Active Elements Research Articles

Robust chromatin state annotation.

With the goal of mapping genomic activity, international projects have recently measured epigenetic activity in hundreds of cell and tissue types. Chromatin state annotations produced by segmentation and genome annotation (SAGA) methods have emerged as the predominant way to summarize these epigenomic data sets in order to annotate the genome. These chromatin state annotations are essential for many genomic tasks, including identifying active regulatory elements and interpreting disease-associated genetic variation. However, despite the widespread applications of SAGA methods, no principled approach exists to evaluate the statistical significance of chromatin state assignments. Here, we propose the first method for assigning calibrated confidence scores to chromatin state annotations. Toward this goal, we performed a comprehensive evaluation of the reproducibility of the two most widely used existing SAGA methods, ChromHMM and Segway. We found that their predictions are frequently irreproducible. For example, when applying the same SAGA method on two sets of experimental replicates, 27%-69% of predicted enhancers fail to replicate. This suggests that a substantial fraction of predicted elements in existing chromatin state annotations cannot be relied upon. To remedy this problem, we introduce SAGAconf, a method for assigning a measure of confidence (r-value) to chromatin state annotations. SAGAconf works with any SAGA method and assigns an r-value to each genomic bin of a chromatin state annotation that represents the probability that the label of this bin will be reproduced in a replicated experiment. Thus, SAGAconf allows a researcher to select only the reliable predictions from a chromatin annotation for use in downstream analyses.

Key indicators of beef safety and quality as important aspects of conservation

Meat cattle breeding should develop in Ukraine as a priority and independent industry to meet beef needs. The meat industry has enormous potential and, as the most promising and attractive, will take a dominant place in the structure of the domestic food industry in the coming years. Beef is one of the most essential elements of the human diet. It contains complete proteins and animal fats, biologically active substances, mineral elements, and vitamins. The most important feature of food products is their quality and safety indicators, that is, the absence of substances harmful to the consumer's health and pathogens of infectious and invasive diseases. In this regard, veterinary and sanitary expertise and product safety control are of particular importance, as they are necessary to ensure the health of the population of Ukraine. Improving the quality of meat and meat products is a primary task in modern conditions. The implementation of this task depends not only on agricultural but also on processing enterprises. The article presents materials on the study of critical indicators of the safety and quality of beef. The study was carried out as part of the research work of the Department of Normal and Pathological Morphology, hygiene, and Expertise: “Monitoring the content of toxic substances in drinking water, feed and their impact on the body of cattle and the quality and safety of products”, state registration number – 0120U101318. The material for the research was the slaughter products of domestic animals, such as cattle, which were supplied to enterprises in the city of Zhytomyr. Pre-slaughter inspection and veterinary-sanitary examination of carcasses and their slaughter products of cattle was carried out following the “Rules of pre-slaughter veterinary examination of animals and veterinary-sanitary examination of meat and meat products”. The study aims to determine the safety and quality indicators of beef obtained in the conditions of meat processing enterprises of the Zhytomyr region. To achieve this goal, a comprehensive survey of beef safety and quality indicators was conducted. As a result of the tests, it was established that the pH level of the meat was 5.7–6.1. Carrying out the reaction with a 5 % solution of CuSO4 in the broth showed that the broth was transparent. A positive response to peroxidase was also detected. The safety parameters corresponded to regulatory documents. Careful control of the safety and quality of beef at every stage of production, starting from the rearing of animals and up to the sale of the product, guarantees a high degree of consumer protection.

Active elastic metamaterials with equidistant solely resonant bandgaps

Elastic metamaterials are man-made structures with properties that transcend naturally occurring materials. One predominant feature of elastic metamaterials is locally resonant bandgaps, i.e., frequency ranges at which wave propagation is blocked. Locally resonant bandgaps appear at relatively low frequency and arise from the existence of periodically placed mechanical local resonators. Typically, elastic metamaterials exhibit both locally resonant and Bragg-scattering bandgaps, which can generally be different in width and frequency ranges. This paper proposes two designs of active elastic metamaterials that only exhibit locally resonant bandgaps, which are infinite in number, evenly spaced in the frequency spectrum, and identical in width. The mathematical model is established using the transfer matrix method and synthesis of locally resonant bandgaps is achieved via an active elastic support with carefully designed frequency-dependent stiffness. A single unit cell of each proposed metamaterials is thoroughly studied, and its dispersion relation is derived analytically, along with the periodically repeating bandgap limits and widths. Following the dispersion analysis and bandgap parametric studies, finite arrays of the proposed metamaterials are considered, and their frequency response is calculated to verify the analytical predictions from dispersion analyses.

Monitoring Redox Processes in Lithium-Ion Batteries by Laboratory-Scale Operando X-ray Emission Spectroscopy.

Tracking changes in the chemical state of transition metals in alkali-ion batteries is crucial to understanding the redox chemistry during operation. X-ray absorption spectroscopy (XAS) is often used to follow the chemistry through observed changes in the chemical state and local atomic structure as a function of the state-of-charge (SoC) in batteries. In this study, we utilize an operando X-ray emission spectroscopy (XES) method to observe changes in the chemical state of active elements in batteries during operation. Operando XES and XAS were compared by using a laboratory-scale setup for four different battery systems: LiCoO2 (LCO), Li[Ni1/3Co1/3Mn1/3]O2 (NMC111), Li[Ni0.8Co0.1Mn0.1]O2 (NMC811), and LiFePO4 (LFP) under a constant current charging the battery in 10 h (C/10 charge rate). We show that XES, despite narrower chemical shifts in comparison to XAS, allows us to fingerprint the battery SOC in real time. We further demonstrate that XES can be used to track the change in net spin of the probed atoms by analyzing changes in the emission peak shape. As a test case, the connection between net spin and the local chemical and structural environment was investigated by using XES and XAS in the case of electrochemically delithiated LCO in the range of 2-10% lithium removal.

유아동의 창의성 증진을 위한 영상매체 기반 미술놀이 콘텐츠 개발

Objectives The purpose of this study is to prove its suitability and effectiveness by developing contents for children that perform actual activities such as art activities along with video viewing.
 Methods For this, based on the narrative-based, case-based, and problem-based learning elements of contextual learning, a creative fairy tale, “The Postman Bobo”, was produced as a video. In addition, the contents were completed by designing an art activities program to be conducted after watching the video focusing on promoting creativity. After that, six children aged 8 to 10 at a child care institution in D area located in Gyeonggi-do were simulated for the application of the content in the field.
 Results First, the application of video media was effective in understanding the content and inducing voluntary participation before conducting the art activities program. Second, prior to conducting the art activities program, stories or elements that appeared in the video had a positive effect on leading to the art activities program, which had a significant effect on the connection between content and context learning. Third, the video media-based art activities contents was effective in that it was an activity that could have a positive effect on the creativity of children.
 Conclusions This study is meaningful in that it revealed that video media-based art activities program through linkage with context learning are effective in enhancing the creativity of children.

Dynamic Hyperspectral Holography Enabled by Inverse-Designed Metasurfaces with Oblique Helicoidal Cholesterics.

Metasurfaces are flat arrays of nanostructures that allow exquisite control of phase and amplitude of incident light. Although metasurfaces offer new active element for both fundamental science and applications, the challenge still remains to overcome their low information capacity and passive nature. Here, by integrating an inverse-designed-metasurface with oblique helicoidal cholesteric liquid crystal (ChOH), simultaneous spatial and spectral tunable metasurfaces with a high information capacity for dynamic hyperspectral holography, are demonstrated. The inverse design facilitates a single-phase map encoding of ten independent holographic images at different wavelengths. ChOH provides precise spectral modulation with narrow bandwidth and wide tunable regime in response to programmed stimuli, thus enabling dynamic switching of the multicolor holography. The results provide simple and generalizable principles for the rational design of interactive metasurfaces that will find numerous applications, including security platform.

Domain Dynamics and Resistive Switching in Ferroelectric Al1–xScxN Thin Film Capacitors

AbstractIn this paper, using a combination of pulse testing measurements and piezoresponse force microscopy (PFM), an investigation of the polarization reversal behavior and the accompanying resistive switching in the Al0.72Sc0.28N thin film capacitors is reported. The obtained results reveal a transition from the nucleation‐limited switching (NLS) in the low field range toward the more uniform switching described by the Kolmogorov–Avrami–Ishibashi (KAI) model in the high field range. It is found that the Al0.72Sc0.28N capacitors exhibit an unusually steep change in the switching time– it decreases by five orders of magnitude with a moderate increase of the applied field. This feature is caused by a significantly higher activation field value (≈126 MV cm−1) in comparison with the conventional perovskite ferroelectrics. PFM visualization of the field‐induced domain dynamics has allowed the evaluation of the nucleation rate and domain wall velocity. Furthermore, capacitors in the polydomain state generated by partial switching of polarization exhibit a significant (up to two orders of magnitude) increase in the steady‐state conductance. This effect is likely caused by the injection of strongly inclined conducting 180° domain walls. Resistance tunability offers additional functionalities to the Al1‐xScxN devices where conductive domain walls are used as active elements.

Deciphering the molecular and functional basis of TMexCD1: the plasmid-encoded efflux pump of resistance-nodulation-division superfamily.

Horizontal gene transfer has been demonstrated to be an important driver for the emergency of multidrug-resistant pathogens. Recently, a transferable gene cluster tmexCD1-toprJ1 of the resistance-nodulation-division (RND) superfamily was identified in the plasmids of animal-derived Klebsiella pneumoniae strains, with a higher efflux capacity for various drugs than the Escherichia coli AcrAB-TolC homolog system. In this study, we focused on the differences in the inner membrane pump of these two systems and identified some key residues that contribute to the robust efflux activity of the TMexCD1 system. With the aid of homologous modeling and molecular docking, eight residues from the proximal binding pocket (PBP) and nine from the distal binding pocket (DBP) were selected and subjected to site-directed mutagenesis. Several of them, such as S134, I139, D181, and A290, were shown to be important for substrate binding in the DBP region, and all residues in PBP and DBP showed certain substrate preferences. Apart from the conservative switch loop (L613-623TMexD1) previously identified in the E. coli AcrB (EcAcrB), a relatively unconservative loop (L665-675TMexD1) at the bottom of PBP was proposed as a critical element for the robust activity of TMexD1, due to variations at sites E669, G670, N673, and S674 compared to EcAcrAB, and the significantly altered efflux activity due to their mutations. The conservation and flexibility of these key factors can contribute to the evolution of the RND efflux pumps and thus serve as potential targets for developing inhibitors to block the widespread of the TMexCD1 system.

Закономерности в распределении химических элементов в листьях березы

Биологическая активность лекарственного растительного сырья и фитопрепаратов обусловлена комплексом биологически активных веществ и химических элементов. Исследование влияния условий призрастания на состав, содержание химических элементов в лекарственных растениях, лекарственном растительном сырье является актуальным. Особый интерес вызывает исследование закономерностей в распределении химических элементов в лекарственных растениях, лекарственном растительном сырье и возможность использования выявленных закономерностей для установления подлинности и чистоты сырья. Объект нашего исследования — листья березы, собранные в экологически чистой зоне и в зонах с различной степенью антропогенной нагрузки. Состав и содержание элементов анализировали методом ИСП–МС (масс-спектрометр ELAN DRC-е ICP-MS, оптико-эмиссионный спектрометр Agilent 715 ICP–OES). Статистическая обработка результатов химического анализа проведена в программе Microsoft ® Excel 2010. Сопоставление концентраций 60 элементов проводили с применением метода наименьших квадратов. Сравнительный анализ логарифмов концентраций в листьях березы, собранных из мест произрастания, различающихся по степени антропогенной нагрузки, показал сильную корреляционную связь между ними (r=0,99; R2=0,9). Диаграмма, отражающая периодическую зависимость логарифма концентраций химических элементов, представляет собой элементный профиль листьев березы и может быть использована для установления их подлинности и чистоты.

Shuttling Active Elements in and out of Ultrathin Nanowires: Toward Rational Design of Multicomponent Catalysts.

One-dimensional nanostructures, with a high ratio of surface-bulk atoms, find applications as active catalysts. Here, we report tunability in ultrathin single-crystalline AuPdPt nanowires by modifying synthesis conditions and postsynthetic treatment in a controlled ambient atmosphere. The surface microstructure modification of these nanostructures has been analyzed by integrating the results of three crucial techniques including Z-contrast HAADF-STEM imaging, X-ray photoelectron spectroscopy, and electrochemically active surface area from cyclic voltammograms.

Epigenetic profiling reveals key genes and cis-regulatory networks specific to human parathyroids

In all terrestrial vertebrates, the parathyroid glands are critical regulators of calcium homeostasis and the sole source of parathyroid hormone (PTH). Hyperparathyroidism and hypoparathyroidism are clinically important disorders affecting multiple organs. However, our knowledge regarding regulatory mechanisms governing the parathyroids has remained limited. Here, we present the comprehensive maps of the chromatin landscape of the human parathyroid glands, identifying active regulatory elements and chromatin interactions. These data allow us to define regulatory circuits and previously unidentified genes that play crucial roles in parathyroid biology. We experimentally validate candidate parathyroid-specific enhancers and demonstrate their integration with GWAS SNPs for parathyroid-related diseases and traits. For instance, we observe reduced activity of a parathyroid-specific enhancer of the Calcium Sensing Receptor gene, which contains a risk allele associated with higher PTH levels compared to the wildtype allele. Our datasets provide a valuable resource for unraveling the mechanisms governing parathyroid gland regulation in health and disease.

Expansion and improvement of ChinaMu by MuT-seq and chromosome-level assembly of the Mu-starter genome.

ChinaMu is the largest sequence-indexed Mutator (Mu) transposon insertional library in maize (Zea mays). In this study, we made significant improvements to the size and quality of the ChinaMu library. We developed a new Mu-tag isolation method Mu-Tn5-seq (MuT-seq). Compared to the previous method used by ChinaMu, MuT-seq recovered 1/3 more germinal insertions, while requiring only about 1/14 of the sequencing volume and 1/5 of the experimental time. Using MuT-seq, we identified 113,879 germinal insertions from 3,168 Mu-active F1 families. We also assembled a high-quality genome for the Mu-active line Mu-starter, which harbors the initial active MuDR element and was used as the pollen donor for the mutation population. Using the Mu-starter genome, we recovered 33,662 (15.6%) additional germinal insertions in 3,244 (7.4%) genes in the Mu-starter line. The Mu-starter genome also improved the assignment of 117,689 (54.5%) germinal insertions. The newly upgraded ChinaMu dataset currently contains 215,889 high-quality germinal insertions. These insertions cover 32,224 pan-genes in the Mu-starter and B73Ref5 genomes, including 23,006 (80.4%) core genes shared by the two genomes. As a test model, we investigated Mu insertions in the pentatricopeptide repeat (PPR) superfamily, discovering insertions for 92% (449/487) of PPR genes in ChinaMu, demonstrating the usefulness of ChinaMu as a functional genomics resource for maize.

Interconnect Stress Testing as a Tool for Assessment of Reliability of Modern PCBs

The of miniaturization can be seen in electronics for some time already. The pinout of active components grows enabling them to have additional functions. The trend in usage of System in a Package (SiP) solutions is also evident thus routing of the active and passive elements became also challenging. To overcome this challenge boards with High Density Interconnection (HDI) where not only through hole, but also different kinds of microvias e.g. blind, buried, stacked, staggered via are used. The standard procedure to test reliability of boards and assemblies is very resource-hungry especially in time and money, as the tests have to be carried out in climatic chambers which lasts for weeks, followed by additional destructive testing like cross-sections. On the other hand IST (Interconnect Stress Testing) is a quick test, that enables to have assessment of the used technology especially the quality of the through holes of all types. Although the coupons are destroyed during the test, it is not necessary to test the manufactured circuits. This saves both materials and time. The technology optimizations and the key findings will be presented within the paper.

Soft switching high step-up three-level boost DC-DC converter with Quasi Z-source for Photovoltaic application

A three-level Boost DC-DC converter is proposed in this paper. Quasi Z-source converter acts as an auxiliary circuit to create soft switching condition for all active elements. Consequently. The converter efficiency is very high. Using a three-level structure in the proposed converter causes the maximum voltage stress across the semiconductor devices is limited to half of the output voltage. The converter has a high voltage gain and a small number of elements. The converter is analyzed with details in all operating modes. Furthermore, the experimental results are obtained to prove the converter performance based on the theoretical considerations.

Silicon in prevention of atherosclerosis and other age-related diseases.

Researchers' interest in silicon as an element important for the functioning of the animal and human body began in the 1970s. Soluble compounds of silicon bioavailable from water and food seem to have important meaning for life processes occurring in the body. So far, researchers have focused on the significance of silicon for the development of bones and connective tissue, and its role in preventing neurodegenerative diseases and atherosclerosis. Despite numerous studies, the role of silicon as an active element in the human body is poorly understood. Since the involvement of lipid oxidation and inflammatory processes in the pathogenesis of atherosclerosis is well known, this article summarizes and discusses the current research and scientific observations regarding silicon, primarily in terms of its beneficial influence on redox and anti-inflammatory reactions and the lipid profile. The association of silicon with the stabilization of the structure of glycosaminoglycans and their protein complexes may also support the anti-atherosclerotic effect. The authors attempted to collect and present existing publications that could confirm the beneficial role of dietary silicon in the prevention of age-related diseases and explain the potential mechanisms of its action.

Higher-order Non-Hermitian skin effect in an acoustic lattice

Non-Hermitian physical systems offer a distinct band topology that gives rise to the interesting phenomenon known as the non-Hermitian skin effect (NHSE). However, the exploration of higher-order NHSE in classical wave systems by leveraging non-reciprocity has been largely unexplored. In this study, we introduce a novel approach to experimentally realize the higher-order NHSE in a two-dimensional non-reciprocal breathing acoustic Kagome lattice. This lattice is composed of acoustic cavities with non-reciprocal coupling achieved through electrically controlled active acoustic elements. We successfully observed second-order corner modes using a 3 × 3 lattice, which manifest as localized pressure distributions at specific frequencies in both parallelogram and triangular topological acoustic lattices. We delve into the underlying mechanisms and their implications, thereby paving the way for a deeper understanding of higher-order NHSE and potentially innovative applications rooted in the acoustic non-reciprocity.

Rummaging in the Attic: Queer Memories and Enduring Activism in the Attic Press/Róisín Conroy Collection

ABSTRACT: This hybrid narrative-historical essay relates the legacy of late-twentieth-century Irish women’s activism as it is documented through the Attic Press/Róisín Conroy Collection (RCC) housed at University College Cork, Ireland. While much of the historical discussion about this era of women’s activism focuses on the Irish Women’s Liberation Movement, in this essay, the author makes the case that the RCC actively presences Irish lesbian women’s activism. The essay highlights specific items in the archive which particularly emphasize the more mundane tasks required to power an enduring social justice movement because these actions are often overlooked in preference for the more obvious public-facing elements of activism. Throughout the piece, the author reflects on her position as an activist and scholar from outside of Ireland in relation to the archive and more recent demonstrations of Irish feminist activism. Ultimately, the history of Irish women’s and lesbian activism as documented by the RCC reminds readers of the need for collaboration and collective rage, thought, and pain. In the post-COVID-19 era, activists will be re-visioning the way they connect, share, care, and fight for justice.

A spatiotemporal deconvolution approach for measurements of therapeutic ultrasound pressures, intensities, and beamwidths

Complete characterization of high intensity focused ultrasound (HIFU) systems includes measurements of transmitted pressure at the focal plane with a hydrophone. However, highly focused, nonlinear HIFU beams can result in considerable spatial averaging artifacts due to finite area of the hydrophone active element. Spatiotemporal deconvolution (STD) can correct for hydrophone spatial averaging (Wear, IEEE Trans. UFFC 69, 1243–1256 (2021)]. The objective of the present work is to extend validation of STD from diagnostic levels (6 MPa) to therapeutic levels (49 MPa). Three HIFU transducers (1.45 MHz F/1, 1.53 MHz F/1.5, and 3.91 MHz F/1) were driven in tone bursts (Agilent HP3314A function generator, ENI 240L amplifier) to generate HIFU fields in a degassed, deionized water tank with focal compressional pressures of 49, 16, and 29 MPa. Fields were measured in focal planes with two hydrophones (Onda HFO 100-μm fiber-optic; Onda HNA-0400 400-μm robust needle). STD reduced inter-hydrophone differences from −18 ± 11% to 0 ± 8% (peak compressional pressure), −8 ± 4% to −5 ± 5% (peak rarefactional pressure), −20% ± 7% to −3 ± 8% (pulse intensity integral), and 21 ± 12% to −2 ± 3% (beam FWHM). STD reduces dependence of measurements on hydrophone active element size. STD reduces reliance on fiber optic hydrophones, which can be expensive, difficult to use, and prone to radiation-force-induced sensor misalignment.

The Mechanism of Fuzheng Xiaoji Decoction in the Treatment of Non-Small Cell Lung Cancer Based on Network Pharmacology and Molecular Docking Technology

With approximately 2 million lung cancer patients and 1.8 million deaths per year, the world ranks among the highest incidence rates in the world. Non-small cell lung cancer (NSCLC) accounts for up to 85% of lung cancer patients and has a poor prognosis. To investigate the mechanism of Fuzheng Xiaoji Decoction in the treatment of NSCLC. Fuzheng Xiaoji Decoction, consisting of ten traditional Chinese medicines, was analyzed using the TCMSP database to identify its active ingredients and their corresponding targets. Simultaneously, NSCLC-related targets were obtained from GeneCards. The study aimed to predict Fuzheng Xiaoji Decoction’s targets in treating NSCLC and establish a network diagram illustrating the relationship between traditional Chinese medicine, active ingredients, targets, and the disease. The STRING platform was used to construct a PPI network, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis and Gene Ontology (GO) function enrichment analysis were performed on the intersecting targets. Based on the interaction network analysis, the core target proteins, represented by the TOP5 nodes with the highest degrees, were selected. These core targets were then subjected to molecular docking with the top five key active components of Fuzheng Xiaoji Decoction to construct the docking model. We identified 132 active components in Fuzheng Xiaoji Decoction and picked the TOP 5 proteins from the PPI network as the primary active elements in Fuzheng Xiaoji Decoction for NSCLC treatment, including kaempferol, quercetin, ingenin, luteolin, and osterol, involving a total of 209 targets. The top five core targets obtained by PPI network were AKT1, TP53, STAT3, TNF and IL6. A total of 7879 targets related to NSCLC were retrieved, and 164 drug-disease intersection targets were identified. GO functional analysis results showed that 164 gene sets were involved in 377 biological processes, mainly involved in 79 processes related to cell composition and 46 molecular function expression processes. KEGG enrichment results showed 132 significantly enriched signaling pathways. Molecular docking findings indicated favorable binding interactions between the receptor and ligand, suggesting a strong affinity between the key NSCLC treatment protein and the primary active ingredient in Fuzheng Xiaoji Decoction. The potential mechanism of Fuzheng Xiaoji Decoction in NSCLC treatment may involve flavonoids, triterpenoids and other compounds regulate lung cancer-related signaling pathways by acting on AKT1, TP53, STAT3 and other proteins to affect the expression of P53, IL6 and other cytokines. This may help regulate immune function and inhibit tumor cell proliferation.

The social media use of college students: Exploring identity development, learning support, and parallel use

Social media has a strong influence on the everyday lives of college students. A particular question of advanced research interest is whether social media also play a role when attending class. This exploratory study was aimed at designing a theoretical model that embraces such concepts. First, we identified that identity development, learning support, and parallel use are general concepts that are relevant when attending class. Next, using a survey with 230 students, we examined whether these general concepts could be empirically validated with factor and correlation analyses. We then applied a literature review to identify and subordinate more specific concepts to these general concepts. The resulting model of social media use when attending class includes active and passive elements related to designing and registering personal information, giving and getting support for learning, as well as posting and browsing during parallel use. We offer three conclusions: (1) identity development is based on impression management, social comparison, and self-concept clarifying, (2) learning support consists of collaborative learning, supporting intrinsic motivation, and promoting self-efficacy, and (3) parallel use during learning is based on entertainment, escapism, and relaxation. Finally, we discuss limitations, especially missing model tests, future research activities, and practical implications of our conceptual model.