bluuebunny/crossref_metadata_2025 huggingface dataset:
Unmasking the immune microecology of ductal carcinoma in situ with deep learning
Authors: Narayanan Priya Lakshmi , Raza Shan E. Ahmed , Hall Allison H. , Marks Jeffrey R. , King Lorraine , West Robert B. , Hernandez Lucia , Guppy Naomi , Dowsett Mitch , Gusterson Barry , Maley Carlo , Hwang E. Shelley , Yuan Yinyin
Published: March 2021

Despite increasing evidence supporting the clinical relevance of tumour infiltrating lymphocytes (TILs) in invasive breast cancer, TIL spatial variability within ductal carcinoma in situ (DCIS) samples and its association with progression are not well understood. To characterise tissue spatial architecture and the microenvironment of DCIS, we designed and validated a new deep learning pipeline, UNMaSk. Following automated detection of individual DCIS ducts using a new method IM-Net, we applied spatial tessellation to create virtual boundaries for each duct. To study local TIL infiltration for each duct, DRDIN was developed for mapping the distribution of TILs. In a dataset comprising grade 2–3 pure DCIS and DCIS adjacent to invasive cancer (adjacent DCIS), we found that pure DCIS cases had more TILs compared to adjacent DCIS. However, the colocalisation of TILs with DCIS ducts was significantly lower in pure DCIS compared to adjacent DCIS, which may suggest a more inflamed tissue ecology local to DCIS ducts in adjacent DCIS cases. Our study demonstrates that technological developments in deep convolutional neural networks and digital pathology can enable an automated morphological and microenvironmental analysis of DCIS, providing a new way to study differential immune ecology for individual ducts and identify new markers of progression.
Automation of diffusion database development in multicomponent alloys from large number of experimental composition profiles
Authors: Zhong Jing , Chen Li , Zhang Lijun
Published: March 2021

Nowadays, the urgency for the high-quality interdiffusion coefficients and atomic mobilities with quantified uncertainties in multicomponent/multi-principal element alloys, which are indispensable for comprehensive understanding of the diffusion-controlled processes during their preparation and service periods, is merging as a momentous trending in materials community. However, the traditional exploration approach for database development relies heavily on expertize and labor-intensive computation, and is thus intractable for complex systems. In this paper, we augmented the HitDIC (high-throughput determination of interdiffusion coefficients,https://hitdic.com) software into a computation framework for automatic and efficient extraction of interdiffusion coefficients and development of atomic mobility database directly from large number of experimental composition profiles. Such an efficient framework proceeds in a workflow of automation concerning techniques of data-cleaning, feature engineering, regularization, uncertainty quantification and parallelism, for sake of agilely establishing high-quality kinetic database for target alloy. Demonstration of the developed infrastructures was finally conducted in fcc CoCrFeMnNi high-entropy alloys with a dataset of 170 diffusion couples and 34,000 composition points for verifying their reliability and efficiency. Thorough investigation over the obtained kinetic descriptions indicated that the sluggish diffusion is merely unilateral interpretation over specific composition and temperature ranges affiliated to limited dataset. It is inferred that data-mining over large number of experimental data with the combinatorial infrastructures are superior to reveal extremely complex composition- and temperature-dependent thermal–physical properties.
Combination of histochemical analyses and micro-MRI reveals regional changes of the murine cervix in preparation for labor
Authors: Chatterjee Antara , Saghian Rojan , Dorogin Anna , Cahill Lindsay S. , Sled John G. , Lye Stephen , Shynlova Oksana
Published: March 2021

The cervix is responsible for maintaining pregnancy, and its timely remodeling is essential for the proper delivery of a baby. Cervical insufficiency, or “weakness”, may lead to preterm birth, which causes infant morbidities and mortalities worldwide. We used a mouse model of pregnancy and term labor, to examine the cervical structure by histology (Masson Trichome and Picrosirius Red staining), immunohistochemistry (Hyaluronic Acid Binding Protein/HABP), and ex-vivo MRI (T2-weighted and diffusion tensor imaging), focusing on two regions of the cervix (i.e., endocervix and ectocervix). Our results show that mouse endocervix has a higher proportion of smooth muscle cells and collagen fibers per area, with more compact tissue structure, than the ectocervix. With advanced gestation, endocervical changes, indicative of impending delivery, are manifested in fewer smooth muscle cells, expansion of the extracellular space, and lower presence of collagen fibers. MRI detected three distinctive zones in pregnant mouse endocervix: (1) inner collagenous layer, (2) middle circular muscular layer, and (3) outer longitudinal muscular layer. Diffusion MRI images detected changes in tissue organization as gestation progressed suggesting the potential application of this technique to non-invasively monitor cervical changes that precede the onset of labor in women at risk for preterm delivery.
Examining modifications of execution strategies during a continuous task
Authors: Cohen Erez James , Wei Kunlin , Minciacchi Diego
Published: March 2021

How strategies are formulated during a performance is an important aspect of motor control. Knowledge of the strategy employed in a task may help subjects achieve better performances, as it would help to evidence other possible strategies that could be used as well as help perfect a certain strategy. We sought to investigate how much of a performance is conditioned by the initial state and whether behavior throughout the performance is modified within a short timescale. In other words, we focus on the process of execution and not on the outcome. To this scope we used a repeated continuous circle tracing task. Performances were decomposed into different components (i.e., execution variables) whose combination is able to numerically determine movement outcome. By identifying execution variables of speed and duration, we created an execution space and a solution manifold (i.e., combinations of execution variables yielding zero discrepancy from the desired outcome) and divided the subjects according to their initial performance in that space into speed preference, duration preference, and no-preference groups. We demonstrated that specific strategies may be identified in a continuous task, and strategies remain relatively stable throughout the performance. Moreover, as performances remained stable, the initial location in the execution space can be used to determine the subject’s strategy. Finally, contrary to other studies, we demonstrated that, in a continuous task, performances were associated with reduced exploration of the execution space.
Integral equation theory for mixtures of spherical and patchy colloids. 2. Numerical results
Authors: Kalyuzhnyi Yurij V. , Nezbeda Ivo , Cummings Peter T.
Published: March 2021

Thermodynamic properties and structure of binary mixtures of patchy and spherical colloids are studied using a recently developed theory [Y. V. Kalyuzhnyi, et al., Soft Matter, 2020, 16, 3456].
Electron transfer pathways in photoexcited lanthanide(iii) complexes of picolinate ligands
Authors: Kovacs Daniel , Kocsi Daniel , Wells Jordann A. L. , Kiraev Salauat R. , Borbas K. Eszter
Published: March 2021

A series of luminescent lanthanide(iii) complexes consisting of 1,4,7-triazacyclononane-1,4-picolinate frameworks and three secondary amidelinked carbostyril antennae were synthesised and characterised.
Palladium(0) complexes of diferrocenylmercury diphosphines: synthesis, X-ray structure analyses, catalytic isomerization, and C–Cl bond activation
Authors: Tagne Kuate Alain C. , Lalancette Roger. A. , Bockfeld Dirk , Tamm Matthias , Jäkle Frieder
Published: March 2021

In trigonal LPd0(dba) complexes with diastereomeric diferrocenylmercury diphosphine ligands the Pd environment and Hg⋯Pd separation are starkly different. The rates of Pd0complex formation and their CH2Cl2oxidative addition vary significantly.
Correction: Rapid synthesis of internal peptidyl α-ketoamides by on resin oxidation for the construction of rhomboid protease inhibitors
Authors: Van Kersavond Tim , Konopatzki Raphael , van der Plassche Merel A. T. , Yang Jian , Verhelst Steven H. L.
Published: March 2021

Correction for ‘Rapid synthesis of internal peptidyl α-ketoamides by on resin oxidation for the construction of rhomboid protease inhibitors’ by Tim Van Kersavond et al., RSC Adv., 2021, 11, 4196–4199, DOI: 10.1039/D0RA10614C.
Reliability of Perceptual Judgments of Phonetic Accuracy and Hypernasality Among Speech-Language Pathologists for Children With Dysarthria
Authors: Allison Kristen M. , Russell Mackenzie , Hustad Katherine C.
Published: March 2021

Purpose

The objectives of this study were to: (a) compare interrater reliability of practicing speech-language pathologists' (SLPs) perceptual judgments of phonetic accuracy and hypernasality between children with dysarthria and those with typical development, and (b) to identify speech factors that influence reliability of these perceptual judgments for children with dysarthria.

Method

Ten SLPs provided ratings of speech samples from twenty 5-year-old children with dysarthria and twenty 5-year-old children with typical development on two tasks via a web-based platform: a hypernasality judgment task and a phonetic accuracy judgment task. Interrater reliability of SLPs' ratings on both tasks was compared between children with dysarthria and children with typical development. For children with dysarthria, four acoustic speech measures, intelligibility, and a measure of phonetic accuracy (percent stops correct) were examined as predictors of reliability of SLPs' perceptual judgments.

Results

Reliability of SLPs' phonetic accuracy judgments and hypernasality ratings was significantly lower for children with dysarthria than for children with typical development. Among children with dysarthria, interrater reliability of perceptual judgments ranged from strong to weak. Percent stops correct was the strongest predictor of interrater reliability for both phonetic accuracy judgments and hypernasality ratings.

Conclusions

Reliability of perceptual phonetic accuracy judgments and hypernasality ratings among practicing SLPs for children with dysarthria is reduced compared to ratings for children with typical development. Findings underscore the need for more reliable methods to assess phonetic accuracy and hypernasality for children with dysarthria.
A Preliminary Investigation of Attention-Deficit/Hyperactivity Disorder Characteristics in Adults Who Stutter
Authors: Tichenor Seth E. , Johnson Chelsea A. , Yaruss J. Scott
Published: March 2021

Purpose

Recent studies have shown that many children who stutter may have elevated characteristics of attention-deficit/hyperactivity disorder (ADHD). Although childhood ADHD commonly persists into adulthood, it is unclear how many adults who stutter experience aspects of ADHD (e.g., inattention or hyperactivity/impulsivity). This study sought to increase understanding of how ADHD characteristics might affect individuals who stutter by evaluating (a) whether elevated ADHD characteristics are common in adults who stutter, (b) whether elevated ADHD characteristics in adults who stutter were significantly associated with greater adverse impact related to stuttering, and (c) whether individual differences in Repetitive Negative Thinking (RNT) and Effortful Control influenced this relationship.

Method

Two hundred fifty-four adults who stutter completed the Adult ADHD Self-Report Scale, the Perseverative Thinking Questionnaire, the Adult Temperament Questionnaire short form, and the Overall Assessment of the Speaker's Experience of Stuttering. Data were analyzed via multiple linear regression to determine whether the number of inattention or hyperactivity/impulsivity characteristics was significantly associated with RNT, Effortful Control, or Adverse Impact related to stuttering.

Results

Almost one quarter of participants (23.2%; 60/254) self-reported experiencing six or more inattention characteristics, while fewer participants (8.3%; 21/254) self-reported experiencing six or more hyperactivity/impulsivity characteristics. Participants with lower Effortful Control and higher levels of both RNT and Adverse Impact were significantly more likely to self-report experiencing more inattention characteristics.

Discussion

Many adults who stutter may exhibit previously unaccounted for characteristics of ADHD, especially inattention. Results highlight the value of continued research on the intersectionality of stuttering, ADHD, and attention, and the importance of individualizing therapy to the needs of each unique person who stutters.
Multiscale, multiwavelength extraction of sources and filaments using separation of the structural components:getsf
Authors: Men’shchikov A.
Published: March 2021

High-quality astronomical images delivered by modern ground-based and space observatories demand adequate, reliable software for their analysis and accurate extraction of sources, filaments, and other structures, containing massive amounts of detailed information about the complex physical processes in space. The multiwavelength observations with highly variable angular resolutions across wavebands require extraction tools that preserve and use the invaluable high-resolution information. Complex fluctuating backgrounds and filamentary structures appear differently on various scales, calling for multiscale approaches for complete and reliable extraction of sources and filaments. The availability of many extraction tools with varying qualities highlights the need to use standard model benchmarks for choosing the most reliable and accurate method for astrophysical research. This paper presentsgetsf, a new method for extracting sources and filaments in astronomical images using separation of their structural components, designed to handle multiwavelength sets of images and very complex filamentary backgrounds. The method spatially decomposes the original images and separates the structural components of sources and filaments from each other and from their backgrounds, flattening their resulting images. It spatially decomposes the flattened components, combines them over wavelengths, detects the positions of sources and skeletons of filaments, and measures the detected sources and filaments, creating the output catalogs and images. The fully automated method has a single user-defined parameter (per image), the maximum size of the structures of interest to be extracted, that must be specified by users. This paper presents a realistic multiwavelength set of simulated benchmark images that can serve as the standard benchmark problem to evaluate qualities of source- and filament-extraction methods. This paper describeshires, an improved algorithm for the derivation of high-resolution surface densities from multiwavelength far-infraredHerschelimages. The algorithm allows creating the surface densities with angular resolutions that reach 5.6″ when the 70 μm image is used. If the shortest-wavelength image is too noisy or cannot be used for other reasons, slightly lower resolutions of 6.8−11.3″ are available from the 100 or 160 μm images. These high resolutions are useful for detailed studies of the structural diversity in molecular clouds. The codesgetsfandhiresare illustrated by their applications to a variety of images obtained with ground-based and space telescopes from the X-ray domain to the millimeter wavelengths.
Platelet-rich plasma as an effective biological therapy in early-stage knee osteoarthritis: One year follow up
Authors: Rai Deepak , Singh Jyotsana , Somashekharappa Thimmappa , Singh Ajit
Published: March 2021

Objective: PRP is produced by centrifugation of whole blood containing highly concentrated platelets, associated growth factors, and other bioactive agents which has been shown to provide some symptomatic relief in early knee osteoarthritis (OA). The principal objective of our study was to evaluate the effectiveness and safety of standardized intra-articular injection of autologous PRP in early osteoarthritis knee. Methods: A total of 98 eligible symptomatic patients received two injections of standardized PRP 3 weeks apart. Clinical outcomes were evaluated using the VAS and Western Ontario and McMaster Universities Arthritis Index (WOMAC) questionnaire before treatment and at 6 weeks, 3 months, 6 months, and 1 year after treatment. Secondary objectives were safety (side effects), and the effect of PRP on the different grades of knee degeneration. Results: There was a statistically significant improvement in mean VAS and WOMAC scores at 6 weeks, 3 months, 6 months, and slight loss of improvement at 1 year follow-up. There was also a correlation between the degree of degeneration and improvement in the mean scores. The decrease in mean pain score is more in grades 1 and 2 (early OA) than in grade 3. The intraarticular injection is safe, with no major complications. Conclusion: PRP is a safe and effective biological regenerative therapy for early OA Knees. It provides a significant clinical improvement in patients with some loss of improvement with time. More studies will be needed to confirm our findings.
Rational limit cycles on generalized Bernouilli polynomial equations
Authors: Valls Clàudia
Published: March 2021

We determine the maximum number of rational limit cycles of the generalized Bernouilli polynomial equations a(x)dy/dx = A(x)yn + B(x)y, where a(x), A(x), and B(x) are real polynomials with a(x)A(x) ≢ 0, n ≥ 3. In particular, we show that when n = 3, there are equations with six rational limit cycles. We also show that the addressed problem can be reduced to know the number of polynomial solutions of a related polynomial equation of arbitrary degree. Then, we approach these equations by applying several tools; in particular, some developed to study extending Fermat problems for polynomial equations.
Self-adaptive enzyme-powered micromotors with switchable propulsion mechanism and motion directionality
Authors: Feng Youzeng , Yuan Yue , Wan Jieshuo , Yang Chenglin , Hao Xiaomeng , Gao Zhixue , Luo Ming , Guan Jianguo
Published: March 2021

Switchable chemotaxis is vital for motile microorganisms seeking benefits or to avoid harm. Inspired by nature, and for the first time, we demonstrate an artificial enzyme-powered micromotor that can autonomously regulate the propulsion mechanism, as well as motion directionality, by solely sensing the change of fuel concentration (Cf) in its surroundings. The as-designed micromotors have a pot-like microstructure with ureases immobilized on the inner surface. With the confined effect of the pot-like microstructure and unique features of the urease catalytic reaction, the molecular products are further reacted into ions, and their propulsion mechanism can be reversibly adjusted between ionic diffusiophoresis and microbubble recoils when Cf changes. Consequently, the as-developed micromotors under magnetic field are able to self-turn back if the local Cf differs greatly in their surroundings, indicating the achievement of positive and negative chemotaxis by sensing local Cf. Meanwhile, the micromotors also show highly enhanced migration speed by microbubble ejection, up to 60 μm/s, around 30 body lengths per second at physiological urea concentrations. Furthermore, they have an outer surface of mesoporous silica which is easily functionalized for applications such as stimuli-responsive delivery-associated therapies. This work will promote “smart” artificial micro/nanomotors for in vivo biomedical applications.
An experimental system to evaluate impact shear failure of rock discontinuities
Authors: Yao Wei , Wang Chonglang , Xia Kaiwen , Zhang Xin
Published: March 2021

Conventionally, the evaluation of shear failure of discontinuities in rocks and other geomaterials has been conducted under static shear loading. In such methods, the shear failure behaviors of rock discontinuities are significantly influenced by loading velocities. To evaluate the shear failure process under dynamic loading, in this paper, we propose a new experimental methodology by taking advantages of recently available high-speed optical and mechanical measurement techniques. The methodology utilizes the Hopkinson bar to apply impact loading, and the diagnostics include a dynamic stress wave acquisition system, a digital image correlation (DIC) system, and an acoustic emission (AE) monitoring system. To improve the accuracy of the DIC analysis, an advanced digital speckle pattern and an updated water transfer printing are used to obtain the optimized and consistent speckle pattern. A flexible piezoelectric film sensor is first introduced to acquire AE signals in order to locate AE events accurately. A dynamic impact shear experiment indicates that the normal stress has a significant effect on the peak shear stress of rock discontinuities and the peak shear stress itself is rate dependent. The displacement field along shear directions is quantified using the DIC method, and the initial AE source locations during the impact shear process are determined using the AE monitoring system. We thus conclude that the dynamic impact shear system can systematically characterize the dynamic impact shear process with quantitative details and can further be implemented to study other dynamic impact failure behaviors of rock discontinuities under in situ stresses.
The reaction of O+(4S) ions with H2, HD, and D2 at low temperatures: Experimental study of the isotope effect
Authors: Kovalenko A. , Roučka Š. , Tran T. D. , Rednyk S. , Plašil R. , Dohnal P. , Glosík J.
Published: March 2021

The reactions of the O+ ions in the 4S electronic ground state with D2 and HD were studied in a cryogenic 22-pole radio-frequency ion trap in the temperature range of 15 K–300 K. The obtained reaction rate coefficients for both reactions are, considering the experimental errors, nearly independent of temperature and close to the values of the corresponding Langevin collisional reaction rate coefficients. The obtained branching ratios for the production of OH+ and OD+ in the reaction of O+(4S) with HD do not change significantly with temperature and are consistent with the results obtained at higher collisional energies by other groups. Particular attention was given to ensure that the O+ ions in the trap are in the ground electronic state.
Lattice-Boltzmann modeling of a turbulent bluff-body stabilized flame
Authors: Tayyab M. , Zhao S. , Boivin P.
Published: March 2021

This Letter reports the first large eddy simulation of a turbulent flame using a lattice-Boltzmann model. To that end, simulation of a bluff-body stabilized propane–air flame is carried out, showing an agreement similar to those available in the literature. Computational costs are also reported, indicating that lattice-Boltzmann modeling of reactive flows is competitive, with around 1000cpuh required to simulate one residence time in the 1.5 m burner.
A comparison of two dynamic power cable configurations for a floating offshore wind turbine in shallow water
Authors: Zhao Shilun , Cheng Yongquan , Chen Pengfei , Nie Yan , Fan Ke
Published: March 2021

For the study of the double wave configuration for the dynamic power cable of a Floating Offshore Wind Turbine (FOWT) in shallow water, this paper presented a comparison of the hydrostatic and hydrodynamic performance between a lazy wave and a double wave configuration. The double wave shape’s parametric presentation was first developed based on an extension of a previous parametric lazy wave shape. An aero-hydro-servo-elastic integrated model fully coupling the FOWT and the dynamic power cable was then proposed in the SIMO/RIFLEX code for numerical simulation. Subsequently, the strain-cycle curve and the rain flow counting method were employed to estimate the copper conductor’s fatigue damage. The bending moment was proved to provide the major fatigue contribution. The results showed that the double wave offered superior performance than the lazy wave. The second arc of the double wave configuration was proved critical for suffering high curvature, tension, and fatigue damage. A lower position and less hogged wave arc were suggested for the determination of the double wave shape.
Role of bulk- and interface-defects in spectrum-dependent energy harvesting of CZTSSe-based indoor photovoltaic devices
Authors: Maria Eymana , Baten Md Zunaid
Published: March 2021

In this work, we theoretically investigate spectrum dependent energy harvesting of a thin-film indoor photovoltaic (PV) device, taking into account the role of defects. By numerically solving Poisson’s equation and the continuity equation under optical generation-recombination conditions, performance characteristics of a Cu2ZnSn(S,Se)4-based thin-film PV device have been evaluated under spectrally varying white light emitting diodes (LEDs). Without any loss of generality, the results of the experimentally validated theoretical model suggest that a thin-film PV device becomes significantly tolerant to both bulk and interface defects when a fraction of blue emission in the white LED spectra remains relatively low. For a white LED having cool white emission characteristics, the efficiency of a CZTSSe-based PV device can equal the efficiency of the CZTSSe solar cell, the experimentally reported champion, while having about two orders of magnitude higher interface defect density, as well as about twenty times higher bulk defect density. In addition, for all practical densities of both types of defects, the efficiency of the indoor PV device remains at least 20% higher than the efficiency obtained under AM1.5 solar irradiation. The underlying reasons behind such observations have been traced back to the wavelength dependent carrier generation recombination dynamics of the thin-film device stack. The results of this work in effect provide guidelines for designing low-cost yet energy-efficient indoor photovoltaic devices with defect-rich thin film material systems.
Caldeira–Leggett model vs ab initio potential: A vibrational spectroscopy test of water solvation
Authors: Rognoni Alessandro , Conte Riccardo , Ceotto Michele
Published: March 2021

We present a semiclassically approximate quantum treatment of solvation with the purpose of investigating the accuracy of the Caldeira–Leggett model. We do that by simulating the vibrational features of water solvation by means of two different approaches. One is entirely based on the adoption of an accurate ab initio potential to describe water clusters of increasing dimensionality. The other one consists of a model made of a central water molecule coupled to a high-dimensional Caldeira–Leggett harmonic bath. We demonstrate the role of quantum effects in the detection of water solvation and show that the computationally cheap approach based on the Caldeira–Leggett bath is only partially effective. The main conclusion of the study is that quantum methods associated with high-level potential energy surfaces are necessary to correctly study solvation features, while simplified models, even if attractive owing to their reduced computational cost, can provide some useful insights but are not able to come up with a comprehensive description of the solvation phenomenon.
A novel fluid–solid coupling model for the oil–water flow in the natural fractured reservoirs
Authors: Zhang Dongxu , Zhang Liehui , Tang Huiying , Yuan Shuwu , Wang Hui , Chen Shengnan (Nancy) , Zhao Yulong
Published: March 2021

The mutual coupling effect between the fluid flow and the in situ stress fields cannot be ignored during the development of natural fractured reservoirs (NFRs), such as in the waterflooding process. In this study, a discrete fracture model is proposed to simulate the rock deformation and two-phase flow behaviors of oil and water in the NFR. The numerical solution of the model is achieved via the finite-element method and control-volume finite-element method. The numerical simulator is verified using commercial software, and a perfect agreement is obtained. Finally, sensitivity analysis is conducted on the key parameters in the model, such as fracture parameters, matrix permeability, and injection intensity. Results show that the fluid–solid coupling effect gradually weakens with production time. The degree of the fluid–solid coupling on cumulative oil production becomes smaller as the permeability of the matrix increases. Fracture connectivity controls the velocity and direction of the water flood front. Water injection intensity directly affects the natural fracture opening deformation and well productivity. The research and the numerical results obtained in this paper can provide theoretical guidance for the optimal design of water flooding operations in NFR.
DNA assembles nano-objects
Authors: Gang Oleg
Published: March 2021

A programmable one-size-fits-all method builds lattices of nanoparticles, proteins, and enzymes.
Human DNA methylation signatures differentiate persistent from resolving MRSA bacteremia
Authors: Chang Yu-Ling , Rossetti Maura , Gjertson David W. , Rubbi Liudmilla , Thompson Michael , Montoya Dennis J. , Morselli Marco , Ruffin Felicia , Hoffmann Alexander , Pellegrini Matteo , Fowler Vance G. , Yeaman Michael R. , Reed Elaine F. ,   with the MRSA Systems Immunology Group, Ahn Richard , Bayer Arnold S. , Chan Liana C. , Chang Yu-Ling , Filler Scott G. , Fowler Vance G. , Gjertson David , Hoffmann Alexander , Medie Felix Mba , Mikkaichi Tsuyoshi , Mitchell Simon , Qin Yan , Reed Elaine F. , Rossetti Maura , Ruffin Felicia , Sharma-Kuinkel Batu K. , Sheu Katherine , Thaden Joshua , Waring Alan J. , Xiong Yan Q. , Zheng Ying , Yeaman Michael R.
Published: March 2021

Significance

Up to 30% of methicillin-resistant
Staphylococcus aureus
(MRSA) bloodstream infections fail to resolve despite appropriate therapy. Such infections are persistent and life threatening. Because persistent MRSA isolates are susceptible to antibiotics in vitro, unique interactions among the pathogen, patient, and antibiotic occur in the body that lead to persistent outcomes. To study host factors involved in persistence, we used state-of-the-art methods to explore how genes are modified by methylation in patients who experience persistent vs. resolving MRSA bacteremia. Findings established distinct methylation patterns in these patients, including differential methylation signatures associated with important immune system and related genes. These results may enable approaches to identify and treat patients prone to persistent infection to improve therapeutic outcomes and save lives.
Adaptive evolution of hybrid bacteria by horizontal gene transfer
Authors: Power Jeffrey J. , Pinheiro Fernanda , Pompei Simone , Kovacova Viera , Yüksel Melih , Rathmann Isabel , Förster Mona , Lässig Michael , Maier Berenike
Published: March 2021

Significance

In a parallel evolution experiment, we probe lateral gene transfer between two
Bacillus subtilis
lineages close to the species boundary. We show that laboratory evolution by horizontal gene transfer can rapidly generate hybrid organisms with broad genomic and functional alterations. By combining genomics, transcriptomics, fitness assays, and statistical modeling, we map the selective effects underlying gene transfer. We show that transfer takes place under genome-wide positive and negative selection, generating a net fitness increase in hybrids. The evolutionary dynamics efficiently navigates this fitness landscape, finding viable paths with increasing fraction of transferred genes.
Ozone pollution in the North China Plain spreading into the late-winter haze season
Authors: Li Ke , Jacob Daniel J. , Liao Hong , Qiu Yulu , Shen Lu , Zhai Shixian , Bates Kelvin H. , Sulprizio Melissa P. , Song Shaojie , Lu Xiao , Zhang Qiang , Zheng Bo , Zhang Yuli , Zhang Jinqiang , Lee Hyun Chul , Kuk Su Keun
Published: March 2021

Significance

The North China Plain experiences severe summer ozone pollution, but ozone during winter haze (particulate) pollution events has been very low. Here, we show that the abrupt decrease in nitrogen oxide (NO
x
) emissions following the COVID-19 lockdown in January 2020 drove fast ozone production during winter haze events to levels approaching the air quality standard. This fast ozone production was driven by formaldehyde originating from high emissions of volatile organic compounds (VOCs). The COVID-19 experience highlights a general 2013 to 2019 trend of rapidly increasing ozone pollution in winter–spring in China as NO
x
emissions have decreased. VOC emission controls would mitigate the spreading of ozone pollution into winter–spring with benefits for public health, crop production, and particulate pollution.
Host genetic control of natural killer cell diversity revealed in the Collaborative Cross
Authors: Dupont Magali S. J. , Guillemot Vincent , Campagne Pascal , Serafini Nicolas , Marie Solenne , Montagutelli Xavier , Di Santo James P. , Vosshenrich Christian A. J.
Published: March 2021

Significance

Our work reveals the breadth of NK cell immune variation present in theMus musculusspecies as represented by the highly diverse Collaborative Cross (CC) mouse resource. We identify unique CC strains that provide an opportunity to study NK cell differentiation and function, and we identify genomic loci driving the variation of relevant NK cell parameters including lung NK cell numbers, frequencies of CD94+NK cells, and expression levels of NKp46. Finally, our results reveal the similarities of NK cell immune variation between genetically highly diverse human and mouse populations, highlighting the potential of CC mice as a preclinical model for the development of immunotherapies targeting NK cells.
Lipid nanoparticle-mediated codelivery of Cas9 mRNA and single-guide RNA achieves liver-specific in vivo genome editing ofAngptl3
Authors: Qiu Min , Glass Zachary , Chen Jinjin , Haas Mary , Jin Xin , Zhao Xuewei , Rui Xuehui , Ye Zhongfeng , Li Yamin , Zhang Feng , Xu Qiaobing
Published: March 2021

Significance

Genome editing technologies enable the permanent repair of disease-causing genetic mutations. However, the application of this technology has been limited by the technical challenge of achieving safe, effective, and specific in vivo delivery of the CRISPR-Cas9 genome editing components. Here, we report the development of a newly identified lipid nanoparticle (LNP) for specific delivery of CRISPR-Cas9 mRNA to the liver. While LNPs have been FDA approved for delivery of siRNA to the liver, here we examine their application for genome editing. When compared head-to-head, our delivery platform significantly outperforms the FDA-approved LNP in the efficient delivery of Cas9 mRNA for knockdown of theAngptl3gene and subsequent regulation of hypercholesterolemia, while matching the safety and specificity of the approved platform.
Anomalous mechanics of Zn
2+
-modified fibrin networks
Authors: Xia Jing , Cai Li-Heng , Wu Huayin , MacKintosh Frederick C. , Weitz David A.
Published: March 2021

Significance

Fibrin forms a three-dimensional network in blood clots during hemostasis that must be strong enough to stop bleeding yet flexible enough to withstand pressure variations of arterial flow. During clotting, activated platelets release Zn
2+
whose effect on the structure and mechanics of fibrin gels is poorly understood. We show that Zn
2+
unexpectedly reduces fibrin gel stiffness even though it induces bundling that coarsens the network. This results from weak interactions between the fibrils that make up the bundle, leading to a loose coupling that results in a softer network. These results provide important insight into the impact of Zn
2+
on the behavior of blood clots and represent a different class of network that becomes weaker even with increasing bundle thickness.
N6-methyladenosine modification of HCV RNA genome regulates cap-independent IRES-mediated translation via YTHDC2 recognition
Authors: Kim Geon-Woo , Siddiqui Aleem
Published: March 2021

Significance

N6-methyladenosine (m
6
A) modification is an emerging topic of RNA biology, and its functional roles are being investigated. m
6
A modification occurs in RNAs cotranscriptionally and regulates RNA stability and translation. m
6
A methylation has been identified in RNA virus genomes and the RNA transcripts of DNA viruses. These m
6
A modifications regulate the viral life cycle in various aspects and pathogeneses associated with individual viral infections. Here, we demonstrated that m
6
A modification of the internal ribosome entry site (IRES) region of the hepatitis C virus (HCV) recruits YTHDC2, which in concert with the cellular La antigen supports the HCV IRES-mediated translation. Our study shows the functional roles of m
6
A modification and YTHDC2 in the IRES-mediated translation.
Spine dynamics of PSD-95-deficient neurons in the visual cortex link silent synapses to structural cortical plasticity
Authors: Yusifov Rashad , Tippmann Anja , Staiger Jochen F. , Schlüter Oliver M. , Löwel Siegrid
Published: March 2021

Significance

During critical periods, restricted time windows in early brain development, cortical neural circuits get refined in an experience-dependent manner. Postsynaptic density protein-95 (PSD-95)-dependent maturation of silent glutamatergic synapses onto principal neurons is required for the termination of the critical period for ocular dominance plasticity (ODP) in the primary visual cortex (V1) of mice. Using chronic in vivo two-photon imaging of dendritic spine dynamics in V1 of awake mice, here we show that adult PSD-95-deficient neurons display increased spine elimination after a brief monocular deprivation, a structural hallmark of juvenile ODP. Thus, adult PSD-95-deficient neurons display both functional and structural hallmarks of critical period plasticity so that PSD-95-dependent silent synapse maturation and stabilization is correlated with critical period closure.
Up-regulation of miR-34b/c by JNK and FOXO3 protects from liver fibrosis
Authors: Piccolo Pasquale , Ferriero Rosa , Barbato Anna , Attanasio Sergio , Monti Marcello , Perna Claudia , Borel Florie , Annunziata Patrizia , Carissimo Annamaria , De Cegli Rossella , Quagliata Luca , Terracciano Luigi M. , Housset Chantal , Teckman Jeffrey H. , Mueller Christian , Brunetti-Pierri Nicola
Published: March 2021

Significance

α1-Antitrypsin deficiency is one of the most common genetic diseases. Homozygous and heterozygous carriers of the Z allele of α1-antitrypsin are susceptible to developing liver fibrosis and cirrhosis. In mouse and human samples expressing the Z allele of α1-antitrypsin, we found both miR-34b and miR-34c are up-regulated by activation of FOXO3 upon JNK phosphorylation on Ser
574
. Deletion of miR-34b/c resulted in early development of liver fibrosis and increased signaling of the PDGF pathway, a target of miR-34b/c. JNK-activated FOXO3 and miR-34b/c up-regulation also occur in several mouse models of liver fibrosis. Fibrosis is a major health problem and unravelling its underlying pathogenic mechanisms has potential for the development of targeted therapeutic agents.
The linguistic landscape and materials development
Authors: Xie Yilan , Buckingham Louisa
Published: March 2021

Despite the wide acceptance of the contributions of linguistic landscape (LL) research to sociolinguistic
analyses, models of how the LL can be exploited to practise specific features of the language system have been lacking. In this
study we focus on Mandarin Chinese, an important community language, to document the development of LL-based materials to practise
language-specific elements of the linguistic system (such as understanding the hierarchical organisation of characters, decoding
characters, identifying tones, and distinguishing different writing systems), in addition to cultural elements. Beginning with
extensive local fieldwork to compile a dataset of Chinese-language signs, materials were developed using the content of signs
considered to be representative for this context. Employing a MALL (Mobile-Assisted Language Learning) approach, materials were
piloted with learners of Chinese. The results of this practical engagement are discussed, and we end with key recommendations for
educationalists concerning the use of the LL as a resource for language acquisition.
Simulation of charge transport in polypropylene-based nano-composites
Authors: Zheng Yuesheng , Huang Huifen , Zhong Xiaoyan , Serdyuk Yuriy V
Published: March 2021

Polypropylene (PP)-based polymers are environmentally friendly and degradable materials that make them attractive alternatives to polyethylene for the electrical insulation systems of power cables in the future. To enhance the insulation performance of PP and to impede leakage currents through the material, different admixtures are utilized. In this paper, the effect of nano-fillers on charge transport characteristics in PP composites under DC electric fields is investigated by using a bipolar charge transport model accounting for mobile and trapped electrons and holes as well as ionic species. The model was validated by comparing the numerical results with the experimental data. The dynamic distributions of space charge densities and electric field in PP with and without nano-fillers are analyzed and compared. The numerical results confirmed that 0.5 phr ZnO nano-fillers can significantly improve the electric field distribution in PP nanocomposites and suppress the bulk current by reducing the charge generation rate and mobilities of charge carriers, thus resulting in a decrease in the volume conductivity. The obtained results provide a theoretical background for tailoring PP-based composites for specific applications by controlling nano-fillers.
Smart Gate Using Android Applications
Authors: Muthmainnah binti Mohd Noor Nurul , Afiq Afifi bin Mohd Zafie Mohamad
Published: March 2021

This paper is about the designing and developing an automatic gate system by implementation Android applications. This is a new improvement to the conventional technique. This project is focused on the development of smart gate prototype in order to improve the current automatic gate that used among the residential houses. The smart gate was controlled by using Android application on a smartphone that connected via a wireless connection. The wireless module ESP8266 was used to set up a server. An Arduino microcontroller was used as an interface between the input and output. The input is the user’s selection from the Android application while the output is the motion of the gate that generated by a DC motor. When the wireless module receiving the incoming signal from the smartphone, the microcontroller will read the signal and trigger the pin to turn on or turn off the DC motor. The ultrasonic sensor was used to detect any intruder that passes through the gate and trigger the buzzer. The limitation of this project is focused on smart gate prototype made of acrylic glass with the base size of 48 cm x 20 cm and a DC motor was used to open or close the gate
Development of Soil Electrical Conductivity (EC) Sensing System in Paddy Field
Authors: Othaman N.N.C. , Isa M.N.Md , Hussin R. , Ismail R.C. , Naziri S.Z.Md , Murad S.A.Z. , Harun A. , Ahmad M.I.
Published: March 2021

The amount of fertilisers affects electrical conductivity (EC), and it is one of the major causes of the paddy yield decrease. The overuse of fertilisers can lead to environmental pollution and contamination. This study designed to develop soil electrical conductivity (EC) sensing system in the paddy field using the smart farming application. In this work, the study conducted in Kampung Ladang, Kuala Perlis, and the soil samples collected from a random location at two different depths from the paddy field. The EC value for the developed system was near the calibration solutions (12880µS and 150000µS) and directly proportional to the temperature. From the laboratory soil results, the EC values of the soils were higher with fertiliser. However, the EC values for 0-10cm soil depth were higher than 10-20cm soil depth. The soil EC is inversely proportional to the depth of soil and directly proportional to the amount of nutrients. It observed that the soil EC is linearly related to the amount of nutrients and temperature. The EC value decreases with the increase of soil depth displays a low amount of salts in the deep soil, while, increases with the increase of temperature indicates high current flow.
Face Recognition and Identification using Deep Learning Approach
Authors: Teoh KH , Ismail RC , Naziri SZM , Hussin R , Isa MNM , Basir MSSM
Published: March 2021

Human face is the significant characteristic to identify a person. Everyone has their own unique face even for twins. Thus, a face recognition and identification are required to distinguish each other. A face recognition system is the verification system to find a person’s identity through biometric method. Face recognition has become a popular method nowadays in many applications such as phone unlock system, criminal identification and even home security system. This system is more secure as it does not need any dependencies such as key and card but only facial image is needed. Generally, human recognition system involves 2 phases which are face detection and face identification. This paper describes the concept on how to design and develop a face recognition system through deep learning using OpenCV in python. Deep learning is an approach to perform the face recognition and seems to be an adequate method to carry out face recognition due to its high accuracy. Experimental results are provided to demonstrate the accuracy of the proposed face recognition system.
Graphical password based mouse behavior technique
Authors: Abdalkareem Zahraa A. , Akif Omar Z. , Abdulatif Firas A. , Amiza A. , Ehkan Phaklen
Published: March 2021

This paper proposes a new password generation technique on the basis of mouse motion and a special case location recognized by the number of clicks to protect sensitive data for different companies. Two, three special locations click points for the users has been proposed to increase password complexity. Unlike other currently available random password generators, the path and number of clicks will be added by admin, and authorized users have to be training on it.

This method aims to increase combinations for the graphical password generation using mouse motion for a limited number of users. A mathematical model is developed to calculate the performance of the password. The proposed technique in this paper allows the user to keep the ease-of-use in the mouse motion, while minimizing the risk of password guessing. A comparative evaluation has been conducted against a traditional password. The results show that the proposed approach improves the complexity 200% for fix position technique and two variants technique but more than 200% for three variants technique.
Development of a monitoring system and power management for an IoT based vaccine carrier
Authors: Hasanat R T , Mansoor N , Mohammed N , Rahman M S , Rasheduzzaman M
Published: March 2021

The development and implementation of automated system to monitor the temperature, humidity, and location of a vaccine carrier in real-time are presented in this paper. All the collected data are sent via SMS and also stored on an SD card to prevent the loss of any data. The weak power infrastructure is one of the challenges in the developing countries which brings into consideration the overall power management and power saving modes of the carrier. The monitoring system and vaccine carrier have been powered from the same source: by either using the vehicle battery or portable batteries. The current consumption of the individual components has been reduced up to 92% and the overall current consumption of the system has been reduced by 8%. Being able to monitor the vaccine storage conditions and the carrier location remotely in real-time, and maintaining low power consumption at the same time, would allow to reduce the vaccine wastage rates and can be very effective in increasing the vaccine outreach in developing and undeveloped countries.