bluuebunny/crossref_metadata_2025 huggingface dataset:
Electromagnetically induced transparency metamaterials: theories, designs and applications
Authors: Zhu Lei , Dong Liang
Published: March 2022

Electromagnetically induced transparency (EIT) stems from a quantum system, where an opaque atomic medium appears the narrow transparent state within a wide absorption area. This phenomenon can be achieved by quantum interference of pumping light and detecting light at different energy levels of transitions. In the generation process of EIT effect, in addition to transparent state, the atomic medium is usually accompanied with a strong dispersion effect, which will bright about a significant reduction of light velocity, thus realizing many important applications, such as slow light propagations. Although the EIT effect has many important applications, its application scenarios are greatly limited due to the fact that EIT realization usually requires specific and complicated conditions, such as refrigeration temperature, high intensity laser, etc. Recently, the analogue of EIT effect in metamaterial has attracted increasing attentions due to its advantages such as controllable room temperature and large operating bandwidth. Metamaterial analogue of EIT effect has become a new research focus. In this article, we review current research progresses on EIT metamaterials. Firstly, we describe the theoretical models for analyzing EIT metamaterials, including the mechanical oscillator model and the equivalent circuit model. Then, we describe the simulations, designs and experiments of passive EIT metamaterials with fixed structures and active EIT metamaterials with tunable elements. Furthermore, the applications of EIT metamaterials in the areas of slow lights, sensings, absorptions and other fields are also reviewed. Finally, the possible directions and key issues of future EIT metamaterial researches are prospected.
Phase fraction measurement of oil–gas–water three-phase flow with stratified gas by ultrasound technique
Authors: Su Qian , Deng Xiangtian , Liu Zhenxing , Tan Chao , Dong Feng
Published: March 2022

Phase fraction is one of important indexes to characterize multiphase flow. In order to measure each phase fraction of oil–gas–water three-phase flow, liquid level height is detected by time-of-flight—TOF of reflected ultrasound at gas–liquid interface, while oil phase fraction in reflection path is calculated according to the ultrasound attenuation. By studying interactions between multiphase flow and the ultrasound propagation in certain flow patterns, a prediction model for phase fraction measurement of three-phase flow is proposed based on ultrasound transmission attenuation and reflection TOF in the process of horizontal flow with actual phase distributions. Simulation and experimental results under conditions of oil–water two-phase structure with stratified gas in a horizontal pipe show that the proposed method and the established model can accurately detect gas–liquid interface, so that measure oil, gas, water phase fraction. The mechanism prediction model and the measurement device effectively solve the nonlinear response of the ultrasonic measurement parameter, so that can estimate phase fractions of liquids and gas in two-phase as well as three-phase flows simultaneously, which extends the measurement range and the applicable scope of ultrasonic technique to multiphase flow.
Discovery of Extended Structure Around Open Cluster COIN-Gaia 13 Based on Gaia EDR3
Authors: Bai Leya , Zhong Jing , Chen Li , Li Jing , Hou Jinliang
Published: March 2022

COIN-Gaia 13 is a newly discovered open cluster revealed by Gaia DR2 data. It is a nearby open cluster with a distance of about 513 pc. Combined with the five-dimensional astrometric data of Gaia EDR3 with higher accuracy, we use the membership assignment algorithm (pyUPMASK) to determine the membership of COIN-Gaia 13 in a large extended spatial region. The cluster has 478 identified candidate members. After obtaining reliable cluster members, we further study its basic properties and spatial distribution. Our results show that there is an obvious extended structure of the cluster in the X–Y plane. This elongated structure is distributed along the spiral arm, and the whole length is about 270 pc. The cluster age is 250 Myr, the total mass is about 439 M
⊙ and the tidal radius of the cluster is about 11 pc. Since more than half of member stars (352 stars) are located outside twice the tidal radius, it is suspected that this cluster is undergoing the dynamic dissolution process. Furthermore, the spatial distribution and kinematic analysis indicate that the extended structure in COIN-Gaia 13 is more likely to be caused by differential rotation of the Galaxy.
Evolution Toward the Observational Features of a Stripped Envelope Type IIb Supernova in a Binary System
Authors: Long Gang , Song Han-Feng , Zhang Rui-Yu , Qin Ying , Zhao Liu-Yan , Qi Shi-Tao , Wu Fang-Wen
Published: March 2022

Type IIb supernovae (SNe IIb) that have a thin layer of hydrogen left in their outer envelope have been believed to belong to core collapse supernovae. Mass transfer via Roche lobe overflow can significantly change the nucleosynthesis and surface chemical elements of the progenitors of SNe IIb. We aim to explore what conditions a close binary can meet with the observational features of SNe IIb. We find that an observed low mass SN IIb cannot be produced by a low mass isolated star with M < 20 M
⊙ due to the existence of a thick hydrogen envelope regardless of rotation. Binaries dominate as progenitors in the mass interval (i.e., M < 20 M
⊙) considered in this paper. The 16 M
⊙ primary with a 14 M
⊙ companion in a binary system with ∼10 days < P
orb < 720 days can reproduce observational features of SNe IIb (i.e., T
eff,

log

L

/

L

⊙

, M
He, M
H, etc.). With the decrease of the hydrogen-rich envelope mass, the radius of the progenitor shrinks. The associated types of SN IIb progenitors from RSGs and YSGs to BSGs are closely related to the amount of hydrogen left in the envelopes. Rotation can bring the production of the CNO reaction to the stellar surface at an early phase, which would explain the nitrogen-rich circumstellar material of SN 1993J and can also explain the large He/H ratio of supernova ejecta. Rotation can increase the corresponding region of the orbital period which can produce an SN IIb.
Tailoring of upconversion luminescence of Al3+ engineered titanate phosphor for non-invasive thermometry
Authors: Pattnaik Sasank , Rai Vineet Kumar
Published: March 2022

The ability of rare-earth-doped ferroelectric oxides to achieve outstanding upconversion (UC) performances under NIR irradiation despite possessing intrinsic electric properties drives researchers all over the globe to work in this field. The structural and spectroscopic characteristics of the Bi4Ti3O12 phosphor integrated with Er3+, Yb3+, and Al3+ have been thoroughly investigated in this study. The considerable increase in UC emission ∼three times caused by the addition of Al3+ ions has been observed and discussed. The processes connected with the UC emission related to the pump power variation have been realized using the rate law equation. Aside from having high sensitivity of 0.011 K−1 at room temperature, the prepared phosphor possesses excellent thermal stability, i.e., it retains ∼73% of its initial intensity with the addition of Al3+ ions.
Theoretical study of encapsulation of diethylstilbestrol drug into the inner surface of BNNT toward designing a new nanocarrier for drug delivery systems
Authors: Hosseinzadeh Maryamossadat , Masoudi Shiva , Masnabadi Nasrin , Azarakhshi Fatemeh
Published: March 2022

In this research, the encapsulation and intermolecular non-bonded interactions of an anticancer drug, Diethylstilbestrol (DES), into the inner surfaces of BNNT (8,8–12) were investigated. All Density Functional Theory (DFT) calculations were performed in a gas phase. So, this research focuses on intermolecular hydrogen bonding, van der Waals and steric interactions between active sites of the BNNT and DES by quantum theory of atom in molecule (QTAIM) theory. QTAIM and non-covalent interaction index (NCI) analyses showed the interactions between the DES drug and the BNNT nanotube. The HOMO-LUMO orbitals, Density of States (DOS) plots, and reduced density gradient (RDG) analyses were carried out to determine the effect of DES adsorption into the nanotube. Furthermore, the effect of the abovementioned interactions between the DES and BNNT (8,8–12) on the electronic characteristics, and natural charges have also been estimated. Based on the results, the thermodynamic parameters of BNNT (8,8-12)/DES are in very close agreement with the NCI analysis and showed that the BNNT (8,8–12) adsorb DES via a physisorption process rather than chemical one and the sorption procedure was exothermic in benign and thermodynamically favorable. Therefore, the use of BNNT (8,8–12) as a carrier for DES drug has been confirmed theoretically.
Strengthening mechanism of Sr element on 6063 Al alloys
Authors: Yang Zhan-Shou , Dong Yaping , Li Wu , Liu Xin
Published: March 2022

The micro-texture, grain size, morphology, size and distribution of the second phase in 6063 Al alloys significantly influence the comprehensive mechanical properties of alloys. By adding Sr to the 6063 Al alloys, this study performed a comparison of the effect exerted by micro-texture and grain refinement and explored the existence of Sr and its influence on the second phase. Inaddition, the influence mechanism for mechanical properties of the Sr-added alloys was also investigated. The results show that the phase structure of 6063 Al alloys is changed after adding Sr The Al2Si2Sr intermetallic compound is formed, and numerous substructures are developed during dynamic recovery and recrystallization. Moreover, after adding Sr element, the grain size of 6063 Al alloys is reduced from 33.45 μm to 24.04 μm. Small-angle grain boundaries increase, while large-angle grain boundaries decrease. Sr element changes the micro-texture of 6063 Al alloys significantly when Cube{100}〈001〉, Goss{110}〈001〉 and S {123}〈634〉 become Cube{100}〈001〉. The tensile strength, yield strength and Brinell hardness of 6063 Al alloys increase by 59.67%, 69.36% and 36.63%, respectively. Taken together, the Sr element strengthens the mechanical properties of 6063 Al alloys through fine-grained strengthening.
Thermal and mechanical analyses of dry clutch disk made of functionally graded aluminum matrix composite
Authors: Ali Ibrahim A , Asiri Saeed
Published: March 2022

This research work presents an innovative utility of Functionally Graded Aluminum Matrix Composite with Silicon Carbide as a friction material in clutches’ plate since it has an acceptable friction coefficient and a high wear resistance which may lead to longer working life. Functionally Graded Aluminum Matrix Composite’s properties are calculated using rule-of-mixture and power law, and simulated as layered geometry. Clutches designed based on the standard size and working conditions of clutches in mid-size and heavy automobiles. Functionally Graded Aluminum Matrix Composite’s behavior is examined considering statics, dynamics, thermal and wear. Analyses are done using Finite Element method, by ANSYS with boundary conditions that represent the actual working conditions of clutch in automobiles. The developed finite element model is validated by comparing it to literature and has achieved good agreement. Results are discussed by comparing functionally graded aluminum matrix composite’s clutch performance to aluminum matrix composite with 20% of silicon carbide clutch and e-glass clutch performances. FGAMC clutch showed excellent behavior considering static analysis where deformations were the least among the three materials. The thermal and free vibrational performance of the FGAMC were not the best but with very small differences compared to aluminum matrix composite and e-glass clutches. Very unwanted performance of FGAMC is recognized in forced vibration analysis, as it has very high stresses, strain and deformation compared to the other two materials. Structural transient behavior of FGAMC is acceptable as it has the lowest deformations and strains from the highest stresses but in small area of the contact surface of the clutch. Volume loss in FGAMC due wear is less compared to traditional aluminum matrix composite by more than 4 times.
A multitask deep representation for Gleason score classification to support grade annotations
Authors: León Fabian , Martínez Fabio
Published: March 2022

The Gleason grade system is the main standard to quantify the aggressiveness and progression of prostate cancer. Currently, exists a high disagreement among experts in the diagnosis and stratification of this disease. Deep learning models have emerged as an alternative to classify and support experts automatically. However, these models are limited to learn a rigid stratification rule that can be biased during training to a specific observer. Therefore, this work introduces an embedding representation that integrates an auxiliary task learning to deal with the high inter and intra appearance of the Gleason system. The proposed strategy implements as a main task a triplet loss scheme that builds a feature embedding space with respect to batches of positive and negative histological training patches. As an auxiliary task is added a cross-entropy that helps with inter-class variability of samples while adding robust representations to the main task. The proposed approach shows promising results achieving an average accuracy of 66% and 64%, for two experts without statistical difference. Additionally, reach and average accuracy of 73% in patches where both pathologists are agree, showing the robustness patterns learning from the approach.
Application of unlaminated EBT3 film dosimeter for quantification of dose enhancement using silver nanoparticle-embedded alginate film
Authors: Kakade Nitin R , Das Abhishek , Kumar Rajesh , Sharma S D , Chadha Ridhima , Maiti Nandita , Kapoor Sudhir
Published: March 2022

Purpose. The paper describes the application of unlaminated Gafchromic EBT3 film dosimeter for quantification of dose enhancement using locally synthesized silver nanoparticle-embedded alginate film (AgNPs-Alg film) for nanoparticles-aided radiotherapy. Materials and Methods. AgNPs-Alg film was synthesized and characterized using standard techniques. The unlaminated Gafchromic EBT3 film was specially customized for dosimetric measurement. The dose enhancements due to AgNPs-Alg film was experimentally determined for ISO wide spectrum x-rays series (average energy ranging from 57–137 keV) and 6 and 10 MV x-rays using laminated and unlaminated Gafchromic EBT3 film. The radiation dose of 1 Gy was delivered to a combination of AgNPs-Alg films and EBT3 film. Results. Ultraviolet-Visible spectroscopy of silver nanoparticles shows a surface plasmon resonance peak at 400 nm. The average particle size of 13 ± 2 nm was measured using Atomic Force Microscopy. For unlaminated film, the dose enhancements of 29%, 23%, 14% and 2% was observed for ISO wide spectrum x-rays having average energy of 57, 79, 104 and 137 keV, respectively. The dose enhancement was negligible for 6 and 10 MV x-rays. In the case of laminated film, no significant dose enhancement was measured for all the x-ray energies. Conclusion. The unlaminated Gafchromic EBT3 film can be a suitable choice for the measurement of dose enhancement. Further, silver nanoparticles can be used during nanoparticle-aided radiotherapy when irradiated at low x-ray energy.
On local conservation of information content in Schwarzschild black holes
Authors: Kanyolo Godwill Mbiti , Masese Titus
Published: March 2022

The central equations in classical general relativity are the Einstein Field equations, which accurately describe not only the generation of pseudo-Riemannian curvature by matter and radiation manifesting as gravitational effects, but more importantly mass-energy dynamics, evolution and distribution on the space-time manifold. Herein, we introduce a geometric phase in general relativity corresponding to Schwarzschild black hole information content. This quantity appropriately satisfies a local conservation law subject to minimal coupling, with other desirable properties such as the quantization of the black hole horizon in units of Planck area. The local conservation law is imposed by field equations, which not only contain the trace of Einstein Field equations, but also a complex-valued function with properties analogous to the quantum-mechanical wave function. Such success attests to the utility of the proposed field equations in capturing key aspects of quantum gravity theories.
Unusual abundance of bloom forming Aulacoseira spp. diatom populations in an anthropogenically impacted stretch of lower part of the River Ganga
Authors: Kumar Chakresh , Ghosh Anwesha , Yash  , Bhadury Punyasloke
Published: March 2022

The River Ganga is reeling from pressures of rapid urbanization and resulting anthropogenic forcings. In this study, phytoplankton community assemblages were deduced from the Dakshineswar site located in the lower stretch of River Ganga to quantify and understand the health status of this river. Surface water samples were collected from six pre-defined stations of Dakshineswar spanning across monsoon and post-monsoon seasons of 2019 and 2020. Stations were categorized into point source and surface water based on proximity to municipal discharges. Measurement of in situ environmental parameters showed significant differences in values for dissolved oxygen, total dissolved solids, electrical conductivity and suspended particulate matter between the two seasons during the study period. In particular, concentrations of dissolved nitrate and silicate were found to be higher in point source stations compared to surface water stations. The concentration of Chlorophyll-a (Chl-a) was found to be higher in post-monsoon compared to monsoon seasons. Phytoplankton communities consisted of 23 diatom taxa and 14 green algal taxa and they showed distinct seasonal and spatial variations in the study site. Phytoplankton communities were dominated by diatom taxa namely Aulacoseira, Bacillaria, Coscinodiscus, and green algal taxa such as Ulothrix, Chlorella, and Scenedesmus. There was a dramatic increase in cell abundance of Aulacoseira spp. in post-monsoon seasons indicating a bloom-like scenario. Moreover, the rapid increase in cell abundance of Aulacoseira spp. also coincided with an increase in Chl-a and a sharp fall in the concentration of dissolved silicate. Some of the encountered phytoplankton taxa such as Tetraedron, Cosmarium, Nitzschia and Scenedesmus showed strong co-occurrence patterns indicating possible association at ecological scales. Four distinct clusters were formed in nMDS ordination plot based on the influences of environmental variables on encountered phytoplankton taxa. Network analysis revealed evidence of co-occurrence patterns between several diatoms and green algal taxa.
Many-body van der Waals interactions in wet MoS2 surfaces
Authors: Shao Xuecheng , Umerbekova Alina , Jiang Kaili , Pavanello Michele
Published: March 2022

Many-body dispersion (MBD), and generally many-body correlation effects, have emerged in recent years as key contributions to intermolecular interactions in condensed phases affecting nearly every field in the molecular sciences. Ab initio electronic structure methods are the golden standard of material science but unfortunately they are too computationally expensive for evaluating MBD in such complex systems as liquid–solid interfaces. In this work, we leverage subsystem time-dependent DFT’s rigorous decomposition of the system’s response function into subsystem contributions to evaluate the effect of many-body correlation effects (which include dispersion) for each water molecule in a model of wet MoS2 surface. The optical spectra and and to a lesser extent the effective molecular C
6 coefficients display a dependence on a handful of order parameters describing the liquid as well as the distance and orientation of the molecules with respect to the surface. Overall, we provide an unprecedented, granular analysis of many-body correlation effects for wet MoS2 which will be useful for developing more approximate models, such as force fields and other multi-scale methods for water–surface interactions.
Photovoltaics module reliability for the terawatt age
Authors: Jordan D C , Haegel Nancy , Barnes Teresa M
Published: March 2022

Photovoltaics (PV), or solar electricity generation, has become the cheapest form of energy in many locations worldwide and, combined with energy storage, has the potential to satisfy most of our electricity needs. PV has grown at an annual compounded growth rate of approximately 30% in the last three decades. Solar energy systems will continue their impressive growth in distributed energy, microgrids, and utility scale, as efforts are made for dependable electricity in an age with increasing extreme weather. However, within this remarkable success lies a new challenge. The growth curve, combined with rapid product innovation and scale up, means that the majority of PV systems are new, without the three years of performance data that have been required in the past to estimate product lifetime. PV reliability has to address this challenge. In this review we present a brief summary of PV reliability starting with brief historical synopsis, detailing some of the technological challenges and present a framework required for long lifetime.
Limitations and suggestions of electric transit charge scheduling
Authors: Zeng Ziling , Daniels David , Qu Xiaobo
Published: March 2022

A major factor hindering the popularization of electric buses (EBs) in the current automotive market is the high ownership cost of batteries and its significant upfront investment. For the daily maintenance of electric fleets, the amortized battery replacement cost is at least six times the charging cost. Thus, ensuring the healthy operation of the battery and prolonging the cycle life are some of the most concerned issues of the bus operators. In order to achieve the best operating mode, the operators are required to formulate an effective charging schedule with minimized battery wear. However, little quantitative formulation exists in prior literature to consider battery wear in bus charge scheduling. In this paper, a general formula is presented for battery wear cost consideration in charge scheduling based on the emerging literature. Then, the existing charge scheduling model is improved based on the proposed approach. A case study illustrates the significant difference in operating costs between charging plans developed with or without consideration of battery wear. The focus of this commentary is to present the crucial factors to improve the efficiency of EB operations and help make the charge scheduling models more realistic.
Modelling, analysis and optimization of design parameter of bump-type gas foil journal bearing
Authors: Mourya Vishal , Bhore Skylab P
Published: March 2022

The bump-type gas foil bearing (GFB) is widely used in various high-speed oil-free turbomachinery due to its extra features such as high-speed capability without any external oil lubricant. Under the high-speed condition, the performance characteristics of GFB are majorly dependent on its design parameter. Thus, this paper briefly analyzes and optimizes the design parameters of bump-type GFB to improve its performance characteristic. The numerical simulation of bump-type GFB is performed in ANSYS software. The effect of various design parameters such as foil thickness, bump half-length, bump pitch, and bump angle on the output responses are analyzed using a response surface methodology based CCD design matrix. Here, the output responses are structural stiffness and the equivalent stress in foil bearing. To optimize it, the multi-objective GRA technique is used. These results show that the foil thickness is the most influencing and the bump angle is the least influencing design parameter. The optimal value of foil thickness, bump angle, bump half-length and bump pitch are 0.14 mm, 63.75 deg., 1.55 mm and 4.6 mm respectively. At these optimal design parameters, the deviation between the predicted regression model and the numerical results are within 3.5%. Moreover, with these optimal design parameters, the structural stiffness of foil bearings increases by 68.4% and stress distribution reduces by 44.22% compared to the general configuration of foil bearings.
Highly efficient resonant length integrated optic photodetector
Authors: Sharma Vinod K
Published: March 2022

A novel integrated optic photodetector with resonant length is theoretically proposed for detection at 1.55 μm. The structure consists of substrate/waveguide/phase matching layer (low index)/absorbing semiconductor layer/air. A general mode expansion and propagation technique based on supermode analysis is used to study the propagation of modes in the device structure. Periodic coupling between the guided mode and the mode supported by the absorbing layer takes place and varies with the length of the detector. We show that resonant coupling between the two super modes takes place for the optimized thickness of the phase matching layer and the absorbing layer at a particular length of the detector which is considered the detector length. An attenuation exceeding 170 dB could be obtained for a detector length of 13 μm for TM polarization. The proposed photodetector exhibits a 3dB bandwidth exceeding 300 GHz and has capacitance of only 0.01 pF. Similar results have been obtained for TE polarization with different thickness of the absorbing layer.
Complex systems for the most vulnerable
Authors: Omodei Elisa , Garcia-Herranz Manuel , Paolotti Daniela , Tizzoni Michele
Published: March 2022

In a rapidly changing world, facing an increasing number of socioeconomic, health and environmental crises, complexity science can help us to assess and quantify vulnerabilities, and to monitor and achieve the UN sustainable development goals. In this perspective, we provide three exemplary use cases where complexity science has shown its potential: poverty and socioeconomic inequalities, collective action for representative democracy, and computational epidemic modeling. We then review the challenges and limitations related to data, methods, capacity building, and, as a result, research operationalization. We finally conclude with some suggestions for future directions, urging the complex systems community to engage in applied and methodological research addressing the needs of the most vulnerable.
The need for agricultural productive uses in the national electrification plan of sub-Saharan African countries—a call to action for Ethiopia
Authors: Van-Hein Sackey Charles , Nock Destenie
Published: March 2022

Access to electricity is a crucial aspect of sub-Saharan Africa’s path towards development. In light of the potential for electricity access to improve quality of life, the United Nations aims to achieve universal access to ‘clean, reliable, affordable and modern’ electricity as Goal 7 of its Sustainable Development Goals (SDG 7). As such, governments of sub-Saharan African (SSA) countries, such as Ethiopia, have developed national electrification plans to outline their pathway to universal access to electricity. In this paper, we identify why it is essential for the national electrification plans of SSA countries to prioritize electricity access for productive uses in its agricultural sector, using Ethiopia as a case study. Reviewing existing literature and using the authors’ research, we point out that there is 3.04 terawatt-hours of latent demand for small-scale pressurized cereal-crop irrigation alone in Ethiopia. Supplying this electricity demand for small-scale irrigation could lead to a reduction in the levelized cost of electricity of up to 95%. We conclude our paper by recommending the creation of a cross-sector national productive use commission that would be tasked with collecting and sharing relevant data from each sector and collaboratively creating a national productive use program that would ensure that Ethiopia reaps the full benefits and potential for wealth creation from access to electricity.
Exploring the impacts of tourism and weather on water consumption at different spatiotemporal scales: evidence from a coastal area on the Adriatic Sea (northern Italy)
Authors: Mazzoni Filippo , Marsili Valentina , Alvisi Stefano , Franchini Marco
Published: March 2022

The growth of tourism in the last decades has left behind a significant footprint on water resources, which is particularly evident in the regions affected by water scarcity or consistent seasonal population fluctuations. However, only limited efforts were spent in evaluating the effects of tourism on water consumption with regard to specific non-residential users such as bathing facilities. The current work aimed at providing an insight into the effects of seaside tourism on water consumption in a case study coastal area in northern Italy that is typically subjected to high tourist fluctuations throughout the year. Analyses were carried out at multiple spatiotemporal scales—from urban to user level, and from yearly to daily scale—by exploiting hourly flow data collected at the inflow points of the area and at some touristic users (i.e. nine bathing facilities and a holiday home). In addition, the impact of weather—temperature and rainfall—on water use was explored. The study revealed consistent inflow fluctuations in the area concerned based on tourism (with a ratio between the maximum and minimum monthly average inflow of about 15.7) and demonstrated that the touristic component of water inflow was considerably higher than the residential component at the height of tourist season (i.e., 176 L/s against 42 L/s). Moreover, significant variations in the water inflow due to tourism and weather were also observed on a daily scale, along with considerable water consumption fluctuations in bathing facilities.
Assessment of chimeric antigen receptor T cytotoxicity by droplet microfluidics in vitro
Authors: Wong Kuan Un , Shi Jingxuan , Li Peng , Wang Haitao , Jia Yanwei , Deng Chuxia , Jiang Lianmei , Wong Ada Hang-Heng
Published: March 2022

Chimeric antigen receptor T (CAR-T) cells are cytotoxic T cells engineered to specifically kill cancer cells expressing specific target receptor(s). Prior CAR-T efficacy tests include CAR expression analysis by qPCR or ELISA, in vitro measurement of interferon-γ (IFNγ) or interleukin-2 (IL-2), and xenograft models. However, the in vitro measurements did not reflect CAR-T cytotoxicity, whereas xenograft models are low throughput and costly. Here, we presented a robust in vitro droplet microfluidic assay for CAR-T cytotoxicity assessment. This method not only enabled assessment of CAR-T cytotoxic activity under different fluid viscosity conditions, but also facilitated measurement of CAR-T expansion and dissection of mechanism of action via phenotype analysis in vitro. Furthermore, our data suggested that label-free cytotoxicity analysis is feasible by acquiring data before and after treatment. Hence, this study presented a novel in vitro method for assessment of cellular cytotoxicity that could potentially be applied to any cytotoxicity experiment with varying solvent composition.
Identifying preeclampsia-associated genes using a control theory method
Authors: Li Xiaomei , Liu Lin , Whitehead Clare , Li Jiuyong , Thierry Benjamin , Le Thuc D , Winter Marnie
Published: March 2022

Preeclampsia is a pregnancy-specific disease that can have serious effects on the health of both mothers and their offspring. Predicting which women will develop preeclampsia in early pregnancy with high accuracy will allow for improved management. The clinical symptoms of preeclampsia are well recognized, however, the precise molecular mechanisms leading to the disorder are poorly understood. This is compounded by the heterogeneous nature of preeclampsia onset, timing and severity. Indeed a multitude of poorly defined causes including genetic components implicates etiologic factors, such as immune maladaptation, placental ischemia and increased oxidative stress. Large datasets generated by microarray and next-generation sequencing have enabled the comprehensive study of preeclampsia at the molecular level. However, computational approaches to simultaneously analyze the preeclampsia transcriptomic and network data and identify clinically relevant information are currently limited. In this paper, we proposed a control theory method to identify potential preeclampsia-associated genes based on both transcriptomic and network data. First, we built a preeclampsia gene regulatory network and analyzed its controllability. We then defined two types of critical preeclampsia-associated genes that play important roles in the constructed preeclampsia-specific network. Benchmarking against differential expression, betweenness centrality and hub analysis we demonstrated that the proposed method may offer novel insights compared with other standard approaches. Next, we investigated subtype specific genes for early and late onset preeclampsia. This control theory approach could contribute to a further understanding of the molecular mechanisms contributing to preeclampsia.
kc-hits: a tool to aid in the evaluation and classification of chemical carcinogens
Authors: Reisfeld Brad , de Conti Aline , El Ghissassi Fatiha , Benbrahim-Tallaa Lamia , Gwinn William , Grosse Yann , Schubauer-Berigan Mary
Published: March 2022

Motivation

The evaluation of chemicals for their carcinogenic hazard requires the analysis of a wide range of data and the characterization of these results relative to the key characteristics of carcinogens. The workflow used historically requires many manual steps that are labor-intensive and can introduce errors, bias and inconsistencies.

Results

The automation of parts of the evaluation workflow using the kc-hits software has led to significant improvements in process efficiency, as well as more consistent and comprehensive results.

Availability and implementation

https://gitlab.com/i1650/kc-hits.git.

Supplementary information

Supplementary data are available at Bioinformatics online.
An extended amygdala circuit at the core of long-term post-sepsis psychiatric disorders
Authors: Desmedt Aline
Published: March 2022

This scientific commentary refers to ‘Silencing of amygdala circuits during sepsis prevents the development of anxiety-related behaviours’, by Bourhy et al. (https://doi.org/10.1093/brain/awab475).
Magnetization transfer ratio for assessing remyelination after transcranial ultrasound stimulation in the lysolecithin rat model of multiple sclerosis
Authors: Huang Li-Hsin , Pan Zih-Yun , Pan Yi-Ju , Yang Feng-Yi
Published: March 2022

It has been shown that transcranial ultrasound stimulation (TUS) is capable of attenuating myelin loss and providing neuroprotection in animal models of brain disorders. In this study, we investigated the ability of TUS to promote remyelination in the lysolecithin (LPC)-induced local demyelination in the hippocampus. Demyelination was induced by the micro-injection of 1.5 μL LPC (1%) into the rat hippocampus and the treated group received daily TUS for 5 or 12 days. Magnetic resonance imaging techniques, including magnetization transfer ratio (MTR) and T2-weighted imaging, were used to longitudinally characterize the demyelination model. Furthermore, the therapeutic effects of TUS on LPC-induced demyelination were assessed by Luxol fast blue (LFB) staining. Our data revealed that reductions in MTR values observed during demyelination recover almost completely upon remyelination. The MTR values in demyelinated lesions were significantly higher in TUS-treated rats than in the LPC-only group after undergoing TUS. Form histological observation, TUS significantly reduced the size of demyelinated lesion 7 days after LPC administration. This study demonstrated that MTR was a sensitive and reproducible quantitative marker to assess remyelination process in vivo during TUS treatment. These findings might open new promising treatment strategies for demyelinating diseases such as multiple sclerosis.
Polydopamine Coating Doped with Graphene Oxide Enhances Enantioseparation of Capillary Column
Authors: Zhao Shiyuan , Miao Panden , Zhang Jian , Gan Jie , Du Yingxiang , Chen Cheng , Sun Xiaodong , Feng Zijie , Ma Xiaofei , Ma Mingxuan , Xi Ying , Ding Wen
Published: March 2022

How to improve the enantiomer separation efficiency of drugs is a hot topic. In this paper, polydopamine (PDA) coating doped with graphene oxide (GO) by physical adsorption was used to modify the capillary column to enhance the enantioseparation efficiency of the drugs. In the capillary electrochromatography (CEC) system, the novel capillary column with carboxymethyl-β-cyclodextrin (CM-β-CD) as a chiral selector has completed the enantioseparation of four basic drugs (propranolol, metoprolol, amlodipine and chlorpheniramine). The optimum separation conditions were obtained by optimizing the pH of the buffer, the concentration of organic modifier, the concentration of the chiral selector and the voltage, and the resolution and peak shape were significantly improved compared with uncoated bare-fused column. The stability and reproducibility of the new capillary column were satisfactory and the relative standard deviation of intra-day and inter-day was <3.2%, and of column-to-column was <4.8%. The rich functional groups of GO are key factors to improve the enantioseparation efficiency, which also indicates that nanomaterials with easy modification of functional groups and large specific surface area are excellent resources for capillary modification applications.
Use of a smartphone electrocardiogram to diagnose arrhythmias during exercise in athletes: a case series
Authors: Jewson Jacob L , Orchard John W , Semsarian Chris , Fitzpatrick Jane , La Gerche Andre , Orchard Jessica J
Published: March 2022

Background

While athletes are generally very fit, intense exercise can increase the risk of atrial fibrillation. Moreover, other arrhythmias such as atrial flutter or supraventricular tachycardia can cause distressing, exercise-related symptoms. Given symptoms are infrequent and may occur during intense exertion, traditional monitoring devices are often impractical to use during exercise. Smartphone electrocardiograms (ECGs) such as the Alivecor Kardia device may be the portable and reliable tool required to help identify arrhythmias in this challenging population. This case series highlights the use of such devices in aiding the diagnosis of arrhythmias in the setting of exercise-related symptoms in athletes.

Case summary

The six cases in this series included one elite non-endurance athlete, two elite cricketers, one amateur middle-distance runner, and two semi-elite ultra-endurance runners, with an age range of 16–48 years. An accurate diagnosis of an arrhythmia was obtained in five cases (atrial fibrillation/flutter and supraventricular tachycardias) using the smartphone ECG, which helped guide definitive treatment. No arrhythmia was identified in the final case despite using the device during multiple symptomatic events.

Discussion

The smartphone ECG was able to accurately detect arrhythmias and provide a diagnosis in cases where traditional monitoring had not. The utility of detecting no arrhythmia during symptoms in one case was also highlighted, providing the athlete with the confidence to continue exercising. This reassurance and confidence across all cases is perhaps the most valuable aspect of this device, where clinicians and athletes can be more certain of reaching a diagnosis and undertaking appropriate management.
Systematic review ofListeria monocytogenesfrom food and clinical samples in Chinese mainland from 2010 to 2019
Authors: Cheng Ying , Dong Qingli , Liu Yangtai , Liu Hong , Zhang Hongzhi , Wang Xiang
Published: March 2022

Listeria monocytogenes (L. monocytogenes), a foodborne pathogen, can cause human listeriosis. Listeriosis is a potentially fatal gastrointestinal illness, which is closely related to the spread of food to humans. We review the literature published during 2010–2019 to better understand the prevalence of L. monocytogenes in food products, incidence of human listeriosis, and their characteristics in Chinese mainland. We found the main sequence types (STs) strains from foods are similar globally, and the prevalence of L. monocytogenes from raw meat was the highest among all food products. The most common STs in food products and clinical cases were ST9 (serogroup I.2) strains and ST87 (serogroup II.2) strains, respectively. The ST87 strains being the most common STs of clinical cases might be related to the existence of Listeria pathogenicity island 4 gene and Chinese eating habits for ready-to-eat foods, among which the prevalence of ST87 strain was the highest in ready-to-eat foods. Therefore, more research should be conducted to explore the reasons for the L. monocytogenes isolates differences in food and clinical sources.
Whole-genome sequence and methylome profiling of the almond [Prunus dulcis (Mill.) D.A. Webb] cultivar ‘Nonpareil’
Authors: D’Amico-Willman Katherine M , Ouma Wilberforce Z , Meulia Tea , Sideli Gina M , Gradziel Thomas M , Fresnedo-Ramírez Jonathan
Published: March 2022

Almond [Prunus dulcis (Mill.) D.A. Webb] is an economically important, specialty nut crop grown almost exclusively in the United States. Breeding and improvement efforts worldwide have led to the development of key, productive cultivars, including ‘Nonpareil,’ which is the most widely grown almond cultivar. Thus far, genomic resources for this species have been limited, and a whole-genome assembly for ‘Nonpareil’ is not currently available despite its economic importance and use in almond breeding worldwide. We generated a 571X coverage genome sequence using Illumina, PacBio, and optical mapping technologies. Gene prediction revealed 49,321 putative genes using MinION Oxford nanopore and Illumina RNA sequencing, and genome annotation found that 68% of predicted models are associated with at least one biological function. Furthermore, epigenetic signatures of almond, namely DNA cytosine methylation, have been implicated in a variety of phenotypes including self-compatibility, bud dormancy, and development of noninfectious bud failure. In addition to the genome sequence and annotation, this report also provides the complete methylome of several almond tissues, including leaf, flower, endocarp, mesocarp, exocarp, and seed coat. Comparisons between methylation profiles in these tissues revealed differences in genome-wide weighted % methylation and chromosome-level methylation enrichment.
Mapping the sex determination region in the Salix F1 hybrid common parent population confirms a ZW system in six diverse species
Authors: Wilkerson Dustin G , Taskiran Bircan , Carlson Craig H , Smart Lawrence B
Published: March 2022

Within the genus Salix, there are approximately 350 species native primarily to the northern hemisphere and adapted to a wide range of habitats. This diversity can be exploited to mine novel alleles conferring variation important for production as a bioenergy crop, but also to identify evolutionarily important genes, such as those involved in sex determination. To leverage this diversity, we created a mapping population by crossing 6 Salix species (Salix viminalis, Salix suchowensis, Salix integra, Salix koriyanagi, Salix udensis, and Salix alberti) to common male and female Salix purpurea parents. Each family was genotyped via genotyping-by-sequencing and assessed for kinship and population structure as well as the construction of 16 backcross linkage maps to be used as a genetic resource for breeding and selection. Analyses of population structure resolved both the parents and F1 progeny to their respective phylogenetic section and indicated that the S. alberti parent was misidentified and was most likely S.suchowensis. Sex determining regions were identified on Salix chromosome 15 in the female-informative maps for seven of the eight families indicating that these species share a common female heterogametic ZW sex system. The eighth family, S. integra × S. purpurea, was entirely female and had a truncated chromosome 15. Beyond sex determination, the Salix F1 hybrid common parent population (Salix F1 HCP) introduced here will be useful in characterizing genetic factors underlying complex traits, aid in marker-assisted selection, and support genome assemblies for this promising bioenergy crop.
GNSS-corrected InSAR displacement time-series spanning the 2019 Ridgecrest, CA earthquakes
Authors: Guns Katherine , Xu Xiaohua , Bock Yehuda , Sandwell David
Published: March 2022

InSAR displacement time-series are emerging as a valuable product to study a number of Earth processes. One challenge to current time-series processing methods, however, is that when large earthquakes occur, they can leave sharp coseismic steps in the time-series. These discontinuities can cause current atmospheric correction and noise smoothing algorithms to break down, as these algorithms commonly assume that deformation is steady through time. Here, we aim to remedy this by exploring two methods for correcting earthquake offsets in InSAR time-series: a simple difference offset estimate (SDOE) process and a multiparameter offset estimate (MPOE) parametric time-series inversion technique. We apply these methods to a 2-yr time-series of Sentinel-1 interferograms spanning the 2019 Ridgecrest, CA earthquake sequence. Descending track results indicate that the SDOE method precisely corrects for only 20 per cent of the coseismic offsets at 62 study locations included in our scene and only partially corrects or sometimes overcorrects for the rest of our study sites. On the other hand, the MPOE estimate method successfully corrects the coseismic offset for the majority of sites in our analysis. This MPOE method allows us to produce InSAR time-series and data-derived estimates of deformation during each phase of the earthquake cycle. In order to better isolate and estimate the signal of post-seismic lithospheric deformation in the InSAR time-series, we apply a GNSS-based correction to our interferograms. This correction ties the interferograms to median-filtered weekly GNSS displacements and removes additional atmospheric artefacts. We present InSAR-based estimates of post-seismic deformation for the area around the Ridgecrest rupture, as well as a 2-yr coseismic-corrected, GNSS-corrected InSAR time-series data set. This GNSS-corrected InSAR time-series will enable future modelling of post-seismic processes such as afterslip in the near field of the rupture, poroelastic deformation at intermediate distances and viscoelastic deformation at longer timescales in the far field.