes by RT-qPCR for murine cementoblasts in mechanical loading experiments simulating orthodontic forces in vitro
Authors: Niederau Christian , Craveiro Rogerio B. , Azraq Irma , Brockhaus Julia , Bastian Asisa , Kirschneck Christian , Wolf Michael
Published: February 2021

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Clinicopathological characteristics and prognostic factors for intrahepatic cholangiocarcinoma: a population-based study
Authors: Yu Tian-hua , Chen Xin , Zhang Xuan-he , Zhang Er-chi , Sun Cai-xia
Published: February 2021

We aimed to explore the clinicopathological features and survival-related factors for intrahepatic cholangiocarcinoma (ICC). Eligible data were extracted from the Surveillance, Epidemiology and End Results (SEER) database from 2004 to 2015. Totally, 4595 ICC patients were collected with a male to female ratio of nearly 1:1. The higher proportion of ICC patients was elderly, tumor size ≥ 5 cm and advanced AJCC stage. Most patients (79.2%) have no surgery, while low proportion of patients receiving radiotherapy (15.1%). The median survival was 7.0 months (range 0–153 months). The 5-year CSS and OS rates were 8.96% and 7.90%. Multivariate analysis found that elderly age (aged ≥ 65 years old), male, diagnosis at 2008–2011, higher grade, tumor size ≥ 5 cm, and advanced AJCC stage were independent factors for poorer prognosis; while API/AI (American Indian/AK Native, Asian/Pacific Islander) race, married, chemotherapy, surgery and radiotherapy were independent favorable factors in both CSS and OS. Furthermore, stratified analysis found that chemotherapy and radiotherapy improved CSS and OS in patients without surgery. Age, sex, race, years of diagnosis, married status, grade, tumor size, AJCC stage, surgery, chemotherapy and radiotherapy were significantly related to prognosis of ICC. Chemotherapy and radiotherapy could significantly improve survival in patients without surgery.
Effects of temperature on the behaviour and metabolism of an intertidal foraminifera and consequences for benthic ecosystem functioning
Authors: Deldicq Noémie , Langlet Dewi , Delaeter Camille , Beaugrand Grégory , Seuront Laurent , Bouchet Vincent M. P.
Published: February 2021

Heatwaves have increased in intensity, duration and frequency over the last decades due to climate change. Intertidal species, living in a highly variable environment, are likely to be exposed to such heatwaves since they can be emerged for more than 6 h during a tidal cycle. Little is known, however, on how temperature affects species traits (e.g. locomotion and behaviour) of slow-moving organisms such as benthic foraminifera (single-celled protists), which abound in marine sediments. Here, we examine how temperature influences motion-behaviour and metabolic traits of the dominant temperate foraminiferaHaynesina germanicaby exposing individuals to usual (6, 12, 18, 24, 30 °C) and extreme (high; i.e. 32, 34, 36 °C) temperature regimes. Our results show that individuals reduced their activity by up to 80% under high temperature regimes whereas they remained active under the temperatures they usually experience in the field. When exposed to a hyper-thermic stress (i.e. 36 °C), all individuals remained burrowed and the photosynthetic activity of their sequestered chloroplasts significantly decreased. Recovery experiments subsequently revealed that individuals initially exposed to a high thermal regime partially recovered when the hyper-thermic stress ceased.H. germanicacontribution to surface sediment reworking substantially diminished from 10 mm3indiv−1day−1(usual temperature) to 0 mm3indiv−1day−1when individuals were exposed to high temperature regimes (i.e. above 32 °C). Given their role in sediment reworking and organic matter remineralisation, our results suggest that heatwaves may have profound long-lasting effects on the functioning of intertidal muddy ecosystems and some key biogeochemical cycles.
Beta synchrony for expressive language lateralizes to right hemisphere in development
Authors: Sharma Vivek V. , Vannest Jennifer , Greiner Hansel M. , Fujiwara Hisako , Tenney Jeffrey R. , Williamson Brady J. , Kadis Darren S.
Published: February 2021

A left perisylvian network is known to support language in healthy adults. Low-beta (13–23 Hz) event-related desynchrony (ERD) has been observed during verb generation, at approximately 700–1200 ms post-stimulus presentation in past studies; the signal is known to reflect increased neuronal firing and metabolic demand during language production. In contrast, concurrent beta event-related synchrony (ERS) is thought to reflect neuronal inhibition but has not been well studied in the context of language. Further, while low-beta ERD for expressive language has been found to gradually shift from bilateral in childhood to left hemispheric by early adulthood, developmental lateralization of ERS has not been established. We used magnetoencephalography to study low beta ERS lateralization in a group of children and adolescents (n = 78), aged 4 to less than 19 years, who performed covert verb generation. We found that the youngest children had bilateral ERD and ERS. By adolescence, low-beta ERD was predominantly left lateralized in perisylvian cortex (i.e., Broca’s and Wernicke’s regions), while beta ERS was predominantly right lateralized. Increasing lateralization was significantly correlated to age for both ERD (Spearman’s r = 0.45, p < 0.01) and ERS (Spearman’s r =  − 0.44, p < 0.01). Interestingly, while ERD lateralized in a linear manner, ERS lateralization followed a nonlinear trajectory, suggesting distinct developmental trajectories. Implications to early-age neuroplasticity and neuronal inhibition are discussed.
Accelerated sonothrombolysis with Definity in a xenographic porcine cerebral thromboembolism model
Authors: Kleven Robert T. , Karani Kunal B. , Hilvert Nicole , Ford Samantha M. , Mercado-Shekhar Karla P. , Racadio John M. , Rao Marepalli B. , Abruzzo Todd A. , Holland Christy K.
Published: February 2021

Adjuvant ultrasound at 2 MHz with or without an ultrasound contrast agent improves the rate of thrombus resolution by recombinant tissue plasminogen activator (rt-PA) in laboratory and clinical studies. A sub-megahertz approach can further expand this therapy to a subset of patients with an insufficient temporal bone window, improving efficacy in unselected patient populations. The aim of this study was to determine if a clinical ultrasound contrast agent (UCA), Definity, and 220 kHz pulsed ultrasound accelerated rt-PA thrombolysis in a preclinical animal model of vascular occlusion. The effect of Definity and ultrasound on thrombus clearance was first investigated in vitro and subsequently tested in a xenographic porcine cerebral thromboembolism model in vivo. Two different microcatheter designs (end-hole, multi-side-hole) were used to infuse rt-PA and Definity at the proximal edge or directly into clots, respectively. Sonothrombolysis with Definity increased clot mass loss relative to saline or rt-PA alone in vitro, only when rt-PA was administered directly into clots via a multi-side-hole microcatheter. Combined treatment with rt-PA, Definity, and ultrasound in vivo increased the rate of reperfusion up to 45 min faster than clots treated with rt-PA or saline. In this porcine cerebral thromboembolism model employing retracted human clots, 220 kHz ultrasound, in conjunction with Definity increased the probability of early successful reperfusion with rt-PA.
Chemical-free and scalable process for the fabrication of a uniform array of liquid-gated CNTFET, evaluated by KCl electrolyte
Authors: Agarwal Pankaj B. , Thakur Navneet Kumar , Sharma Rishi , Singh Parul , Joseph Joshy , Tripura Chaturvedula
Published: February 2021

Biosensors based on liquid-gated carbon nanotubes field-effect transistors (LG-CNTFETs) have attracted considerable attention, as they offer high sensitivity and selectivity; quick response and label-free detection. However, their practical applications are limited due to the numerous fabrication challenges including resist-based lithography, in which after the lithography process, the resist leaves trace level contaminations over the CNTs that affect the performance of the fabricated biosensors. Here, we report the realization of LG-CNTFET devices using silicon shadow mask-based chemical-free lithography process on a 3-in. silicon wafer, yielding 21 sensor chips. Each sensor chip consists of 3 × 3 array of LG-CNTFET devices. Field emission scanning electron microscope (FESEM) and Raman mapping confirm the isolation of devices within the array chip having 9 individual devices. A reference electrode (Ag/AgCl) is used to demonstrate the uniformity of sensing performances among the fabricated LG-CNTFET devices in an array using different KCl molar solutions. The average threshold voltage (Vth) for all 9 devices varies from 0.46 to 0.19 V for 0.1 mM to 1 M KCl concentration range. This developed chemical-free process of LG-CNTFET array fabrication is simple, inexpensive, rapid having a commercial scope and thus opens a new realm of scalable realization of various biosensors.
A comparative study on the chloride effectiveness of synthetic rutile and natural rutile manufactured from ilmenite ore
Authors: Jung Eun Jin , Kim Jinyoung , Lee Ye Rin
Published: February 2021

Studies on continuous and selective chlorination by using ilmenite have been actively conducted because the efficient removal of FeO from ilmenite(FeTiO3) ore using selective chlorination not only improves the reaction purity of TiCl4 but it also leads to price competitiveness compared to TiCl4 synthesized from natural rutile. The chlorination of synthetic rutile with FeO removed was compared with that of natural rutile to examine the reaction efficiency. The selective chlorination efficiency depends on the input amounts of coke and Cl2, as shown by thermodynamic calculation, when FeO is selectively removed. It was found that manufacturing of TiCl4 was easier by using the synthetic rutile, because it had greater porosity than natural rutile. Relatively greater pore volumes were found in the synthetic rutile than in natural rutile. It was confirmed that the reaction efficiency of chlorination for TiCl4 production was directly related to the difference in the porosity distribution between the titanium ores, as verified by a kinetic comparison of synthetic and natural rutiles.
Development and validation of a multiplex qPCR assay for detection and relative quantification of HPV16 and HPV18 E6 and E7 oncogenes
Authors: Bordigoni Alexia , Motte Anne , Tissot-Dupont Hervé , Colson Philippe , Desnues Christelle
Published: February 2021

Human papillomaviruses (HPV) play a key role in promoting human anogenital cancers. Current high-risk HPV screening or diagnosis tests involve cytological or molecular techniques mostly based on qualitative HPV DNA detection. Here, we describe the development of a rapid quantitative polymerase chain reaction (qPCR) detection test of HPV16 and HPV18 oncogenes (E6 and E7) normalized on human gene encoding GAPDH. Optimized qPCR parameters were defined, and analytical specificities were validated. The limit of detection was 101 for all genes tested. Assay performances were evaluated on clinical samples (n = 96). Concordance between the Xpert HPV assay and the triplex assay developed here was 93.44% for HPV16 and 73.58% for HPV18. HPV co-infections were detected in 15 samples. The systems developed in the present study can be used in complement to traditional HPV tests for specifically validating the presence of HPV16 and/or HPV18. It can also be used for the follow-up of patients with confirmed infection and at risk of developing lesions, through the quantification of E6 and E7 oncogene expression (mRNA) normalized on the GAPDH expression levels.
Automatic classification of canine thoracic radiographs using deep learning
Authors: Banzato Tommaso , Wodzinski Marek , Burti Silvia , Osti Valentina Longhin , Rossoni Valentina , Atzori Manfredo , Zotti Alessandro
Published: February 2021

The interpretation of thoracic radiographs is a challenging and error-prone task for veterinarians. Despite recent advancements in machine learning and computer vision, the development of computer-aided diagnostic systems for radiographs remains a challenging and unsolved problem, particularly in the context of veterinary medicine. In this study, a novel method, based on multi-label deep convolutional neural network (CNN), for the classification of thoracic radiographs in dogs was developed. All the thoracic radiographs of dogs performed between 2010 and 2020 in the institution were retrospectively collected. Radiographs were taken with two different radiograph acquisition systems and were divided into two data sets accordingly. One data set (Data Set 1) was used for training and testing and another data set (Data Set 2) was used to test the generalization ability of the CNNs. Radiographic findings used as non mutually exclusive labels to train the CNNs were: unremarkable, cardiomegaly, alveolar pattern, bronchial pattern, interstitial pattern, mass, pleural effusion, pneumothorax, and megaesophagus. Two different CNNs, based on ResNet-50 and DenseNet-121 architectures respectively, were developed and tested. The CNN based on ResNet-50 had an Area Under the Receive-Operator Curve (AUC) above 0.8 for all the included radiographic findings except for bronchial and interstitial patterns both on Data Set 1 and Data Set 2. The CNN based on DenseNet-121 had a lower overall performance. Statistically significant differences in the generalization ability between the two CNNs were evident, with the CNN based on ResNet-50 showing better performance for alveolar pattern, interstitial pattern, megaesophagus, and pneumothorax.