bluuebunny/crossref_metadata_2025 huggingface dataset:
Amendment with Burkina Faso phosphate rock-enriched composts alters soil chemical properties and microbial structure, and enhances sorghum agronomic performance
Authors: Sagnon Adama , Iwasaki Shinya , Tibiri Ezechiel Bionimian , Zongo Nongma Armel , Compaore Emmanuel , Bonkoungou Isidore Juste O. , Nakamura Satoshi , Traore Mamoudou , Barro Nicolas , Tiendrebeogo Fidele , Sarr Papa Saliou
Published: August 2022

Low soil available phosphorus (P) severely limits crop production in sub-Saharan Africa. The present study evaluated phosphate rock-enriched composts as locally available low-cost fertilizers for sorghum production. The treatments consisted of sorghum straw, compost (COMP), phosphate rock (BPR), BPR-enriched compost (P-COMP), BPR-rhizosphere soil-enriched compost (P-COMP-SOIL), nitrogen-phosphorus-potassium treatment (NPK, 60–39–25), and control (NK, 60–25). Sorghum straw and compost were applied at 1.34 tons ha−1. N, P, and K in all treatments, excluding the control, were adjusted to 60, 39, and 25 kg ha−1, with urea, BPR, and KCl, respectively. Sorghum vr. kapelga was cultivated and soil samples were collected at the S5, S8, and S9 growth stages. P-COMP-SOIL and NPK yielded better sorghum yields than the other treatments. The rhizosphere soil of P-COMP-SOIL had high abundance of soil bacteria and AMF, and genes involved in P solubilization, such as: acid phosphatase (aphA), phosphonatase (phnX), glucose dehydrogenase (gcd), pyrroloquinoline quinone (pqqE), phosphate-specific transporter (pstS). The superior performance of the P-COMP-SOIL was associated with its higher available P content and microbial abundance. Multivariate analysis also revealed vital contributions of N, carbon, and exchangeable cations to sorghum growth. Soils could be amended with phosphate rock-rhizosphere soil-enriched composts, as an alternative to chemical fertilizers.
Synaptic branch stability is mediated by non-enzymatic functions of MEC-17/αTAT1 and ATAT-2
Authors: Teoh Jean-Sébastien , Vasudevan Amruta , Wang Wenyue , Dhananjay Samiksha , Chandhok Gursimran , Pocock Roger , Koushika Sandhya P. , Neumann Brent
Published: August 2022

Microtubules are fundamental elements of neuronal structure and function. They are dynamic structures formed from protofilament chains of α- and β-tubulin heterodimers. Acetylation of the lysine 40 (K40) residue of α-tubulin protects microtubules from mechanical stresses by imparting structural elasticity. The enzyme responsible for this acetylation event is MEC-17/αTAT1. Despite its functional importance, however, the consequences of altered MEC-17/αTAT1 levels on neuronal structure and function are incompletely defined. Here we demonstrate that overexpression or loss of MEC-17, or of its functional paralogue ATAT-2, causes a delay in synaptic branch extension, and defective synaptogenesis in the mechanosensory neurons of Caenorhabditis elegans. Strikingly, by adulthood, the synaptic branches in these animals are lost, while the main axon shaft remains mostly intact. We show that MEC-17 and ATAT-2 regulate the stability of the synaptic branches largely independently from their acetyltransferase domains. Genetic analyses reveals novel interactions between both mec-17 and atat-2 with the focal adhesion gene zyx-1/Zyxin, which has previously been implicated in actin remodelling. Together, our results reveal new, acetylation-independent roles for MEC-17 and ATAT-2 in the development and maintenance of neuronal architecture.
Evaluation of antimicrobial resistance and risk factors for recovery of intrauterine Escherichia coli from cows with metritis on California commercial dairy farms
Authors: Basbas Carl , Garzon Adriana , Silva-del-Rio Noelia , Byrne Barbara A. , Karle Betsy , Aly Sharif S. , Champagne John D. , Williams Deniece R. , Lima Fabio S. , Machado Vinicius S. , Pereira Richard V.
Published: August 2022

The goals of this study were to evaluate factors affecting recovery and antimicrobial resistance (AMR) in intrauterine E. coli in post-partum dairy cows with and without metritis from commercial California dairy farms. Using a cross-sectional study design, a total of 307 cows were sampled from 25 farms throughout California, from which a total of 162 intrauterine E. coli isolates were recovered. During farm visits, cows within 21 days post-partum were categorized in one of three clinical presentation groups before enrollment: metritis (MET, n = 86), defined as a cow with watery, red or brown colored, and fetid vaginal discharge; cows with purulent discharge (PUS, n = 106), defined as a non-fetid purulent or mucopurulent vaginal discharge; and control cows, (CTL, n = 115) defined as cows with either no vaginal discharge or a clear, non-purulent mucus vaginal discharge. Cows diagnosed as MET had significantly higher odds for recovery of E. coli compared to cows diagnosed as CTL (OR = 2.16, 95% CI: 1.17–3.96), with no significant difference observed between PUS and CTL, and PUS and MET. An increase in days in milk (DIM) at the time of sampling was significantly associated with a decrease in the odds ratio for E. coli recovery from intrauterine swabs (OR = 0.94, 95% CI: 0.89–0.98). All intrauterine E. coli were resistant to ampicillin (AMP), with an AMR prevalence of 30.2% and 33.9% observed for chlortetracycline and oxytetracycline, respectively. Only 8.6% of isolates were resistant to ceftiofur (CEFT), one of the most common drugs used to treat cows on farms sampled. No significant difference in the prevalence of AMR was observed among clinical groups at the individual cow level. At the farm level, a significantly higher odds for isolating intrauterine E. coli resistant to chlortetracycline (OR: 2.6; 95% CI: 3.7–58.0) or oxytetracycline (OR: 1.9; 95% CI: 1.4–33.8) was observed at farms that used an intrauterine infusion of oxytetracycline as a treatment for metritis when compared to those farms that did not use this practice. Findings from this study indicate the need for further research supporting a broader understanding of farm practices driving AMR in cows with metritis, as well as data to increase the accuracy of breakpoints for AMR classification of intrauterine E. coli from cattle.
Investigation of pathogenesis of hyperuricemia based on untargeted and targeted metabolomics
Authors: Qin Nankun , Qin Ming , Shi Wenjun , Kong Lingbo , Wang Liting , Xu Guang , Guo Yuying , Zhang Jiayu , Ma Qun
Published: August 2022

Hyperuricemia (HUA) seriously harms human health but the exact etiology and pathogenesis of HUA are not fully understood. Therefore, it is still of great significance to find effective biomarkers and explore the pathogenesis of HUA. Metabolomics reflects the influence of internal and external factors on system metabolism, explains the changes in metabolite levels during the development of diseases, and reveals the molecular mechanism of pathogenesis. Metabolomics is divided into untargeted metabolomics and targeted metabolomics according to different research modes. Each other's advantages can be fully utilized by combining the two so that the results of metabolomics research can be consummated. 20 HUA patients and 20 healthy individuals participated in the experiment, and untargeted metabolomics was employed to find 50 differential metabolites in HUA serum samples. Twelve candidate biomarkers were screened based on literature research and ROC Curve analysis for subsequent verification. Based on the UPLC-TQ-MS analysis platform, the targeted metabolomics detection methods were established and the content of 12 candidate biomarkers was precisely quantified. Compare with the results of untargeted metabolomics, the targeted metabolomics results were considered more reliable.
Salidroside alleviates hepatic ischemia–reperfusion injury during liver transplant in rat through regulating TLR-4/NF-κB/NLRP3 inflammatory pathway
Authors: Liu Yanyao , Lei Zilun , Chai Hao , Kang Quan , Qin Xiaoyan
Published: August 2022

Salidroside has anti-inflammatory, antioxidant and hepatoprotective properties. However, its effect on hepatic ischemia–reperfusion injury (IRI), an unavoidable side effect associated with liver transplantation, remains undefined. Here, we aimed to determine whether salidroside alleviates hepatic IRI and elucidate its potential mechanisms. We used both in vivo and in vitro assays to assess the effect and mechanisms of salidroside on hepatic IRI. Hepatic IRI rat models were pretreated with salidroside (5, 10 or 20 mg/kg/day) for 7 days following liver transplantation while hypoxia/reoxygenation (H/R) model of RAW 264.7 macrophages were pretreated with salidroside (1, 10 or 50 μM). The effect of salidroside on hepatic IRI was assessed using hematoxylin–eosin staining, terminal deoxynucleotidyl transferase dUTP nick-end labeling staining, qRT-PCR, immunosorbent assay and western blotting. Our in vivo assays showed that salidroside significantly reduced pathological liver damage, serum aminotransferase levels and serum levels of IL-1, IL-18 and TNF-α. Besides, salidroside reduced the expression of TLR-4/NF-κB/NLRP3 inflammatory pathway associated proteins (TLR-4, MyD88, p-IKKα, p-IKKβ, p-IKK, p-IκBα, p-P65, NLRP3, ASC, Cleaved caspase-1, IL-1β, IL-18, TNF-α and IL-6) in rats after liver transplantation. On the other hand, data from the in vitro analysis demonstrated that salidroside blocks expression of TLR-4/NF-κB/NLRP3 inflammatory pathway related proteins in the RAW264.7 cells treated with H/R. The salidroside-specific anti-inflammatory effects were partially inhibited by the TLR-4 agonist lipopolysaccharide. Taken together, our study showed that salidroside inhibits hepatic IRI following liver transplantation by modulating the TLR-4/NF-κB/NLRP3 inflammatory pathway.
Comparative analysis of the plastid and mitochondrial genomes of Artemisia giraldii Pamp.
Authors: Yue Jingwen , Lu Qianqi , Ni Yang , Chen Pinghua , Liu Chang
Published: August 2022

Artemisia giraldii Pamp. is an herbaceous plant distributed only in some areas in China. To understand the evolutionary relationship between plastid and mitochondria in A. giraldii, we sequenced and analysed the plastome and mitogenome of A. giraldii on the basis of Illumina and Nanopore DNA sequencing data. The mitogenome was 194,298 bp long, and the plastome was 151,072 bp long. The mitogenome encoded 56 genes, and the overall GC content was 45.66%. Phylogenetic analysis of the two organelle genomes revealed that A. giraldii is located in the same branching position. We found 13 pairs of homologous sequences between the plastome and mitogenome, and only one of them might have transferred from the plastid to the mitochondria. Gene selection pressure analysis in the mitogenome showed that ccmFc, nad1, nad6, atp9, atp1 and rps12 may undergo positive selection. According to the 18 available plastome sequences, we found 17 variant sites in two hypervariable regions that can be used in completely distinguishing 18 Artemisia species. The most interesting discovery was that the mitogenome of A. giraldii was only 43,226 bp larger than the plastome. To the best of our knowledge, this study represented one of the smallest differences between all sequenced mitogenomes and plastomes from vascular plants. The above results can provide a reference for future taxonomic and molecular evolution studies of Asteraceae species.
Convolution neural network with batch normalization and inception-residual modules for Android malware classification
Authors: Liu TianYue , Zhang HongQi , Long HaiXia , Shi Jinmei , Yao YuHua
Published: August 2022

Deep learning technology is changing the landscape of cybersecurity research, especially the study of large amounts of data. With the rapid growth in the number of malware, developing of an efficient and reliable method for classifying malware has become one of the research priorities. In this paper, a new method, BIR-CNN, is proposed to classify of Android malware. It combines convolution neural network (CNN) with batch normalization and inception-residual (BIR) network modules by using 347-dim network traffic features. CNN combines inception-residual modules with a convolution layer that can enhance the learning ability of the model. Batch Normalization can speed up the training process and avoid over-fitting of the model. Finally, experiments are conducted on the publicly available network traffic dataset CICAndMal2017 and compared with three traditional machine learning algorithms and CNN. The accuracy of BIR-CNN is 99.73% in binary classification (2-classifier). Moreover, the BIR-CNN can classify malware by its category (4-classifier) and malicious family (35-classifier), with a classification accuracy of 99.53% and 94.38%, respectively. The experimental results show that the proposed model is an effective method for Android malware classification, especially in malware category and family classifier.
Fuel cell performance improvement via the steric effect of a hydrocarbon-based binder for cathode in proton exchange membrane fuel cells
Authors: Cha Jung-Eun , Cho Won Jae , Hwang Jeemin , Seo Dong-Jun , Choi Young-Woo , Kim Won Bae
Published: August 2022

In this study, a sulfonated poly(ether sulfone) having cardo-type fluorenyl groups (FL-SPES) was investigated as a cathodic binder to improve fuel cell performance via increased the oxygen diffusion in the cathode. The maximum power density achieved by using the membrane electrode assembly (MEA) prepared with FL-SPES with a low ion exchange capacity (IEC) of 1.31 meq g–1 was 520 mW cm–2, which is more than twice as high as that of BP-SPES (210 mW cm–2) having typical biphenyl groups with a similar IEC. At high IEC of 1.55 meq g–1, the power density obtained by using BP-SPES was improved to 454 mW cm–2 but remained lower than that of FL-SPES. In addition, although the IEC, swelling degree, and specific resistance were similar to each other, the gas permeability of FL-SPES was improved by approximately three times compared to that of BP-SPES. The steric structure of cardo-type FL-SPES increased the free volume between the polymer backbones, leading to an increase in gas transfer. Consequently, oxygen diffusion was promoted at the cathode, resulting in improved fuel cell performance.
Towards phase-stabilized Fourier domain mode-locked frequency combs
Authors: Grill Christin , Blömker Torben , Schmidt Mark , Kastner Dominic , Pfeiffer Tom , Kolb Jan Philip , Draxinger Wolfgang , Karpf Sebastian , Jirauschek Christian , Huber Robert
Published: August 2022

Fourier domain mode-locked (FDML) lasers are some of the fastest wavelength-swept light sources, and used in many applications like optical coherence tomography (OCT), OCT endoscopy, Raman microscopy, light detection and ranging, and two-photon microscopy. For a deeper understanding of the underlying laser physics, it is crucial to investigate the light field evolution of the FDML laser and to clarify whether the FDML laser provides a frequency comb structure. In this case, the FDML would output a coherent sweep in frequency with a stable phase relation between output colours. To get access to the phase of the light field, a beat signal measurement with a stable, monochromatic laser is performed. Here we show experimental evidence of a well-defined phase evolution and a comb-like structure of the FDML laser. This is in agreement with numerical simulations. This insight will enable new applications in jitter-free spectral-scanning, coherent, synthetic THz-generation and as metrological time-frequency ruler.
Temporal lineage replacements and dominance of imported variants of concern during the COVID-19 pandemic in Kenya
Authors: Kimita Gathii , Nyataya Josphat , Omuseni Esther , Sigei Faith , Lemtudo Alan , Muthanje Eric , Andika Brian , Liyai Rehema , Githii Rachel , Masakwe Clement , Ochola Stephen , Awinda George , Kifude Carol , Mutai Beth , Gatata Robert M. , Waitumbi John
Published: August 2022

Background

Kenya’s COVID-19 epidemic was seeded early in March 2020 and did not peak until early August 2020 (wave 1), late-November 2020 (wave 2), mid-April 2021 (wave 3), late August 2021 (wave 4), and mid-January 2022 (wave 5).

Methods

Here, we present SARS-CoV-2 lineages associated with the five waves through analysis of 1034 genomes, which included 237 non-variants of concern and 797 variants of concern (VOC) that had increased transmissibility, disease severity or vaccine resistance.

Results

In total 40 lineages were identified. The early European lineages (B.1 and B.1.1) were the first to be seeded. The B.1 lineage continued to expand and remained dominant, accounting for 60% (72/120) and 57% (45/79) in waves 1 and 2 respectively. Waves three, four and five respectively were dominated by VOCs that were distributed as follows: Alpha 58.5% (166/285), Delta 92.4% (327/354), Omicron 95.4% (188/197) and Beta at 4.2% (12/284) during wave 3 and 0.3% (1/354) during wave 4. Phylogenetic analysis suggests multiple introductions of variants from outside Kenya, more so during the first, third, fourth and fifth waves, as well as subsequent lineage diversification.

Conclusions

The data highlights the importance of genome surveillance in determining circulating variants to aid interpretation of phenotypes such as transmissibility, virulence and/or resistance to therapeutics/vaccines.
Theory and Applications of NMR Spectroscopy in Biomolecular Structures and Dynamics of Proteins
Authors: Chandra Kousik , Emwas Abdul Hamid , Al-Harthi Samah , Al-Talla Zeyad , Hajjar Dina , Makki Arwa Abdulaziz , Khouqeer Ghada , Jaremko Mariusz
Published: August 2022

Structural biology has come a long way since the first inception of multidimensional NMR. The dipole–dipole interaction between two spatially closed spins provides a powerful tool to probe macromolecules’ three-dimensional (3D) structure, such as proteins. However, the main challenge for macromolecules is to assign the NMR chemical shifts of all signals of the investigated protein. This chapter presents different 3D triple-resonance NMR experiments dedicated to assignments of NMR signals of protein backbone structure. In addition, the through-space correlation experiments, namely NOESY, ROESY, and HOESY, are presented with detailed information about the advantages and limitations of each. The main strength of NMR lies in obtaining molecular structures under natural conditions and detailed information on the molecular dynamics at different timescales. The detailed characterization of sub-nanosecond segmental motions in proteins was characterized long before the advent of the first solution structure by NMR. Herein, the basic concept behind structure determination and elucidating protein dynamics on different timescales is presented. This chapter also highlights the NMR methodologies regarding characterizing sparsely populated protein conformations and transient states, vital for macromolecular functions.
Protein Backbone and Side-chain 15N Spin Relaxation Techniques to Study Biomacromolecular Interactions
Authors: Kharchenko V. , Ejchart A. , Jaremko L.
Published: August 2022

Biomacromolecular dynamics studies based on 15N spin relaxation are well established among the atomic-level structural biology techniques, accessing molecular mobility at a wide range of time scales spanning over ten orders of magnitude. The 15N labelling constitutes the simplest, most accessible, stable isotope labelling strategy for numerous proteins and nucleic acids. Therefore, it has become a convenient method to experimentally target the atomic and sub-atomic levels of molecular mobility. Here we present the currently available experimental techniques to access the dynamics of the protein backbone and side-chains, and the numerical methods of interpretation. The complexity of molecular motional models has led to separate measurements and interpretation of the dynamics for well-folded globular proteins and domains, highly dynamic, flexible, intrinsically disordered regions, and entirely flexible, intrinsically disordered proteins. In addition, separate approaches have been developed to detect and interpret the mobility of various amino acid side-chains. The advantages and limitations of the available tools and the emerging need for a more in-depth understanding of molecular functional dynamics are discussed.
NMR-based Ligand–Receptor Interaction Studies under Conventional and Unconventional Conditions
Authors: Ciaramelli C. , Palmioli A. , Airoldi C.
Published: August 2022

Many biologically relevant molecular recognition processes are highly dynamic and rely on the equilibrium between ligands’ association and dissociation from their receptor(s), because of the reversible nature of the majority of them. Over the last few decades, several NMR experiments allowing the characterization of these interactions have been developed. They are very useful tools for the study of naturally occurring binding events, but also for the screening of both natural and synthetic compounds that, through the interaction with relevant targets, can exert biological and pharmacological activities. The aim of this chapter is to provide a general presentation of the most commonly used NMR experiments based on ligand resonance observation, together with the descriptions of specific examples of their advanced applications in the analysis of unconventional samples, such as those containing complex compound mixtures, multivalent ligands, liposomes, nanoparticles and living cells.
Multi-frequency Saturation Transfer Difference NMR to Characterize Weak Protein–Ligand Complexes
Authors: Monaco Serena , Angulo Jesús
Published: August 2022

Weak protein–ligand interactions have been demonstrated to play key roles in biological processes, particularly in those involving quick cellular responses after certain stimuli (e.g. signal transduction). Although powerful biophysical techniques are available to gain high-resolution structural information of protein–ligand complexes of high affinity, NMR spectroscopy has been demonstrated to stand out among them for protein–ligand studies within the limit of weak affinity. In particular, ligand-based NMR techniques allow the detection and quantification of weak biomolecular binding processes, where saturation transfer difference (STD) NMR techniques have demonstrated through the years their strong ability to not only detect binding processes but also to provide structural information about the ligand mode of binding in the receptor-binding pocket, a highly valuable piece of information for the further development of enhanced binders along the process of drug discovery. This is particularly useful in fragment-based drug-discovery approaches, where the binding of the identified initial small fragments tends to fall within the low affinity range of the spectrum. In this chapter we briefly introduce the different classical STD NMR approaches, and later focus in detail on novel developments based on multi-frequency STD NMR experiments, which expand further the analytical capabilities of STD NMR, exemplified by the DEEP-STD NMR protocol, by providing also some key information on the nature of the protein residues in contact with the ligands in the bond state.
Dynamics of Protein–Nanoparticle Interactions Using NMR
Authors: Brahmkhatri Varsha , Atreya Hanudatta S.
Published: August 2022

The rapid advancement in nanoparticle-based therapeutics and their presence as diagnostic probes, drug-delivery systems, biosensors, and many others proposes the imperative need to understand and investigate the bio–nanointerfaces. Recently various novel nanoparticles with unique properties with different shapes, sizes and functionalities have arisen for diverse biomedical applications. Although the activities of nanoparticles as therapeutic agents are investigated in detail, the nature of their interactions with biological systems remains poorly understood. The interactions of nanoparticles with biological entities like proteins can be explored by various spectroscopic and non-spectroscopic techniques. Amongst these, solution NMR spectroscopy is an established technique to investigate the protein structure, dynamics and confirmational changes, however its applications in protein–nanoparticle interaction studies are only occasional and highly challenging. Therefore, this chapter is intended to provide readers with comprehensive information about protein–nanoparticle interactions, various characterization techniques and special emphasis on solution NMR spectroscopy to study the transient interactions between various nanoparticle systems (gold, silver, silica, polymer, carbon and lipid based) with proteins.
Structure- and Dynamics-guided Drug Development Using NMR and its Application to Diverse Pharmaceutical Modalities
Authors: Takeuchi Koh
Published: August 2022

Nuclear magnetic resonance (NMR) has the unique strength to provide quantitative dynamics information of the systems of interest at atomic resolution under various physiological conditions. Taking advantage of these unique characteristics, solution-state NMR spectroscopy has unveiled the functional dynamics of biological systems and now opens a new avenue to advanced structure-guided drug development that actively utilizes conformational dynamics information. Conformational dynamics revealed by NMR have been utilized to develop better ligands with preferable thermodynamics and kinetics. In addition, the characteristics of conformational dynamics information from NMR are suitable to promote the development of new pharmaceutical modalities, such as biomedicines and medium-size molecules. These new modalities are intrinsically more flexible than small molecule ligands and thus require non-destructive measurements under physiological conditions. Toward this end, we overview recent developments in NMR strategies and the applications of the NMR techniques for higher-ordered structure analysis of biopharmaceuticals, improvement of protein druggability, and understanding the cell permeabilization activity of medium-size molecules. We also discuss a future perspective toward in vivo structure-guided drug development based on the structure and dynamics analysis using in-cell NMR techniques.
Membranes, Minerals and Magnets: Application of NMR Spectroscopy to Biological Interfaces
Authors: Kent J. E. , Shin K. , Marassi F. M.
Published: August 2022

Nuclear magnetic resonance (NMR) spectroscopy is a powerful technique for studying the structures and interactions of macromolecules and their assemblies with atomic resolution. It is the premier technology for characterizing the complex biology occurring at interfacial regions, a challenging task where samples are often not amenable for X-ray crystallography or electron microscopy (EM) methods. This chapter describes examples of the successful application of NMR spectroscopy to complex biological systems ranging from membrane-embedded proteins to mineral-associated proteins and describes advancements in the field to obtain native and near-native systems.
Solid-state NMR Shows That the Structure and Dynamics of Specific Residues in the Membrane Receptor CXCR1 Are Altered by Interactions with Specific Residues in Its Agonist IL-8
Authors: Rai R. K. , De Angelis A. A. , Park S. H. , Berkamp S. , Opella S. J.
Published: August 2022

The recruitment and activation of neutrophils are essential steps in the immune response. These actions are triggered by the release of chemokines that direct the neutrophils to the affected site where they combat inflammation and kill bacteria. Here we utilize the example of chemokine interleukin-8 (IL-8) interacting with the G protein-coupled receptor CXCR1 to demonstrate the use of NMR spectroscopy to describe key protein components of the immune system in terms of their structures, dynamics, and molecular interactions within membrane bilayers. The IL-8 binding site in CXCR1 is often envisioned as being comprised of two distinct parts of the receptor: Binding Site-I is associated with the receptor's flexible N-terminal domain and Binding Site-II is associated with the second and third extracellular loops near the middle of the 350-residue polypeptide. We also describe how the dynamics of 1TM-CXCR1, a CXCR1 construct consisting of the N-terminal residues 1–72, change upon interaction with IL-8. Most of the residues in the flexible N-terminal domain undergo chemical shift perturbations; residues 1–37 also undergo changes in dynamics upon binding the chemokine. Little evidence of changes was observed in residues located more distal to the N-terminus in the first transmembrane helix of the receptor. These interpretations are possible because of the foundation laid by previous results, which determined the three-dimensional structures of IL-8 and CXCR1, characterized the global and local dynamics of both proteins, and described how their structures and dynamics are affected by their interactions.
High-resolution NMR Studies of Antibiotics in Membranes
Authors: Derks Maik , Smid Leanna , Kumar Raj , Becker Lea Marie , Shukla Rhythm , Breukink Eefjan , Weingarth Markus
Published: August 2022

The rapid rise of antimicrobial resistance calls for the development of new antibiotics. Ideal templates for next-generation antibiotics could be drugs that target the cell wall precursor, Lipid II, with vancomycin, nisin, or teixobactin being well-known examples. In this chapter the authors review a selection of NMR studies on the mode of action of Lipid II-binding antibiotics with an emphasis on solid-state NMR findings in lipid membranes that are vital to obtain physiologically relevant drug-binding modes.
The Lipid Phase of the Stratum Corneum Studied by Solid-state NMR: A Not So Rigid Barrier
Authors: Engberg Oskar , Huster Daniel
Published: August 2022

The lipid phase of the stratum corneum (SC), the outermost layer of mammalian skin, represents a unique assembly of lipids organized in stacked layers representing the most important permeation barrier to protect the body from excessive water loss. What makes this lipid assembly so unique is the fact that its main molecular species are represented by ceramides of varying chain lengths, free fatty acids, and cholesterol. Also, the packing and lateral organization of these lipids is quite special, forming short and long periodicity phases of densely packed lipids in an orthorhombic phase at very low hydration. Most lipids are considered to be highly rigid in this assembly. Recent biophysical investigations have revealed that some lipid segments are more dynamic than originally assumed, giving rise to a reconsideration of the current models of the SC lipid phase. This chapter summarizes the NMR view of the SC lipid phase. We also discuss modifications of the rigid lipid phase model considering more mobile lipid segments within the rigid SC lipid phase and possibly dynamic domain formation.
Engineering of small molecular organic nanoparticles for mitochondria-targeted mild photothermal therapy of malignant breast cancers
Authors: Hu Qinglian , He Chao , Lu Zhuoting , He Ying , Xie Hui , Li Jingyu , Fu Zhengwei , Guo Bing
Published: August 2022

Mitochondria-targeted mild photothermal therapy provides opportunities for regulating cell apoptosis and autophagy via localized minimal-invasive mild photothermal treatment.
The effect of halogenated spacer cations on structural symmetry-breaking in 2D halide double perovskites
Authors: Siwach Puneet , Sikarwar Poonam , Rajput Shubham Ajaykumar , Antharjanam Sudhadevi , Chandiran Aravind Kumar
Published: August 2022

Herein, we present a strategy to introduce above-room temperature non-centrosymmetry into two-dimensional halide double perovskites (A′4M′M′′X8) using a halogenated A′-site organic linker, 3-chloro/bromo propyl amine.
Dual amplification of a bio-barcode and auto-cycling primer extension for highly sensitive detection of miRNA
Authors: Xie Nuli , Wang Huimin , Li Jing , Wang Kemin , Huang Jin
Published: August 2022

A dual amplification strategy for the sensitive detection of miRNA targets in complex biological samples is proposed based on the bio-barcode technique (BCA) and auto-cycling primer extension (APE).
New venues in electron density analysis
Authors: Landeros-Rivera Bruno , Gallegos Miguel , Munárriz Julen , Laplaza Rubén , Contreras-García Julia
Published: August 2022

Advanced electron density-based descriptors for obtaining chemical information are addressed. Three of the most important sources for obtaining them are discussed: quantum mechanical calculations, machine learning and X-ray diffraction experiments.
Tailored ternary hydrophobic deep eutectic solvents for synergistic separation of yttrium from heavy rare earth elements
Authors: Ni Shuainan , Gao Yun , Yu Guisu , Zhang Sijia , Zeng Zhiyuan , Sun Xiaoqi
Published: August 2022

Clean, efficient and economical separation of yttrium (Y) from heavy rare earth elements (HREEs) has always attracted attention.
XRFast a new software package for processing of MA-XRF datasets using machine learning
Authors: Vermeulen Marc , McGeachy Alicia , Xu Bingjie , Chopp Henry , Katsaggelos Aggelos , Meyers Rebecca , Alfeld Matthias , Walton Marc
Published: August 2022

XRFast is a new software package written in Julia to decompose XRF imaging dataset.
Ultra-trace Hg determination in crude oils by CV-ICP-MS: overcoming the limitations of sample preparation to determine sub-ppb levels
Authors: Druzian Gabriel T. , Nascimento Mariele S. , Picoloto Rochele S. , Mesko Marcia F. , Flores Erico M. M. , Mello Paola A.
Published: August 2022

A method was developed to determine Hg in crude oil at sub-ppb levels by cold vapor generation inductively coupled plasma mass spectrometry (CV-ICP-MS) after wet digestion in a microwave-assisted system with a pressurized cavity.
Femtosecond induced third-order optical nonlinearity in quasi 2D Ruddlesden–Popper perovskite film deciphered using Z-scan
Authors: Mushtaq Aamir , Pradhan Bapi , Kushavah Dushyant , Zhang Yiyue , Naumenko Denys , Amenitsch Heinz , Hofkens Johan , Pal Suman Kalyan
Published: August 2022

A quasi 2D Ruddlesden–Popper perovskite, (PEA)2Cs4Pb5Br16 exhibits superior third-order nonlinear optical properties, which is promising for the development of ultrafast photonic devices.
Moisture-sensitive mechanical metamaterials with unusual and re-programmable hygroscopic deformation modes
Authors: Bai Yisong , Liu Chuanbao , Li Yang , Li Jinxu , Qiao Lijie , Zhou Ji , Bai Yang
Published: August 2022

We design 2D moisture-sensitive mechanical metamaterials with unusual hygroscopic deformation modes and re-programmable capability, providing a route of tunable hygroscopic expansion for applications responding to moisture.
Shape dependent sensing potential of gold nanoparticles in etching based multicolorimetric plasmonic-ELISA
Authors: Yadav Sangeeta , Satija Jitendra
Published: August 2022

Assessment of three different shapes of gold nanoparticles (AuNPs), viz. nanorods (AuNRs), nanotriangles (AuNTs), and nanospheres (AuNSs), towards the development of horseradish peroxidase (HRP) enzyme-mediated etching-based plasmonic ELISA strategy.
A new chromone-based fluorescent probe for ratiometric detection of Pd2+
Authors: Naskar Rahul , Gharami Saswati , Mandal Subrata , Mondal Tapan Kumar
Published: August 2022

A new chromone-based fluorescent probe (HMPM) is developed for the selective detection of Pd2+.
Sustainable synthesis of pyrazoles using alcohols as the primary feedstock by an iron catalyzed tandem C–C and C–N coupling approach
Authors: Mondal Rakesh , Guin Amit Kumar , Pal Subhasree , Mondal Sucheta , Paul Nanda D.
Published: August 2022

We report two new efficient iron-catalyzed synthetic strategies for multicomponent synthesis of tri-substituted pyrazoles using biomass-derived alcohols as the primary feedstock.
The incipient denaturation mechanism of DNA
Authors: Xu Min , Dai Tinghui , Wang Yanwei , Yang Guangcan
Published: August 2022

The persistent length of DNA decreases significantly by adding small amount of DMSO. Local DNA denaturation occurs even at very low DMSO concentration, which can be observed by atomic force microscopy directly.
Compositional and structural control in LLZO solid electrolytes
Authors: Parascos Kade , Watts Joshua L. , Alarco Jose A. , Chen Yan , Talbot Peter C.
Published: August 2022

Enhanced precursor homogeneity is achieved through a novel solution-based synthesis approach to enable precise control over material structure and composition.
β-cyclodextrin dendritic derivatives as permeation mediators to enhance the in vitro albendazole cysticidal activity by the improvement of the diffusion component
Authors: López-Méndez Luis José , Palomares-Alonso Francisca , González-Hernández Iliana , Jung-Cook Helgi , Cabrera-Quiñones Neyra Citlali , Guadarrama Patricia
Published: August 2022

βCD dendritic derivatives are stable and suitable nanocarriers to enhance ABZ potency by improving solubility and permeation.
On-demand electrochemically controlled compound release from an ultrasonically powered implant
Authors: Wang Max L. , Chamberlayne Christian F. , Xu Haixia , Mofidfar Mohammad , Baltsavias Spyridon , Annes Justin P. , Zare Richard N. , Arbabian Amin
Published: August 2022

Controlled release using electroresponsive nanoparticles and an ultrasonically powered battery-free implant demonstrate a potential implantable drug delivery system platform.
Fischer–Helferich glycosidation mechanism of glucose to methyl glycosides over Al-based catalysts in alcoholic media
Authors: Yu Mengting , Li Yao , Zhang Cheng , Luo Huaying , Ge Chengsheng , Chen Xiaobin , Fu Lanlan , Ju Zhaoyang , Yao Xiaoqian
Published: August 2022

The reaction mechanism of conversion of glucose to methyl glycosides (MDGP) catalyzed by Al-based catalysts through Fischer–Helferich glycosidation has been probed by DFT calculations.
UiO-66-NH2 based fluorescent sensing for detection of tetracyclines in milk
Authors: Wang Xiaohui , Wang Xufeng
Published: August 2022

We have developed a UiO-66-NH2 fluorescent sensor by a simple microwave-assisted method. The synthetic UiO-66-NH2 sensor has good sensitivity and selectivity for tetracyclines determination in milk samples.
Functionalization of a stable AIE-based hydrogen-bonded organic framework for white light-emitting diodes
Authors: Lin Yu-Xin , Wang Jia-Xin , Liang Cong-Cong , Jiang Chenghao , Li Bin , Qian Guodong
Published: August 2022

We successfully fabricated a white light-emitting diode by coating functionalized AIE-based HOF-76 material on a 460 nm blue LED chip.
Exploiting angled thin film vortex microfluidics for expeditious syntheses of iminosugars
Authors: Duczynski Jeremy , Raston Colin L. , Stubbs Keith A.
Published: August 2022

Iminosugars are important compounds in the area of carbohydrate-based therapeutics. The vortex fluidic thin film microfluidic reactor is effective in the synthesis of such compounds.
Construction of a photothermal controlled-release microcapsule pesticide delivery system
Authors: Cen Jun , Li Linhuai , Huang Lingling , Jiang Guangqi
Published: August 2022

A photothermal controlled-release microcapsule pesticide delivery system was constructed using chitosan and polydopamine as the wall materials to encapsulate avermectin, the utilization rate of avermectin was improved.
Heterofunctional epoxy support development for immobilization of fructosyltransferase from Pectinex® Ultra SP-L: batch and continuous production of fructo-oligosaccharides
Authors: Veljković Milica , Simović Milica , Banjanac Katarina , Ćorović Marija , Milivojević Ana , Milivojević Milan , Bezbradica Dejan
Published: August 2022

The FTase from Pectinex® Ultra SP-L was immobilized using a newly developed epoxy-Purolite support with amino and epoxy groups. Continuous production of FOS in the air-lift reactor was established for 7 days (52.47% FOS of total carbohydrates).
Modulating membrane fusion through the design of fusogenic DNA circuits and bilayer composition
Authors: Paez-Perez Miguel , Russell I. Alasdair , Cicuta Pietro , Di Michele Lorenzo
Published: August 2022

Control over lipid-membrane fusion is valuable in nanomedicine and synthetic biology. Here we provide guiding principles to program it by using fusogenic DNA nanostructures and exploring the effect of lipid composition on fusion efficiency.
Investigation of low molecular weight sulfur–limonene polysulfide electrodes in Li–S cells
Authors: Djuandhi Lisa , Cowie Bruce C. C. , Rawal Aditya , Sharma Neeraj
Published: August 2022

Solid-state NMR methods revealed quantifiable impact on lithium shielding and molecular mobility when using limonene polysulfide copolymeric cathodes in Li–S batteries.
Molecular engineering accelerated polarity switching enabling high-performance n-type organic thermoelectrics
Authors: Zhong Fei , Yin Xiaojun , Wu Jiatao , Gao Chunmei , Zhong Cheng , Wang Lei
Published: August 2022

Molecular engineering of indaceno[1,2-b:5,6-b′]dithiophene-based copolymers enables a robust approach to accelerate polarity switching during p-doping, affording a high power factor of over 20 μW m−1 K−2 (n-type).
Niobium tellurium as a novel broadband saturable absorber for pulsed fiber lasers
Authors: Zhang Kang , Feng Ming , Yang Jiaxin , Li Yan , Xie Jinyue , Li Yuanhao , Han Dongdong , Song Feng , Huang Wei
Published: August 2022

NbTe2 has been proven to possess excellent nonlinear optical properties in this work. It performs well as a novel broadband mode-locker to generate stable laser pulses in both Er- and Yb-doped fiber lasers.
Biomimetic directional transport for sustainable liquid usage
Authors: Ma Jie , Dong Zhichao
Published: August 2022

Through hundreds of millions of evolution, animals and plants have possessed their unique structures to adapt to natural variations. As a familiar process, liquid transportation plays an important part in both production and life, and researchers focus on how to achieve this process in a convenient and efficient way without energy input. Inspired by nature, various bioinspired structures are reported and have won multiple achievements. This review starts from basic theory about surface wettability, and then summarises the creatures with special liquid transport functions as well as crucial structures that cause this phenomenon. Next, the recent articles about transporting liquid by bioinspired materials are introduced. Finally, we proposed a brief conclusion and the prospect of bionic materials in the future.
Developing phoneme‐based lip‐reading sentences system for silent speech recognition
Authors: El‐Bialy Randa , Chen Daqing , Fenghour Souheil , Hussein Walid , Xiao Perry , Karam Omar H. , Li Bo
Published: August 2022

Lip‐reading is a process of interpreting speech by visually analysing lip movements. Recent research in this area has shifted from simple word recognition to lip‐reading sentences in the wild. This paper attempts to use phonemes as a classification schema for lip‐reading sentences to explore an alternative schema and to enhance system performance. Different classification schemas have been investigated, including character‐based and visemes‐based schemas. The visual front‐end model of the system consists of a Spatial‐Temporal (3D) convolution followed by a 2D ResNet. Transformers utilise multi‐headed attention for phoneme recognition models. For the language model, a Recurrent Neural Network is used. The performance of the proposed system has been testified with the BBC Lip Reading Sentences 2 (LRS2) benchmark dataset. Compared with the state‐of‐the‐art approaches in lip‐reading sentences, the proposed system has demonstrated an improved performance by a 10% lower word error rate on average under varying illumination ratios.
Decomposition mechanism of environmentally friendly insulating medium HFO1234zeE/N2 gas mixture under partial discharge
Authors: Lin Lin , Chen Qingguo , Wang Xinyu , Zhang Hui , Li Huiyong
Published: August 2022

Hydrofluoroolefin HFO1234zeE (trans‐1,3,3,3‐tetrafluoroprop‐1‐ene) is an environmentally friendly gas insulating medium that has the potential to replace SF6. To clarify the decomposition paths and products of an HFO1234zeE/N2 gas mixture under partial discharge, the decomposition mechanism is explored with density functional theory. The results indicate that only HFO1234zeE molecules decompose in the range of low‐temperature plasma, and electrons with different energies interact with molecules and cause them to decompose through different paths. Then, products are generated by free radical recombination, addition reactions and internal configurational conversions of the molecule. An experimental investigation of decomposition of the HFO1234zeE/N2 gas mixture with different discharge modes is carried out, and it is found that the products calculated with density functional theory are consistent with those seen experimentally. The results show the decomposition mechanism of the insulating gas under partial discharge and provide a theoretical basis for the application of HFO1234zeE.
Traffic emissions management using capacity formulation and multi‐modal road space allocation
Authors: Abubakar Amina Baby , Tenekeci Goktug
Published: August 2022

The ever‐rising traffic volumes and congestion in cities have long constituted concerns for traffic safety and the economy. Moreover, traffic has been recognised as a significant contributor to emissions leading to serious environmental and public health problems, becoming the greatest contributor to premature deaths. In response to global policies, this paper introduces unique evaluation of road capacity with studied impediment factors, demonstrating the need for better road space allocation. Speed and capacity formulation for each factor is a unique contribution to knowledge as presented. The developed formulation depicts poor road space allocation along Birmingham's routes as speed reduces by 13 km/h, and capacity reduction of 400 vehicles/lane/h. A proven method of integrating microsimulation and environmental assessment tools show that CO2 increases by 18%, NOx by 23%, and PM by 6%, with reduced traffic movement due to poor road space allocation. This analysis bridges the gap in knowledge so far reported on road space allocation, showing evidence of significant contribution to European Union Directive on air pollution exceedance. Lastly, evidence from this analysis is used to develop traffic management proposals for a more sustainable road space re‐allocation. This provides a unique and measurable impact on the environment for the ‘Birmingham Transport Plan’.
Multi-frequency angular power spectrum of the 21 cm signal from the Epoch of Reionisation using the Murchison Widefield Array
Authors: Trott Cathryn M. , Mondal Rajesh , Mellema Garrelt , Murray Steven G. , Greig Bradley , Line Jack L. B. , Barry Nichole , Morales Miguel F.
Published: August 2022

Context. The Multi-frequency Angular Power Spectrum (MAPS) is an alternative to spherically averaged power spectra, and computes local fluctuations in the angular power spectrum without need for line-of-sight spectral transform.

Aims. We aimed to test different approaches to MAPS and treatment of the foreground contamination, and compare with the spherically averaged power spectrum, and the single-frequency angular power spectrum.

Methods. We applied the MAPS to 110 h of data in z = 6.2 − 7.5 obtained for the Murchison Widefield Array Epoch of Reionisation experiment to compute the statistical power of 21 cm brightness temperature fluctuations. In the presence of bright foregrounds, a filter was applied to remove large-scale modes prior to MAPS application, significantly reducing MAPS power due to systematics.

Results. The MAPS showed a contrast of 102–103 to a simulated 21 cm cosmological signal for spectral separations of 0−4 MHz after application of the filter, reflecting results for the spherically averaged power spectrum. The single-frequency angular power spectrum was also computed. At z = 7.5 and l = 200, we found an angular power of 53 mK2, exceeding a simulated cosmological signal power by a factor of one thousand. Residual spectral structure, inherent to the calibrated data, and not spectral leakage from large-scale modes, was the dominant source of systematic power bias. The single-frequency angular power spectrum yielded slightly poorer results compared with the spherically averaged power spectrum, having applied a spectral filter to reduce foregrounds. Exploration of other filters may improve this result, along with consideration of wider bandwidths.