bluuebunny/crossref_metadata_2025 huggingface dataset:
Study of Urbach energy and Kramers–Kronig on Mn and Zn doped NiFe2O4 ferrite nanopowder for the determination of structural and optical characteristics
Authors: Nazari N. , Golzan M. M. , Mabhouti Kh.
Published: March 2024

MxNi1-xFe2O4 spinel ferrite (M = Mn, Zn, and x = 0, 0.05) has been successfully synthesized by co-precipitation technique with hydrazine hydrate reduction agent (instead of NaOH) and Ethylene glycol surfactant. The XRD spectra of the samples illustrated high crystallinity. The structural characterization of pure and doped fcc NiFe2O4 were calculated by Scherrer, Modified Scherrer, Williamson–Hall, and SSP methods. In comparison of several methods, the Scherrer method is unreasonable method and W–H method has an acceptable range and can calculate both < L > and strain without restriction. The specific surface area in Zn-doped increased, demonstrate increment of adsorption properties in Ni ferrite structure. TEM images revealed the shape of grains is spherical, cubic, and irregular, with a grain size in the range of 35–65 nm. Hysteresis loops illustrated the magnetic behavior of samples. From the reflectance data, the band gap energies were estimated at 1.984, 1.954, and 1.973 eV for un-doped, Mn, and Zn-doped NiFe2O4 respectively (red shift). The almost low value of Urbach energy for pure, Mn, and Zn -doped NiFe2O4 indicates low structural disorder, which can approve the high crystallinity of samples. Direct band gap energy (Eg), refractive index, and extinction coefficient were estimated by the Kramers–Kronig method with linear optical evaluations. The Eg by K-K method is in good agreement with the Eg by Kubelka–Munk function.
Using shock generator for the fuel mixing of the extruded single 4-lobe nozzle at supersonic combustion chamber
Authors: Alizadeh As’ad , Jasim Dheyaa J. , Sohrabi Neaman , Ahmed Mohsen , Ameer S. Abdul , Ibrahim Safaa Mohammed , Dabis Hasan Khalid , Hussein Ali Adhab , Sultan Abbas J.
Published: March 2024

The importance of the fuel injection configuration on the propulsion efficiency of high-speed vehicles is apparent. In this article, the use of an annular extruded 4-lobe nozzle for the injection of fuel jet in a supersonic combustor of a scramjet engine in the existence of a shock generator is examined. The main aim of this study is to obtain the efficient jet arrangement for efficient fuel mixing inside the engine of hypersonic vehicles. A numerical approach is used to model the supersonic air stream and cross-jet flow with the SST turbulence model. The role of nozzle altitude and internal air jet on the fuel mixing of the hydrogen within the high-speed domain are disclosed. The importance of the horseshoe vortex and counter-rotating vortex on the fuel distribution is also presented. Our results show that the usage of a coaxial jet instead of an annular jet would increase fuel mixing by more than 40% in the combustion chamber.
Prediction of compressive strength of concrete based on improved artificial bee colony-multilayer perceptron algorithm
Authors: Li Ping , Zhang Yanru , Gu Jiming , Duan Shiwei
Published: March 2024

There are many factors that affect the compressive strength of concrete. The relationship between compressive strength and these factors is a complex nonlinear problem. Empirical formulas commonly used to predict the compressive strength of concrete are based on summarizing experimental data of several different mix proportions and curing periods, and their generality is poor. This article proposes an improved artificial bee colony algorithm (IABC) and a multilayer perceptron (MLP) coupled model for predicting the compressive strength of concrete. To address the shortcomings of the basic artificial bee colony algorithm, such as easily falling into local optima and slow convergence speed, this article introduces a Gaussian mutation operator into the basic artificial bee colony algorithm to optimize the initial honey source position and designs an MLP neural network model based on the improved artificial bee colony algorithm (IABC-MLP). Compared with traditional strength prediction models, the ABC-MLP model can better capture the nonlinear relationship of the compressive strength of concrete and achieve higher prediction accuracy when considering the compound effect of multiple factors. The IABC-MLP model built in this study is compared with the ABC-MLP and particle swarm optimization (PSO) coupling algorithms. The research shows that IABC can significantly improve the training and prediction accuracy of MLP. Compared with the ABC-MLP and PSO-MLP coupling models, the training accuracy of the IABC-MLP model is increased by 1.6% and 4.5%, respectively. This model is also compared with common individual learning algorithms such as MLP, decision tree (DT), support vector machine regression (SVR), and random forest algorithms (RF). Based on the comparison of prediction results, the proposed method shows excellent performance in all indicators and demonstrates the superiority of heuristic algorithms in predicting the compressive strength of concrete.
Benchmarking machine learning and parametric methods for genomic prediction of feed efficiency-related traits in Nellore cattle
Authors: Mota Lucio F. M. , Arikawa Leonardo M. , Santos Samuel W. B. , Fernandes Júnior Gerardo A. , Alves Anderson A. C. , Rosa Guilherme J. M. , Mercadante Maria E. Z. , Cyrillo Joslaine N. S. G. , Carvalheiro Roberto , Albuquerque Lucia G.
Published: March 2024

Genomic selection (GS) offers a promising opportunity for selecting more efficient animals to use consumed energy for maintenance and growth functions, impacting profitability and environmental sustainability. Here, we compared the prediction accuracy of multi-layer neural network (MLNN) and support vector regression (SVR) against single-trait (STGBLUP), multi-trait genomic best linear unbiased prediction (MTGBLUP), and Bayesian regression (BayesA, BayesB, BayesC, BRR, and BLasso) for feed efficiency (FE) traits. FE-related traits were measured in 1156 Nellore cattle from an experimental breeding program genotyped for ~ 300 K markers after quality control. Prediction accuracy (Acc) was evaluated using a forward validation splitting the dataset based on birth year, considering the phenotypes adjusted for the fixed effects and covariates as pseudo-phenotypes. The MLNN and SVR approaches were trained by randomly splitting the training population into fivefold to select the best hyperparameters. The results show that the machine learning methods (MLNN and SVR) and MTGBLUP outperformed STGBLUP and the Bayesian regression approaches, increasing the Acc by approximately 8.9%, 14.6%, and 13.7% using MLNN, SVR, and MTGBLUP, respectively. Acc for SVR and MTGBLUP were slightly different, ranging from 0.62 to 0.69 and 0.62 to 0.68, respectively, with empirically unbiased for both models (0.97 and 1.09). Our results indicated that SVR and MTGBLUBP approaches were more accurate in predicting FE-related traits than Bayesian regression and STGBLUP and seemed competitive for GS of complex phenotypes with various degrees of inheritance.
Modelling of surface brightness fluctuation measurements
Authors: Rodríguez-Beltrán P. , Cerviño M. , Vazdekis A. , Beasley M. A.
Published: March 2024

Aims. The goal of this work is to scrutinise the surface brightness fluctuation (SBF) calculation methodology. We analysed the SBF derivation procedure, measured the accuracy of the fitted SBF under controlled conditions, retrieved the uncertainty associated with the variability of a system that is inherently stochastic, and studied the SBF reliability under a wide range of conditions. Additionally, we address the possibility of an SBF gradient detection. We also examine the problems related with biased measurements of the SBF and low luminosity sources. All of this information allows us to put forward guidelines to ensure a valid SBF retrieval.

Methods. To perform all the experiments described above, we carried out Monte Carlo simulations of mock galaxies as an ideal laboratory. Knowing its underlying properties, we attempted to retrieve SBFs under different conditions. The uncertainty was evaluated through the accuracy, the precision, and the standard deviation of the fitting.

Results. We demonstrate how the usual mathematical approximations taken in the SBF theoretical derivation have a negligible impact on the results and how modelling the instrumental noise reduces the uncertainty. We conducted various studies where we varied the size of the mask applied over the image, the surface and fluctuation brightness of the galaxy, its size and profile, its point spread function, and the sky background. It is worth highlighting that we find a strong correlation between having a high number of pixels within the studied mask and retrieving a low uncertainty result. We address how the standard deviation of the fitting underestimates the actual uncertainty of the measurement. Lastly, we find that, when studying SBF gradients, the result is a pixel-weighted average of all the SBFs present within the studied region. Retrieving an SBF gradient requires high-quality data and a sufficient difference in the fluctuation value through the different radii. We show how the SBF uncertainty can be obtained and we present a collection of qualitative recommendations for a safe SBF retrieval.

Conclusions. Our main findings are as follows. It is important to model the instrumental noise, rather than fitting it. The target galaxies must be observed under appropriate observational conditions. In a traditional SBF derivation, one should avoid pixels with fluxes lower than ten times the SBF estimate to prevent biased results. The uncertainty associated with the intrinsic variability of the system can be obtained using sets of Monte Carlo mock galaxy simulations. We offer our computational implementation in the form of a simple code designed to estimate the uncertainty of the SBF measurement. This code can be used to predict the quality of future observations or to evaluate the reliability of those already conducted.
Hunting for complex cyanides in protostellar ices with the JWST
Authors: Nazari P. , Rocha W. R. M. , Rubinstein A. E. , Slavicinska K. , Rachid M. G. , van Dishoeck E. F. , Megeath S. T. , Gutermuth R. , Tyagi H. , Brunken N. , Narang M. , Manoj P. , Watson D. M. , Evans N. J. , Federman S. , Muzerolle Page J. , Anglada G. , Beuther H. , Klaassen P. , Looney L. W. , Osorio M. , Stanke T. , Yang Y.-L.
Published: March 2024

Nitrogen-bearing complex organic molecules have been commonly detected in the gas phase but not yet in interstellar ices. This has led to the long-standing question of whether these molecules form in the gas phase or in ices. The James Webb Space Telescope (JWST) offers the sensitivity, spectral resolution, and wavelength coverage needed to detect them in ices and investigate whether their abundance ratios are similar in gas and ice. We report the first tentative detection of CH3CN, C2H5CN and the simple molecule, N2O, based on the CN-stretch band in interstellar ices toward three (HOPS 153, HOPS 370, and IRAS 20126+4104) out of the five protostellar systems observed as part of the Investigating Protostellar Accretion (IPA) GO program with JWST-NIRSpec. We also provide upper limits for the two other sources with smaller luminosities in the sample. We detect OCN− in the ices of all sources with typical CH3CN/OCN− ratios of around 1. Ice and gas column density ratios of the nitrogen-bearing species with respect to each other are better matched than those with respect to methanol, which are a factor of ~5 larger in the ices than the gas. We attribute the elevated ice column densities with respect to methanol to the difference in snowline locations of nitrogen-bearing molecules and of methanol, biasing the gas-phase observations toward fewer nitrogen-bearing molecules. Moreover, we find tentative evidence of the enhancement of OCN−, CH3CN, and C2H5CN in warmer ices; although, the formation of these molecules likely starts along with methanol in the cold prestellar phase. Future surveys combining NIRSpec and MIRI, and additional laboratory spectroscopic measurements of C2H5CN ice, are necessary for robust detection and conclusions on the formation history of complex cyanides.
Outshining in the spatially resolved analysis of a strongly lensed galaxy at z = 6.072 with JWST NIRCam
Authors: Giménez-Arteaga C. , Fujimoto S. , Valentino F. , Brammer G. B. , Mason C. A. , Rizzo F. , Rusakov V. , Colina L. , Prieto-Lyon G. , Oesch P. A. , Espada D. , Heintz K. E. , Knudsen K. K. , Dessauges-Zavadsky M. , Laporte N. , Lee M. , Magdis G. E. , Ono Y. , Ao Y. , Ouchi M. , Kohno K. , Koekemoer A. M.
Published: March 2024

We present JWST/NIRCam observations of a strongly lensed, sub-L*, multiply imaged galaxy at z = 6.072, with magnification factors μ ≳ 20 across the galaxy. The galaxy has rich HST, MUSE, and ALMA ancillary observations across a broad wavelength range. Aiming to quantify the reliability of stellar mass estimates of high redshift galaxies, we performed a spatially resolved analysis of the physical properties at scales of ∼200 pc, inferred from spectral energy distribution (SED) modelling of five JWST/NIRCam imaging bands covering 0.16 μm < λrest < 0.63 μm on a pixel-by-pixel basis. We find young stars surrounded by extended older stellar populations. By comparing Hα+[N II] and [O III]+Hβ maps inferred from the image analysis with our additional NIRSpec integral field unit (IFU) data, we find that the spatial distribution and strength of the line maps are in agreement with the IFU measurements. We explore different parametric star formation history (SFH) forms with BAGPIPES on the spatially integrated photometry, finding that a double power-law (DPL) star formation history retrieves the closest value to the spatially resolved stellar mass estimate, and other SFH forms suffer from the dominant outshining emission from the youngest stars, thus underestimating the stellar mass – up to ∼0.5 dex. On the other hand, the DPL cannot match the IFU-measured emission lines. Additionally, the ionising photon production efficiency may be overestimated in a spatially integrated approach by ∼0.15 dex, when compared to a spatially resolved analysis. The agreement with the IFU measurements implies that our pixel-by-pixel results derived from the broadband images are robust, and that the mass discrepancies we find with spatially integrated estimates are not just an effect of SED-fitting degeneracies or the lack of NIRCam coverage. Additionally, this agreement points towards the pixel-by-pixel approach as a way to mitigate the general degeneracy between the flux excess from emission lines and underlying continuum, especially when lacking photometric medium-band coverage and/or IFU observations. This study stresses the importance of studying galaxies as the complex systems that they are, resolving their stellar populations when possible, or using more flexible SFH parameterisations. This can aid our understanding of the early stages of galaxy evolution by addressing the challenge of inferring robust stellar masses and ionising photon production efficiencies of high redshift galaxies.
Damped kink motions in a system of two solar coronal tubes with elliptic cross sections
Authors: Shi Mijie , Li Bo , Chen Shaoxia , Yu Hui , Guo Mingzhe
Published: March 2024

Aims. This study is motivated by observations of coordinated transverse displacements in neighboring solar active region loops, addressing specifically how the behavior of kink motions in straight two-tube equilibria is impacted by tube interactions and tube cross-sectional shapes.

Methods. We worked with linear, ideal, pressureless magnetohydrodynamics. Axially standing kink motions were examined as an initial value problem for transversely structured equilibria involving two identical, field-aligned, density-enhanced tubes with elliptic cross sections (elliptic tubes). Continuously nonuniform layers were implemented around both tube boundaries. We numerically followed the system response to external velocity drivers, largely focusing on the quasi-mode stage of internal flows to derive the pertinent periods and damping times.

Results. The periods and damping times that we derive for two-circular-tube setups justify the available modal results found with the T-matrix approach. Regardless of cross-sectional shapes, our nonuniform layers feature the development of small-scale shears and energy accumulation around Alfvén resonances, indicative of resonant absorption and phase mixing. As with two-circular-tube systems, our configurational symmetries still make it possible to classify lower-order kink motions by the polarization and symmetric properties of the internal flows; hence, such motions are labeled as S​x and Ax. However, the periods and damping times for two-elliptic-tube setups further depend on cross-sectional aspect ratios, with Ax motions occasionally damped less rapidly than S​x motions. We find uncertainties up to ∼20% (∼50%) for the axial Alfvén time (the inhomogeneity lengthscale) if the periods (damping times) computed for two-elliptic-tube setups are seismologically inverted with canonical theories for isolated circular tubes.

Conclusions. The effects of loop interactions and cross-sectional shapes need to be considered when the periods, and in particular the damping times, are seismologically exploited for coordinated transverse displacements in adjacent coronal loops.
Towards the epitaxial growth of Au thin films on MgO substrates for plasmonic applications
Authors: Celebrano Michele , Savoini Matteo , Biagioni Paolo , Della Valle Giuseppe , Pellegrini Giovanni , Cantoni Matteo , Rinaldi Christian , Cattoni Andrea , Petti Daniela , Bertacco Riccardo , Duò Lamberto , Finazzi Marco
Published: March 2024

Surface Plasmon Polaritons (SPPs) in Au thin films are nowadays intensively exploited for sensing applications that leverage the strong optical field confinement at the metal/dielectric interface and the easy functionalization of the Au surface. Moreover, Au thin films represent one of the common starting points for the top-down nanofabrication of plasmonic nanostructures supporting localized resonances. In this framework, strategies for the growth of high-quality Au films on transparent substrates are crucial and not yet fully established. In this study, we exploit MgO(001) substrates for the growth of thin (about 45 nm) Au films, also including an additional buffer layer of Fe. We successfully demonstrate Au samples with reduced roughness and presenting Low-Energy Electron Diffraction (LEED) features, indicating a high degree of crystalline ordering. This is supported by the experimental evidence of an increased (by almost a factor of 3) propagation length compared to a reference Au sample grown on standard glass slides, which is however still significantly lower than the one expected from first principles.
Germanium Fabry-Perot nanoresonators investigated by cathodoluminescence spectroscopy
Authors: Mignuzzi Sandro , Wu Xiaofei , Hecht Bert , Frigerio Jacopo , Isella Giovanni , Celebrano Michele , Finazzi Marco , Sapienza Riccardo , Biagioni Paolo
Published: March 2024

We report on the experimental investigation, by means of spatially-resolved cathodoluminescence spectroscopy, of rectangular all-dielectric Ge nanoantennas sustaining Fabry-Perot resonances. The combination of spatial and spectral resolution allows us to directly image the standing-wave pattern of the local density of optical states inside the nanoantennas, which is the fingerprint of the resonant Purcell contribution to the overall emission enhancement previously reported in the literature for the same structures. Our results confirm that the emission properties of Ge nanostructures can be effectively tuned by engineering the local density of optical states and that cathodoluminescence provides valuable information to experimentally address such modulation in their emission properties.
Lessons Learnt from Imaging Review of Interval Breast Cancers in a Single Center in the UK National Breast Screening Program
Authors: Lee Jia Mang , Jantarang Palida , Rengabashyam Bhavani
Published: March 2024

False-negative mammograms are a part of any screening program and the National Breast Screening Program in the United Kingdom is no exception. Every year, 2.5 million women have screening mammograms in the United Kingdom. Around 8 per 1,000 women screened are diagnosed with a breast cancer and 3 per 1,000 women will present with an interval breast cancer following a negative screening mammogram and before their next mammogram.

Robust quality standards have to be adhered to at every stage in the screening pathway in order to maintain the fine balance between detecting cancers early and avoiding unnecessary false-positive results. As part of this process, there is a mandatory requirement for screening units to review all breast cancers. We present a pictorial illustration of the lessons learnt from such a review in this essay. The cases described here are from one large breast screening unit in the North of England. In this unit, 30,000 to 40,000 women have a screening mammogram each year and these are all double read by human readers. All cases requiring recall and those where there is a disagreement between the first and second human reader go through a consensus/arbitration process involving a minimum of two human readers. Interval cancers are identified through a consistent process outlined by the screening program and are then subjected to a review by a minimum of two reviewers. In this process, the reviewers have access to the false-negative mammograms along with all priors that were available at the time of initial read. The reviewers make a decision on whether the initial mammogram is normal or abnormal without seeing the diagnostic mammogram with the interval cancer. They also categorize the density of the breast and describe the mammographic abnormality if there is any on a standardized interval cancer data collection form. Finally, they categorize the interval cancer into one of three types—“satisfactory,” “satisfactory with learning points,” or “unsatisfactory.”
Driving value-based healthcare through a new vision for Queensland’s health system
Authors: Wellington Madeleine , Whiting Elizabeth , Searle Damien , Kreis Megan , Cross Emily
Published: March 2024

The purpose of this case study is to explain the development of Queensland’s strategic approach to health system reform, which promotes partnership across the health system to better deliver integrated and value-based health care across the continuum of care. The new health system vision was informed by undertaking literature searches on national and international health system approaches to reform and supported by extensive consultation across Queensland with more than 1100 stakeholders. Thematic analysis was undertaken to identify key themes that were translated into a high-level vision document that communicated Queensland’s renewed focus on wellness and delivering more care in the community. This was circulated to stakeholders for iterative and collaborative refinement before final approvals. Collaboratively and iteratively developing the new health system vision for Queensland with key stakeholders has contributed to a shared understanding and ownership of a vision that is committed to system reform, focused on delivering high-value care that reflects what is important to consumers and health system stakeholders.
Ensemble forecasting of Persian leopard (Panthera pardus saxicolor) distribution and habitat suitability in south-western Iran
Authors: Jamali Fatemeh , Amininasab Seyed Mehdi , Taleshi Hamid , Madadi Hossein
Published: March 2024

Context Habitat loss and fragmentation are major threats to global biodiversity, especially for wide-ranging apex carnivores. The Persian leopard (Panthera pardus saxicolor) is an endangered species. Although populations of Persian leopards are declining, the species remains widely distributed across large areas of Iran. Aims This study aimed to determine habitat suitability for Persian leopards in the Khaeiz and Sorkh protected area of south-western Iran and to identify the most significant factors influencing their habitat use/selection and spatial distribution. Methods We performed species distribution modelling in two stages: First, we ran the model with three abiotic predictors: slope; aspect; and distance from water resources. In the second stage, modelling was conducted using three ecological predictors: caracal distribution; wild goat distribution; and livestock distribution. Ensemble modelling was applied based on five replicates of eight SDMs (species distribution models; GLM, CTA, FDA, GBM, ANN, MARS, RF and MaxEnt). Key results We observed only minor differences in habitat suitability between the abiotic and ecological models. Habitat suitability for Persian leopards was higher in steeper areas, close to water resources and near the distribution of caracals, livestock and wild goats. The ecological model predicted 2.03% (329 ha) more suitable habitat than the abiotic model did. Conclusions Most habitat suitability models focus on abiotic variables, but we found that ecological variables offer similar predictive power for determining the habitat suitability of Persian leopards. Implications Habitat suitability models for Persian leopards can be used to guide conservation and management decisions. They are also useful indicating where conflicts between predators and humans may occur.
Accelerating Asteroidal Period and Pole Inversion from Multiple Lightcurves Using Parallel Differential Evolution and Cellinoid Shape Model
Authors: Zhang Yong-Xiong , Guo Wen-Xiu , Lu Xiao-Ping , Zheng Hua , Zhao Hai-Bin , Tian Jun , Wang Wei-Lin
Published: March 2024

Determining asteroid properties provides valuable physical insights but inverting them from photometric lightcurves remains computationally intensive. This paper presents a new approach that combines a simplified Cellinoid shape model with the Parallel Differential Evolution (PDE) algorithm to accelerate inversion. The PDE algorithm is more efficient than the Differential Evolution algorithm, achieving an extraordinary speedup of 37.983 with 64 workers on multicore CPUs. The PDE algorithm accurately derives period and pole values from simulated data. The analysis of real asteroid lightcurves validates the method’s reliability: in comparison with results published elsewhere, the PDE algorithm accurately recovers the rotational periods and, given adequate viewing geometries, closely matches the pole orientations. The PDE approach converges to solutions within 20,000 iterations and under one hour, demonstrating its potential for large-scale data analysis. This work provides a promising new tool for unveiling asteroid physical properties by overcoming key computational bottlenecks.
The multi-peak point phenomenon of broadband microwave reflection caused by inhomogeneous plasma
Authors: YANG 杨 Min 敏 , QI 齐 Kaixuan 凯旋 , YANG 杨 Jiuwen 玖文 , JIA 贾 Sa 飒 , LIU 刘 Haoyan 浩岩 , CHEN 陈 Yanyang 燕扬 , LI 李 Jin 瑾 , (李小平) Xiaoping LI
Published: March 2024

During spacecraft re-entry, the challenge of measuring plasma sheath parameters directly contributes to difficulties in addressing communication blackout. In this work, we have discovered a phenomenon of multiple peaks in reflection data caused by the inhomogeneous plasma. Simulation results show that the multi-peak points fade away as the characteristic frequency is approached, resembling a series of gradually decreasing peaks. The positions and quantities of these points are positively correlated with electron density, yet they show no relation to collision frequency. This phenomenon is of significant reference value for future studies on the spatial distribution of plasmas, particularly for using microwave reflection signals in diagnosing the plasma sheath.
Incorporating network diffusion and peak location information for better single-cell ATAC-seq data analysis
Authors: Yu Jiating , Leng Jiacheng , Hou Zhichao , Sun Duanchen , Wu Ling-Yun
Published: March 2024

Single-cell assay for transposase-accessible chromatin using sequencing (scATAC-seq) data provided new insights into the understanding of epigenetic heterogeneity and transcriptional regulation. With the increasing abundance of dataset resources, there is an urgent need to extract more useful information through high-quality data analysis methods specifically designed for scATAC-seq. However, analyzing scATAC-seq data poses challenges due to its near binarization, high sparsity and ultra-high dimensionality properties. Here, we proposed a novel network diffusion–based computational method to comprehensively analyze scATAC-seq data, named Single-Cell ATAC-seq Analysis via Network Refinement with Peaks Location Information (SCARP). SCARP formulates the Network Refinement diffusion method under the graph theory framework to aggregate information from different network orders, effectively compensating for missing signals in the scATAC-seq data. By incorporating distance information between adjacent peaks on the genome, SCARP also contributes to depicting the co-accessibility of peaks. These two innovations empower SCARP to obtain lower-dimensional representations for both cells and peaks more effectively. We have demonstrated through sufficient experiments that SCARP facilitated superior analyses of scATAC-seq data. Specifically, SCARP exhibited outstanding cell clustering performance, enabling better elucidation of cell heterogeneity and the discovery of new biologically significant cell subpopulations. Additionally, SCARP was also instrumental in portraying co-accessibility relationships of accessible regions and providing new insight into transcriptional regulation. Consequently, SCARP identified genes that were involved in key Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways related to diseases and predicted reliable cis-regulatory interactions. To sum up, our studies suggested that SCARP is a promising tool to comprehensively analyze the scATAC-seq data.
Benchmarking multi-omics integration algorithms across single-cell RNA and ATAC data
Authors: Xiao Chuxi , Chen Yixin , Meng Qiuchen , Wei Lei , Zhang Xuegong
Published: March 2024

Recent advancements in single-cell sequencing technologies have generated extensive omics data in various modalities and revolutionized cell research, especially in the single-cell RNA and ATAC data. The joint analysis across scRNA-seq data and scATAC-seq data has paved the way to comprehending the cellular heterogeneity and complex cellular regulatory networks. Multi-omics integration is gaining attention as an important step in joint analysis, and the number of computational tools in this field is growing rapidly. In this paper, we benchmarked 12 multi-omics integration methods on three integration tasks via qualitative visualization and quantitative metrics, considering six main aspects that matter in multi-omics data analysis. Overall, we found that different methods have their own advantages on different aspects, while some methods outperformed other methods in most aspects. We therefore provided guidelines for selecting appropriate methods for specific scenarios and tasks to help obtain meaningful insights from multi-omics data integration.
scENCORE: leveraging single-cell epigenetic data to predict chromatin conformation using graph embedding
Authors: Duan Ziheng , Xu Siwei , Sai Srinivasan Shushrruth , Hwang Ahyeon , Lee Che Yu , Yue Feng , Gerstein Mark , Luan Yu , Girgenti Matthew , Zhang Jing
Published: March 2024

Dynamic compartmentalization of eukaryotic DNA into active and repressed states enables diverse transcriptional programs to arise from a single genetic blueprint, whereas its dysregulation can be strongly linked to a broad spectrum of diseases. While single-cell Hi-C experiments allow for chromosome conformation profiling across many cells, they are still expensive and not widely available for most labs. Here, we propose an alternate approach, scENCORE, to computationally reconstruct chromatin compartments from the more affordable and widely accessible single-cell epigenetic data. First, scENCORE constructs a long-range epigenetic correlation graph to mimic chromatin interaction frequencies, where nodes and edges represent genome bins and their correlations. Then, it learns the node embeddings to cluster genome regions into A/B compartments and aligns different graphs to quantify chromatin conformation changes across conditions. Benchmarking using cell-type-matched Hi-C experiments demonstrates that scENCORE can robustly reconstruct A/B compartments in a cell-type-specific manner. Furthermore, our chromatin confirmation switching studies highlight substantial compartment-switching events that may introduce substantial regulatory and transcriptional changes in psychiatric disease. In summary, scENCORE allows accurate and cost-effective A/B compartment reconstruction to delineate higher-order chromatin structure heterogeneity in complex tissues.
FusionNW, a potential clinical impact assessment of kinases in pan-cancer fusion gene network
Authors: Yang Chengyuan , Kumar Himansu , Kim Pora
Published: March 2024

Kinase fusion genes are the most active fusion gene group in human cancer fusion genes. To help choose the clinically significant kinase so that the cancer patients that have fusion genes can be better diagnosed, we need a metric to infer the assessment of kinases in pan-cancer fusion genes rather than relying on the sample frequency expressed fusion genes. Most of all, multiple studies assessed human kinases as the drug targets using multiple types of genomic and clinical information, but none used the kinase fusion genes in their study. The assessment studies of kinase without kinase fusion gene events can miss the effect of one of the mechanisms that enhance the kinase function in cancer. To fill this gap, in this study, we suggest a novel way of assessing genes using a network propagation approach to infer how likely individual kinases influence the kinase fusion gene network composed of ~5K kinase fusion gene pairs. To select a better seed of propagation, we chose the top genes via dimensionality reduction like a principal component or latent layer information of six features of individual genes in pan-cancer fusion genes. Our approach may provide a novel way to assess of human kinases in cancer.
Translational bioinformatics and data science for biomarker discovery in mental health: an analytical review
Authors: Bhuvaneshwar Krithika , Gusev Yuriy
Published: March 2024

Translational bioinformatics and data science play a crucial role in biomarker discovery as it enables translational research and helps to bridge the gap between the bench research and the bedside clinical applications. Thanks to newer and faster molecular profiling technologies and reducing costs, there are many opportunities for researchers to explore the molecular and physiological mechanisms of diseases. Biomarker discovery enables researchers to better characterize patients, enables early detection and intervention/prevention and predicts treatment responses. Due to increasing prevalence and rising treatment costs, mental health (MH) disorders have become an important venue for biomarker discovery with the goal of improved patient diagnostics, treatment and care. Exploration of underlying biological mechanisms is the key to the understanding of pathogenesis and pathophysiology of MH disorders. In an effort to better understand the underlying mechanisms of MH disorders, we reviewed the major accomplishments in the MH space from a bioinformatics and data science perspective, summarized existing knowledge derived from molecular and cellular data and described challenges and areas of opportunities in this space.
Development and Validation of a New Reversed Phase HPLC Method for the Quantitation of Azithromycin and Rifampicin in a Capsule Formulation
Authors: Patel Foram , Kotadiya Rajendra , Patel Rashmin , Patel Mrunali
Published: March 2024

This research aimed to develop a new method for simultaneously estimating the presence of azithromycin (AZT) and rifampicin (RIF) in a capsule formulation using reverse-phase high-performance liquid chromatography. The developed method utilized a Gemini column with a 60:40% v/v acetonitrile and potassium dihydrogen phosphate mobile phase, a flow rate of 1 mL/min, and an injection volume of 20 μL. The detection wavelengths of 210 and 254 nm for AZT and RIF, respectively, were used. Validation ensures specificity with a peak purity index > 0.99999 for AZT and >0.99995 for RIF, affirming unambiguous analyte detection. The system suitability test, within acceptable limits, validates method reliability. Linearity calibration curves (R2 = 0.998) cover a 25–150% target concentration range. Accuracy studies employing the standard addition method yield recovery values between 96.6 and 103.9% for both drugs, confirming method accuracy. Precision studies reveal % relative standard deviation values consistently below 2%, highlighting reproducibility. Robustness testing supports method reliability under varying conditions. Application to a pharmaceutical capsule formulation demonstrates the method’s practicality, accurately quantifying AZT (98.30%) and RIF (99.37%). This study provides a validated analytical approach for simultaneous quantification in commercial pharmaceutical products containing both drugs, enhancing pharmaceutical quality control for critical antibiotics in complex formulations.
Glucagon-like Peptide 1 Receptor Agonists Promote Weight Loss Among People With HIV
Authors: Nguyen Quynh , Wooten Darcy , Lee Daniel , Moreno Manuel , Promer Katherine , Rajagopal Amutha , Tan Matthew , Tang Michael , Duren Kye , Yin Jeffrey , Hill Lucas
Published: March 2024

Background

Weight gain and associated metabolic complications are increasingly prevalent among people with human immunodeficiency virus (PWH). Glucagon-like peptide 1 receptor agonists (GLP-1RAs) are incretin-based therapies for diabetes and weight management that have been shown to result in substantial weight loss; however, studies of their effects in PWH are limited.

Methods

A retrospective single-center cohort study was conducted among PWH who were taking GLP-1RAs at the University of California, San Diego Owen Clinic between 1 February 2021 and 1 February 2023. Baseline clinical data were collected and changes in weight, body mass index (BMI), and hemoglobin A1C (A1C) before starting GLP-1RAs compared to the most recent clinic visit were calculated (with a minimum of 3 months follow-up time required). Logistic regression was performed to identify variables associated with >5% of total body weight loss.

Results

A total of 225 patients received on average 13 months of GLP-1RA therapy, with 85 (37.8%) achieving the maximum GLP-1RA dose. GLP-1RA therapy resulted, on average, in a weight loss of 5.4 kg, decrease in BMI by 1.8 kg/m2, and decrease in A1C by 0.6%. In the multivariable analysis, higher baseline BMI (odds ratio [OR], 1.10 [95% confidence interval {CI}, 1.03–1.16]), treatment duration of GLP-1RA therapy >6 months (OR, 3.12 [95% CI, 1.49–6.49]), and use of tirzepatide (OR, 5.46 [95% CI, 1.44–20.76]) were significantly more likely to be associated with >5% weight loss.

Conclusions

Use of GLP-1RAs led to declines in weight, BMI, and A1C among PWH and offers an additional strategy to address weight gain and diabetes.
Partial trailside Japanese barberry (Ranunculales: Berberidaceae) removal did not reduce the abundance of questing blacklegged ticks (Acari: Ixodidae)
Authors: Elias Susan P , Rand Peter W , Lubelczyk Charles B , McVety Melanie R , Smith Robert P
Published: March 2024

In a nature reserve in southern Maine, we removed invasive Japanese barberry (Berberis thunbergii de Candolle) along sections of forested recreational trails that ran through dense barberry infestations. Barberry thickets provide questing substrate and a protective microclimate for blacklegged ticks (Ixodes scapularis Say), and trail users could brush up against encroaching barberry and acquire ticks. Trailside barberry removal will reduce or eliminate encroaching tick questing substrate and could reduce trailside questing tick abundance by creating a microclimate more hostile to ticks. The same-day cut-and-spray treatment comprised mechanical cutting of barberry clumps (individual plants with numerous ramets) followed immediately by targeted herbicide application to the resulting root crowns. The treatment created trail shoulders to a lateral width of 1–2 m on both sides of 100-m trail sections, with initial treatment in the fall of 2013 and one retreatment in the summer of 2014. Our aim was to remove 90% of barberry clumps to achieve a 50% or better reduction in questing tick abundance on trail shoulders. However, by the fall of 2015, there were only 41% fewer barberry clumps on treated vs. untreated trail sections and there was no reduction in either adults or nymphs. We concluded that our barberry treatment protocol was not sufficiently aggressive since the resulting ecotone habitat on trail shoulders proved suitable for questing I. scapularis. In principle, cutting back barberry along trails should reduce trail user contact with questing deer ticks, but we were unable to demonstrate a reduction in trailside tick abundance.
Differential feeding on ornamental plants by Duponchelia fovealis (Lepidoptera: Crambidae) larvae
Authors: Copeman Sophia M , Frank Steven D
Published: March 2024

Duponchelia fovealis (Zeller) (Lepidoptera: Crambidae) is a polyphagous pest that feeds on a variety of ornamental and crop plants. At least 47 plant families have been identified as hosts for D. fovealis in literature based on empirical data and observations. This list is surely incomplete based on the broad feeding habits of D. fovealis. We sought to expand the list of known D. fovealis host plants and to identify species that may be less preferred or not fed upon by D. fovealis. We used laboratory feeding assays to measure D. fovealis consumption rate of leaf disks from 32 herbaceous plant species and 32 woody species grown outdoors throughout the Southeastern United States, and 24 tropical species typically grown as house plants. These plants were from 65 genera and 36 families. Between the 3 ornamental plant groups, we tested (herbaceous, woody, and tropical) that, after 24 h, plants in the tropical group were the least consumed by D. fovealis. After 24 h, the average proportion of leaf disks eaten by D. fovealis was 0.80 or higher for 5 herbaceous and 12 woody species. Proportions of leaf disks eaten varied at the family and genus level in many cases. Our research can improve integrated pest management of D. fovealis by informing growers that plants may be at more or less risk of infestation and damage by larvae.
Dominance between self-incompatibility alleles determines the mating system of Capsella allopolyploids
Authors: Duan Tianlin , Zhang Zebin , Genete Mathieu , Poux Céline , Sicard Adrien , Lascoux Martin , Castric Vincent , Vekemans Xavier
Published: March 2024

The shift from outcrossing to self-fertilization is one of the main evolutionary transitions in plants and has broad effects on evolutionary trajectories. In Brassicaceae, the ability to inhibit self-fertilization is controlled by 2 genes, SCR and SRK, tightly linked within the S-locus. A series of small non-coding RNAs also encoded within the S-locus regulates the transcriptional activity of SCR alleles, resulting in a linear dominance hierarchy between them. In Brassicaceae, natural allopolyploid species are often self-compatible (SC) even when one of the progenitor species is self-incompatible, but the reason why polyploid lineages tend to lose self-incompatibility (SI) and the timing of the loss of SI (immediately after ancestral hybridization between the progenitor species, or at a later stage after the formation of allopolyploid lineages) have generally remained elusive. We used a series of synthetic diploid and tetraploid hybrids obtained between self-fertilizing Capsella orientalis and outcrossing Capsella grandiflora to test whether the breakdown of SI could be observed immediately after hybridization, and whether the occurrence of SC phenotypes could be explained by the dominance interactions between S-haplotypes inherited from the parental lineages. We used RNA-sequencing data from young inflorescences to measure allele-specific expression of the SCR gene and infer dominance interactions in the synthetic hybrids. We then evaluated the seed set from autonomous self-pollination in the synthetic hybrids. Our results demonstrate that self-compatibility of the hybrids depends on the relative dominance between S-alleles inherited from the parental species, confirming that SI can be lost instantaneously upon formation of the ancestral allopolyploid lineage. They also confirm that the epigenetic regulation that controls dominance interactions between S-alleles can function between subgenomes in allopolyploids. Together, our results illustrate how a detailed knowledge of the mechanisms controlling SI can illuminate our understanding of the patterns of co-variation between the mating system and changes in ploidy.
A loss of function mutation in CLDN25 causing Pelizaeus-Merzbacher-like leukodystrophy
Authors: Hashimoto Yosuke , Besmond Claude , Boddaert Nathalie , Munnich Arnold , Campbell Matthew
Published: March 2024

Claudin-25 (CLDN-25), also known as Claudin containing domain 1, is an uncharacterized claudin family member. It has less conserved amino acid sequences when compared to other claudins. It also has a very broad tissue expression profile and there is currently a lack of functional information from murine knockout models. Here, we report a de novo missense heterozygous variant in CLDN25 (c. 745G>C, p. A249P) found in a patient diagnosed with Pelizaeus-Merzbacher-like leukodystrophy and presenting with symptoms such as delayed motor development, several episodes of tonic absent seizures and generalized dystonia. The variant protein does not localize to the cell-cell borders where it would normally be expected to be expressed. Amino acid position 249 is located 4 amino acids from the C-terminal end of the protein where most claudin family members have a conserved binding motif for the key scaffolding protein ZO-1. However, CLDN-25 does not contain this motif. Here, we show that the C-terminal end of CLDN-25 is required for its junctional localization in a ZO-1 independent manner. The A249P mutant protein as well as a deletion mutant lacking its last 5 C-terminal amino acids also failed to localize to the cell-cell border in vitro. Intriguingly, cellular knockout of CLDN25, in vitro, appeared to increase the integrity of the tight junction between 2 contacting cells, while driving highly unusual increased movement of solutes between cells. We propose that the barrier function of CLDN-25 is akin to a decoy claudin, whereby decreasing its expression in “leaky” epithelial cells and endothelial cells will drive dynamic changes in the adhesion and interaction capacity of cell-cell contact points. While it remains unclear how this de novo CLDN-25 mutant induces leukodystrophy, our findings strongly suggest that this mutation induces haploinsufficiency of CLDN-25. Elucidating the function of this uncharacterized claudin protein will lead to a better understanding of the role of claudin proteins in health and disease.
On a sharp estimate of overlapping Schwarz methods in H(curl; Ω) and H(div; Ω)
Authors: Liang Qigang , Xu Xuejun , Zhang Shangyou
Published: March 2024

The previously proved upper bound is $C\big(1+\frac{H^{2}}{\delta ^{2}}\big)$ for the condition number of the discrete system arising from the classical two-level overlapping Schwarz method for symmetric positive definite problems in $\boldsymbol{H}(\textbf{curl}; \varOmega )$ and $\boldsymbol{H}(\textrm{div}; \varOmega )$, where $H$ and $\delta $ are the sizes of subdomains and overlap, respectively. But all numerical results indicate that a sharper bound is $C\big (1+ \frac{H}{\delta } \big )$. In this work, we prove that the condition number is indeed bounded above by $C\big(1+\frac{H}{\delta }\big)$.