bluuebunny/crossref_metadata_2025 huggingface dataset:
Impact of artisanal refining activities on bacterial diversity in a Niger Delta fallow land
Authors: Fenibo Emmanuel Oliver , Nkuna Rosina , Matambo Tonderayi
Published: February 2024

Hydrocarbon pollution is a major ecological problem facing oil-producing countries, especially in the Niger Delta region of Nigeria. In this study, a site that had been previously polluted by artisanal refining activity was investigated using 16S rRNA Illumina high-throughput sequencing technology and bioinformatics tools. These were used to investigate the bacterial diversity in soil with varying degrees of contamination, determined with a gas chromatography-flame ionization detector (GC-FID). Soil samples were collected from a heavily polluted (HP), mildly polluted (MP), and unpolluted (control sample, CS) portion of the study site. DNA was extracted using the Zymo Research (ZR) Fungi/Bacteria DNA MiniPrep kit, followed by PCR amplification and agarose gel electrophoresis. The microbiome was characterized based on the V3 and V4 hypervariable regions of the 16S rRNA gene. QIIME (Quantitative Insights Into Microbial Ecology) 2 software was used to analyse the sequence data. The final data set covered 20,640 demultiplexed high-quality reads and a total of 160 filtered bacterial OTUs. Proteobacteria dominated samples HP and CS, while Actinobacteria dominated sample MP. Denitratisoma, Pseudorhodoplanes, and Spirilospora were the leading genera in samples HP, CS, and MP respectively. Diversity analysis indicated that CS [with 25.98 ppm of total petroleum hydrocarbon (TPH)] is more diverse than HP (with 490,630 ppm of TPH) and MP (with 5398 ppm of TPH). A functional prediction study revealed that six functional modules dominated the dataset, with metabolism covering up to 70%, and 11 metabolic pathways. This study demonstrates that a higher hydrocarbon concentration in soil adversely impacts microbial diversity, creating a narrow bacterial diversity dominated by hydrocarbon-degrading species, in addition to the obvious land and ecosystem degradation caused by artisanal refining activities. Overall, the artisanal refining business is significantly driving ecosystem services losses in the Niger Delta, which calls for urgent intervention, with focus on bioremediation.
Dynamic facial emotion recognition and affective prosody recognition are associated in patients with temporal lobe epilepsy
Authors: Metternich Birgitta , Gehrer Nina , Wagner Kathrin , Geiger Maximilian J. , Schütz Elisa , Seifer Britta , Schulze-Bonhage Andreas , Schönenberg Michael
Published: February 2024

Deficits in facial emotion recognition have frequently been established in temporal lobe epilepsy (TLE). However, static, rather than dynamic emotion recognition paradigms have been applied. Affective prosody has been insufficiently studied in TLE, and there is a lack of studies investigating associations between auditory and visual emotion recognition. We wished to investigate potential deficits in a dynamic morph task of facial emotion recognition and in an affective prosody recognition task, as well as associations between both tasks. 25 patients with TLE and 24 healthy controls (CG) performed a morph task with faces continuously changing in their emotional intensity. They had to press a button, as soon as they were able to recognize the emotion expressed, and label it accordingly. In the auditory task, subjects listened to neutral sentences spoken in varying emotional tones, and labeled the emotions. Correlation analyses were conducted across both tasks. TLE patients showed significantly reduced prosody recognition compared to CG, and in the morph task, there was a statistical trend towards significantly reduced performance for TLE. Recognition rates in both tasks were significantly associated. TLE patients show deficits in affective prosody recognition, and they may also be impaired in a morph task with dynamically changing facial expressions. Impairments in basic social-cognitive tasks in TLE seem to be modality-independent.
Defect detection by multi-axis infrared process monitoring of laser beam directed energy deposition
Authors: Herzog T. , Brandt M. , Trinchi A. , Sola A. , Hagenlocher C. , Molotnikov A.
Published: February 2024

Laser beam directed energy deposition (DED-LB) is an attractive additive manufacturing technique to produce versatile and complex 3D structures on demand, apply a cladding, or repair local defects. However, the quality of manufactured parts is difficult to assess by inspection prior to completion, and parts must be extensively inspected post-production to ensure conformance. Consequently, critical defects occurring during the build go undetected. In this work, a new monitoring system combining three infrared cameras along different optical axes capable of monitoring melt pool geometry and vertical displacement throughout deposition is reported. By combining multiple sensor data, an automated algorithm is developed which is capable of identifying the formation of structural features and defects. An intersecting, thin-walled geometry is used to demonstrate the capability of the system to detect process-induced porosity in samples with narrow intersection angles, which is validated using micro-CT observations. The recorded results indicate the root cause of this process-induced porosity at the intersection, and it is shown that advanced toolpath planning can eliminate such defects. The presented methodology demonstrates the value of multi-axis monitoring for identifying both defects and structural features, providing an advancement towards automated detection and alert systems in DED-LB.
Soil fertility impact on recruitment and diversity of the soil microbiome in sub-humid tropical pastures in Northeastern Brazil
Authors: Paes da Costa Diogo , das Graças Espíndola da Silva Thallyta , Sérgio Ferreira Araujo Ademir , Prudêncio de Araujo Pereira Arthur , William Mendes Lucas , dos Santos Borges Wisraiane , Felix da França Rafaela , Alberto Fragoso de Souza Carlos , Alves da Silva Bruno , Oliveira Silva Renata , Valente de Medeiros Erika
Published: February 2024

Soil fertility is key point to pastures systems and drives the microbial communities and their functionality. Therefore, an understanding of the interaction between soil fertility and microbial communities can increase our ability to manage pasturelands and maintain their soil functioning and productivity. This study probed the influence of soil fertility on microbial communities in tropical pastures in Brazil. Soil samples, gathered from the top 20 cm of twelve distinct areas with diverse fertility levels, were analyzed via 16S rRNA sequencing. The soils were subsequently classified into two categories, namely high fertility (HF) and low fertility (LF), using the K-Means clustering. The random forest analysis revealed that high fertility (HF) soils had more bacterial diversity, predominantly Proteobacteria, Nitrospira, Chloroflexi, and Bacteroidetes, while Acidobacteria increased in low fertility (LF) soils. High fertility (HF) soils exhibited more complex network interactions and an enrichment of nitrogen-cycling bacterial groups. Additionally, functional annotation based on 16S rRNA varied between clusters. Microbial groups in HF soil demonstrated enhanced functions such as nitrate reduction, aerobic ammonia oxidation, and aromatic compound degradation. In contrast, in the LF soil, the predominant processes were ureolysis, cellulolysis, methanol oxidation, and methanotrophy. Our findings expand our knowledge about how soil fertility drives bacterial communities in pastures.
JAXA’s new high-resolution land use land cover map for Vietnam using a time-feature convolutional neural network
Authors: Truong Van Thinh , Hirayama Sota , Phan Duong Cao , Hoang Thanh Tung , Tadono Takeo , Nasahara Kenlo Nishida
Published: February 2024

Land use land cover (LULC) maps are crucial for various applications, such as disaster management, natural resource conservation, biodiversity evaluation, climate modeling, etc. The Japan Aerospace Exploration Agency (JAXA) has released several high-resolution LULC maps for national and regional scales. Vietnam, due to its rich biodiversity and cultural diversity, is a target country for the production of high-resolution LULC maps. This study introduces a high-resolution and high-accuracy LULC map for Vietnam, utilizing a CNN approach that performs convolution over a time-feature domain instead of the typical geospatial domain employed by conventional CNNs. By using multi-temporal data spanning 6 seasons, the produced LULC map achieved a high overall accuracy of 90.5% ± 1.2%, surpassing other 10-meter LULC maps for Vietnam in terms of accuracy and/or the ability to capture detailed features. In addition, a straightforward and practical approach was proposed for generating cloud-free multi-temporal Sentinel-2 images, particularly suitable for cloudy regions. This study marks the first implementation of the time-feature CNN approach for the creation of a high-accuracy LULC map in a tropical cloudy country.
Ensemble averaging deep neural network for botnet detection in heterogeneous Internet of Things devices
Authors: Wardana Aulia Arif , Kołaczek Grzegorz , Warzyński Arkadiusz , Sukarno Parman
Published: February 2024

The botnet attack is one of the coordinated attack types that can infect Internet of Things (IoT) devices and cause them to malfunction. Botnets can steal sensitive information from IoT devices and control them to launch another attack, such as a Distributed Denial-of-Service (DDoS) attack or email spam. This attack is commonly detected using a network-based Intrusion Detection System (NIDS) that monitors the network device’s activity. However, IoT network is dynamic and IoT devices have many types with different configurations and vendors in IoT environments. Therefore, this research proposes an Intrusion Detection System (IDS) by ensemble-ing traffic from heterogeneous IoT devices. This research proposes Deep Neural Network (DNN) to create a training model from each heterogeneous IoT device. After that, each training model from each heterogeneous IoT device is used to predict the traffic. The prediction results from each training model are averaged using the ensemble averaging method to determine the final result. This research used the N-BaIoT dataset to validate the proposed IDS model. Based on experimental results, ensemble averaging DNN can detect botnet attacks in heterogeneous IoT devices with an average accuracy of 97.21, precision of 91.41, recall of 87.31, and F1-score 88.48.
Efficient inhibition of amyloid fibrillation and cytotoxicity of α-synuclein and human insulin using biosynthesized silver nanoparticles decorated by green tea polyphenols
Authors: Mirzaei-Behbahani Behnaz , Meratan Ali Akbar , Moosakhani Beitollah , Mohammad-Zaheri Mahya , Mousavi-Jarrahi Zahra , Nikfarjam Nasser , Shahsavani Mohammad Bagher , Saboury Ali Akbar
Published: February 2024

Green tea polyphenols (GTPs), particularly epigallocatechin-3-gallate, stand out among natural small molecules screened for their ability to target protein aggregates due to their potent anti-amyloidogenic and neuroprotective activities against various disease-related peptides and proteins. However, the clinical applications of GTPs in amyloid-related diseases have been greatly limited by drawbacks such as poor chemical stability and low bioavailability. To address these limitations, this study utilized an Iranian green tea polyphenolic extract as a reducing agent to neutralize silver ions and facilitate the formation of silver nanoparticle capped by GTPs (GTPs-capped AgNPs). The results obtained from this study demonstrate that GTPs-capped AgNPs are more effective than free GTPs at inhibiting amyloid fibrillation and reducing cytotoxicity induced by amyloid fibrils of human insulin and α-synuclein (α-syn). This improved efficacy is attributed to the increased surface/volume ratio of GTPs-capped AgNPs, which can enhance their binding affinity to amyloidogenic species and boosts their antioxidant activity. The mechanism by which GTPs-capped AgNPs inhibit amyloid fibrillation appears to vary depending on the target protein. For structured protein human insulin, GTPs-capped AgNPs hinder fibrillation by constraining the protein in its native-like state. In contrast, GTPs-capped AgNPs modulate fibrillation of intrinsically disordered proteins like α-syn by redirecting the aggregation pathway towards the formation of non-toxic off-pathway oligomers or amorphous aggregates. These findings highlight polyphenol-functionalized nanoparticles as a promising strategy for targeting protein aggregates associated with neurodegenerative diseases.
Reconstruction and validation of ground motions across dip-slip faults: an application to response analysis of a long-span suspension bridge
Authors: Jia Hongyu , Cheng Wei , Jia Kang , Zhai Yikun , Zheng Shixiong
Published: February 2024

Recent seismic events have unequivocally highlighted the susceptibility of fault-crossing bridges to the synergistic effects of ground surface vibrations on either side of the fault plane and the tectonic dislocations arising from fault-induced surface ruptures. This study delineates both seismic and parametric response analyses of fault-crossing suspension bridges, employing a straightforward yet efficacious method for simulating desired ground motions near fault-rupture zones. Herein, we introduce a user-friendly method to incorporate predicted fault-induced displacements, accounting for both fling-step and directivity effects, into processed ground motion chronologies, enabling the generation of dip-slip fault ground motions. The accuracy and efficacy of the proposed method are affirmed by juxtaposing the generated ground motions with the observed ones (MGM). An exhaustive parametric analysis, addressing factors like fault-crossing location, fault-crossing angle, and frequency components of fault-crossing ground motions, of a suspension bridge over a rupture fault, is executed using the fashionable ANSYS software. This study provides clear and specific guidelines for the seismic design of suspension bridges traversing rupture faults.
Life course plasma metabolomic signatures of genetic liability to Alzheimer’s disease
Authors: Compton Hannah , Smith Madeleine L. , Bull Caroline , Korologou-Linden Roxanna , Ben-Shlomo Yoav , Bell Joshua A. , Williams Dylan M. , Anderson Emma L.
Published: February 2024

Mechanisms through which most known Alzheimer’s disease (AD) loci operate to increase AD risk remain unclear. Although Apolipoprotein E (APOE) is known to regulate lipid homeostasis, the effects of broader AD genetic liability on non-lipid metabolites remain unknown, and the earliest ages at which metabolic perturbations occur and how these change over time are yet to be elucidated. We examined the effects of AD genetic liability on the plasma metabolome across the life course. Using a reverse Mendelian randomization framework in two population-based cohorts [Avon Longitudinal Study of Parents and Children (ALSPAC, n = 5648) and UK Biobank (n ≤ 118,466)], we estimated the effects of genetic liability to AD on 229 plasma metabolites, at seven different life stages, spanning 8 to 73 years. We also compared the specific effects of APOE ε4 and APOE ε2 carriage on metabolites. In ALSPAC, AD genetic liability demonstrated the strongest positive associations with cholesterol-related traits, with similar magnitudes of association observed across all age groups including in childhood. In UK Biobank, the effect of AD liability on several lipid traits decreased with age. Fatty acid metabolites demonstrated positive associations with AD liability in both cohorts, though with smaller magnitudes than lipid traits. Sensitivity analyses indicated that observed effects are largely driven by the strongest AD instrument, APOE, with many contrasting effects observed on lipids and fatty acids for both ε4 and ε2 carriage. Our findings indicate pronounced effects of the ε4 and ε2 genetic variants on both pro- and anti-atherogenic lipid traits and sphingomyelins, which begin in childhood and either persist into later life or appear to change dynamically.
Reducing image artifacts in sparse projection CT using conditional generative adversarial networks
Authors: Usui Keisuke , Kamiyama Sae , Arita Akihiro , Ogawa Koichi , Sakamoto Hajime , Sakano Yasuaki , Kyogoku Shinsuke , Daida Hiroyuki
Published: February 2024

Reducing the amount of projection data in computed tomography (CT), specifically sparse-view CT, can reduce exposure dose; however, image artifacts can occur. We quantitatively evaluated the effects of conditional generative adversarial networks (CGAN) on image quality restoration for sparse-view CT using simulated sparse projection images and compared them with autoencoder (AE) and U-Net models. The AE, U-Net, and CGAN models were trained using pairs of artifacts and original images; 90% of patient cases were used for training and the remaining for evaluation. Restoration of CT values was evaluated using mean error (ME) and mean absolute error (MAE). The image quality was evaluated using structural image similarity (SSIM) and peak signal-to-noise ratio (PSNR). Image quality improved in all sparse projection data; however, slight deformation in tumor and spine regions was observed, with a dispersed projection of over 5°. Some hallucination regions were observed in the CGAN results. Image resolution decreased, and blurring occurred in AE and U-Net; therefore, large deviations in ME and MAE were observed in lung and air regions, and the SSIM and PSNR results were degraded. The CGAN model achieved accurate CT value restoration and improved SSIM and PSNR compared to AE and U-Net models.
The effect of genetic variants of SLC22A18 on proliferation, migration, and invasion of colon cancer cells
Authors: Song Hyo Sook , Ha Seung Yeon , Kim Jin-Young , Kim Minsuk , Choi Ji Ha
Published: February 2024

Solute carrier family (SLC) transporters are expressed in the digestive system and play important roles in maintaining physiological functions in the body. In addition, SLC transporters act as oncoproteins or tumor-suppressor proteins during the development, progression, and metastasis of various digestive system cancers. SLC22A18, a member of the SLC22 gene family, is an orphan transporter with an unknown endogenous substrate. Previous study revealed that SLC22A18 is downregulated in colorectal cancer tissues and that it acts as a suppressor in colorectal cancer, although the effects of SLC22A18 variants on colon cancer cell proliferation, migration, and invasion are unknown. Therefore, in this study, we identified SLC22A18 variants found in multiple populations by searching public databases and determined the in vitro effects of these missense variations on transporter expression and cancer progression. Our results indicated that three missense SLC22A18 variants—p.Ala6Thr, p.Arg12Gln, and p.Arg86His—had significantly lower cell expression than the wild type, possibly owing to intracellular degradation. Furthermore, these three variants caused significantly higher proliferation, migration, and invasion of colon cancer cells than the wild type. Our findings suggest that missense variants of SLC22A18 can potentially serve as biomarkers or prognostic tools that enable clinicians to predict colorectal cancer progression.
The preliminary study suggests an association between NF-ĸB pathway activation and increased plasma 20S proteasome activity in intracranial aneurysm patients
Authors: Kamińska Joanna , Tylicka Marzena , Sutkowska Kinga , Gacuta Karolina Marta , Sawicka Magdalena Maria , Kowalewska Ewa , Ćwiklińska-Dworakowska Magdalena , Maciejczyk Mateusz , Łysoń Tomasz , Kornhuber Johannes , Lewczuk Piotr , Matowicka-Karna Joanna , Koper-Lenkiewicz Olga Martyna
Published: February 2024

The significant role of increased activation of 20S proteasomes in the development of abdominal aortic aneurysms has been well-established in a mouse model. The available literature lacks similar studies concerning brain aneurysms. The aim of the study was to verify the hypothesis that patients with unruptured intracranial aneurysms (UIA) have increased 20S proteasome ChT-L activity compared to the control group of individuals without vascular lesions in the brain. In the next step, the relationship between the activity of 20S proteasomes ChT-L and precursor proteins from the nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) family, namely NF-κB1 (p105), NF-κB2 (p100), NF-κB p65, and the inflammatory chemokine MCP-1, was examined. Patients with UIA had significantly higher 20S ChT-L proteasome activity compared to the control group. Patients with multiple aneurysms had significantly higher 20S proteasome ChT-L activity compared to those with single aneurysms. In patients with UIA, the activity of the 20S proteasome ChT-L negatively correlated with the concentration of NF-κB1 (p105) and NF-κB p65 precursor proteins and positively correlated with the concentration of the cerebrospinal fluid chemokine MCP-1. Our results may suggest that increased 20S proteasome ChT-L activity in UIA patients modulates inflammation in the cerebral arterial vessel via the MCP-1 chemokine as a result of activation of the canonical NF-κB pathway.
Dietary macronutrient composition impacts gene regulation in adipose tissue
Authors: Farris Kathryn M. , Senior Alistair M. , Sobreira Débora R. , Mitchell Robert M. , Weber Zachary T. , Ingerslev Lars R. , Barrès Romain , Simpson Stephen J. , Crean Angela J. , Nobrega Marcelo A.
Published: February 2024

Diet is a key lifestyle component that influences metabolic health through several factors, including total energy intake and macronutrient composition. While the impact of caloric intake on gene expression and physiological phenomena in various tissues is well described, the influence of dietary macronutrient composition on these parameters is less well studied. Here, we use the Nutritional Geometry framework to investigate the role of macronutrient composition on metabolic function and gene regulation in adipose tissue. Using ten isocaloric diets that vary systematically in their proportion of energy from fat, protein, and carbohydrates, we find that gene expression and splicing are highly responsive to macronutrient composition, with distinct sets of genes regulated by different macronutrient interactions. Specifically, the expression of many genes associated with Bardet-Biedl syndrome is responsive to dietary fat content. Splicing and expression changes occur in largely separate gene sets, highlighting distinct mechanisms by which dietary composition influences the transcriptome and emphasizing the importance of considering splicing changes to more fully capture the gene regulation response to environmental changes such as diet. Our study provides insight into the gene regulation plasticity of adipose tissue in response to macronutrient composition, beyond the already well-characterized response to caloric intake.
Tumor-targeted nanodrug FSGG/siGal-9 for transdermal photothermal immunotherapy of melanoma
Authors: Ren Huihong , Zhang Yujuan , Huang Wei , Xu Haiyan , He Weixiong , Hao Nan , Zhang Cong
Published: February 2024

Photothermal therapy (PTT) is a cancer-targeted treatment approach.The occurrence of tumors may be related to microbial infections (Viruses, bacteria, fungi, etc.), which probably provokes anti-tumor immunity. However, T cells in the context of cancer become exhausted and dysfunctional. Galectin-9 (Gal-9) is highly expressed in normal tissues and associates with body immune tolerance, and was firstly evidenced with much higher expression on the primary solid tumors than CD80/86 (B7) and CD274 (PD-L1) here, which suggests that Gal-9 may be a key factor in inhibiting the anti-tumor immunity, and its receptor T cell immunoglobulin and mucin domain 3 (TIM-3) was discovered on the cytotoxic T lymphocytes (CTL) with high expression as well based on the single cell analysis. The immune checkpoint communications showed that the Gal-9/TIM-3 axis played the most vital role on negatively regulating the anti-tumor immunity of CTL for melanoma. Then, we used a novel transdermal photothermal nanosensitizer (FSGG) loading Gal-9 siRNA (FSGG/siGal-9) for knocking the tumor cells down Gal-9 to block the Gal-9/TIM-3 axis and prohibit CTL exhaustion synergizing PTT against melanoma, which evidenced good effects on inhibiting tumor growth and enhancing anti-tumor immunity, named “photothermal immunotherapy”. This paper provides a new perspective for tumor prevention and treatment.
Identification of lubricant viscosity to minimize the frictional impact of colonoscopy on colonic mucosa
Authors: Watanabe Naoto , Hirose Ryohei , Ikegaya Hiroshi , Yamauchi Katsuma , Miyazaki Hajime , Yoshida Takuma , Bandou Risa , Inoue Ken , Dohi Osamu , Yoshida Naohisa , Nakaya Takaaki , Itoh Yoshito
Published: February 2024

Applying a lubricant to the colonic mucosa and reducing the dynamic friction coefficient (DFC) between the endoscopic shaft and colonic mucosa may reduce colonoscopy invasiveness. However, the ideal lubricant viscosity remains unknown. Here, we developed a DFC measurement model integrating samples of colonic mucosa from forensic autopsy specimens into a simulated bowel bend and determined the low-friction lubricant viscosity that minimizes the DFC. Carboxymethyl cellulose, xanthan gum, hydroxyethyl cellulose, sodium alginate, and sodium polyacrylate aqueous solutions of various concentrations were used as lubricants. Low-friction lubricants minimized the load on the colonic mucosa during colonoscope insertion and reduced the total endoscopy insertion time. The highest correlation was between the DFC and the lubricant viscosity at a shear rate of 100 1/s. The lowest DFC was almost constant at approximately 0.09, irrespective of the chemical composition of the lubricant, and the low-friction lubricant viscosity (100 1/s) was 0.031–0.086 (median: 0.059). The viscosities of conventional colonoscopic lubricants were suitable for lubricating the anorectal skin owing to their low DFC, but too high for lubricating the colonic mucosa because of their high DFC. The utilization of the low-friction lubricants with the optimal viscosity can reduce the stress on colonic mucosa during colonoscopy.
External Media for Inducing Weak Alignment in Biomacromolecules
Authors: Meier Sebastian , Grzesiek Stephan
Published: February 2024

Residual dipolar couplings (RDCs) or more generally residual tensorial couplings (RTCs) have allowed protein and other molecular solution structures to be defined at an accuracy and precision that rivals the best crystal structures, while additionally providing information on protein dynamics at submicrosecond to millisecond timescales, which are central to biological function. These benefits derive from the high sensitivity of the RTC measurement even for large molecules and the straightforward mathematical dependence of the RTC on the orientation of the local atom group relative to a common molecular reference frame. A prerequisite for observing RTCs at high sensitivity in solution is a suitable second-rank molecular orientation, which deviates on the order of 10−4–10−3 from isotropy. While in favorable cases such orientations may be obtained via the intrinsic magnetic anisotropy of molecules, the addition of small amounts of orienting substances to the liquid medium provides a simple, general mechanism to achieve suitable orientation for RTC measurements for all classes of solute molecules. In this chapter, we describe the theory of rotational ordering and the practical aspects of using external orienting substances for the measurement of RTCs.
Prediction of Weak Alignment from Molecule Structure
Authors: Zweckstetter M.
Published: February 2024

Residual dipolar couplings arise from the preferential orientation of a molecule in the anisotropic environment of an alignment medium. The characteristics and degree of alignment, transmitted from the alignment medium to the solute molecule, depend on the molecular properties of both the solute molecule and the alignment medium. Computational tools are today available that accurately simulate the weak alignment of molecules in different alignment media. Particularly powerful are the methods named Prediction of Alignment from Structure (PALES) and P3D which represent the solute molecule or both the solute molecule and the alignment medium in atomic detail. Prediction of weak alignment from molecule structure can improve the analysis of the configuration, conformation and dynamics of proteins, nucleic acids, oligosaccharides, natural products and small molecules.
Consistent Protein Structure Determination Using Sparse NMR Data
Authors: Shen Yang
Published: February 2024

Conventional NMR structure determination for proteins typically is labor-intensive and usually is challenging for larger proteins because only sparse NMR restraint data are generally available. Numerous alternative protein structure determination protocols have been developed to utilize inputs from a sparse set of experimental NMR data, comprising mainly backbone chemical shifts, residual dipolar couplings (RDCs) and sparse 1H–1H NOEs if available. These structure determination approaches directly exploit the powerful bioinformatics algorithms previously developed for sequence-based protein structure prediction and homology modeling, implemented with the essential structural information provided by a variety of sparse NMR data, and have been demonstrated for routinely generating accurate high-resolution full-atom structures for proteins with size up to ca. 40 kDa and with varying fold complexity and oligomeric states. This review aims to highlight the central concepts and important aspects of these sparse NMR data based protein structure determination protocols, represented by those consistent approaches developed within the CS-Rosetta framework.
RNA Conformational Ensembles from NMR Residual Dipolar Couplings
Authors: Roy Rohit , Geng Ainan , Pratihar Supriya , Shi Honglue , Al-Hashimi Hashim M.
Published: February 2024

Knowing the 3D structures formed by the various conformations populating the RNA free energy landscape and their relative abundance is required to obtain a quantitative and predictive understanding of how RNAs fold and function at the atomic level. Here, we describe how NMR residual dipolar couplings (RDCs) measured in partially aligned RNA molecules in conjunction with computational modeling enable the determination of RNA conformational ensembles at near-atomic resolution. We review various strategies for modulating alignment and measuring multiple sets of RDCs and the schemes used to integrate RDCs with computational models. We also examine the approaches used to test the accuracy of RDC-derived ensembles and highlight recurrent themes in RNA ensembles that have been determined thus far. Additionally, we briefly discuss the applications of conformational ensembles in developing a quantitative understanding of RNA cellular activity and in RNA-targeted drug discovery.
Chiral nanoparticle separation and discrimination using radially polarized circular Airy vortex beams with orbital-induced spin angular momentum
Authors: Wu Hao , Wang Tao , Hu Yi
Published: February 2024

Local angular momentum induced by the orbital angular momentum endows radially polarized circular Airy vortex beams with positive and negative annular optical chirality densities, enabling the separation and discrimination of chiral nanoparticles.
Influence of temperatures and loadings on olefin diffusion in MFI-type zeolites in one- to three-dimensions
Authors: Tong Jiahuan , Miyakage Takumi , Toyao Takashi , Shimizu Ken-ichi
Published: February 2024

A detailed understanding of the molecular diffusion in zeolite frameworks is crucial for analysing the factors controlling their catalytic performance in alkenes.
Formoxyboranes as hydroborane surrogates for the catalytic reduction of carbonyls through transfer hydroboration
Authors: Durin Gabriel , Romero R. Martin , Godou Timothé , Chauvier Clément , Thuéry Pierre , Nicolas Emmanuel , Cantat Thibault
Published: February 2024

A new class of Lewis base stabilized formoxyboranes demonstrates the feasibility of catalytic transfer hydroboration.
Oxidation pathways and kinetics of the 1,1,2,3-tetrafluoropropene (CF2CF–CH2F) reaction with Cl-atoms and subsequent aerial degradation of its product radicals in the presence of NO
Authors: Kakati Udeshna Priya , Dowerah Dikshita , Deka Ramesh Chandra , Gour Nand Kishor , Paul Subrata
Published: February 2024

To give a comprehensive account of the environmental acceptability of CF2CF–CH2F in the troposphere, we have examined the oxidation reaction pathways and kinetics of CF2CF–CH2F initiated by Cl-atoms employing quantum chemical calculations.
Unravelling parameter interactions in calcium alginate/polyacrylamide double network hydrogels using a design of experiments approach for the optimization of mechanical properties
Authors: Gorke Oliver , Stuhlmüller Marc , Tovar Günter E. M. , Southan Alexander
Published: February 2024

Systematic variation of the composition of calcium alginate/polyacrylamide double network hydrogels paves the way for the optimization of mechanical properties.
Superior optical and thermoelectric properties of bilayer β12-like phase borophene synthesized on Cu(111) film
Authors: Ali Sajid , Rahman Amin Ur , Sun Mengtao
Published: February 2024

In this work we theoretically investigate the electronic properties, optical properties, and thermoelectric characteristics of bilayer (BL) β12-like phase borophene synthesized on a Cu(111) substrate.
Synthesis, dyeing performance and evaluation of the antimicrobial and antioxidant activities of azo dye derivatives incorporated with 1,3,4-thiadiazole combined within silicocomputational studies
Authors: Mezgebe Kibrom , Melaku Yadessa , Ramachandran Venkatesha Perumal , Mulugeta Endale
Published: February 2024

The incorporation of heterocyclic moieties into azo dye derivatives influences the bioactive properties of synthesized derivatives.
A bio-inspired approach for the synthesis of few-layer graphene using beetle defensive gland extract
Authors: Ajaykumar A. P. , Nikhila K. , Sabira Ovungal , Jayaraj Kodangattil Narayanan , Varma Sudhir Rama , Rasheed V. A. , Binitha V. S. , Sreeja Kalapparambil , Ramakrishnan Resmi M. , Babu Annet
Published: February 2024

Exfoliation of graphite.
Unveiling the local structure of doubly doped CeO2: a synchrotron X-ray pair distribution function study
Authors: Martinelli Alberto , Massardo Sara , Artini Cristina , Carnasciali Maria M. , Pani Marcella
Published: February 2024

For the first time the structural properties at the local scale of doubly-doped ceria systems are discussed.
Distribution of dual additives enables efficient semi-transparent layer-by-layer architecture of organic solar cells
Authors: Kim Ji Youn , Jeon Sung Jae , Lee Hyoung Seok , Han Yong Woon , Kim Ye Chan , Yang Nam Gyu , Kim Gang Wook , Jang Eun Mi , Kim Ji Hyeon , Moon Doo Kyung
Published: February 2024

We combined the layer-by-layer technique with dual additives introduction, which showed a PCE of 16.51% in opaque OSCs. Also, high efficiency of 11.33% was achieved under a notable AVT of 19.28% in semitransparent OSCs.
Dynamic video recognition for cell-encapsulating microfluidic droplets
Authors: Mao Yuanhang , Zhou Xiao , Hu Weiguo , Yang Weiyang , Cheng Zhen
Published: February 2024

Droplet microfluidics is a highly sensitive and high-throughput technology extensively utilized in biomedical applications, such as single-cell sequencing and cell screening.
Correction: MnO2/Ce6 microbubble-mediated hypoxia modulation for enhancing sono-photodynamic therapy against triple negative breast cancer
Authors: Li Ping , Tan Xiao , Dan Qing , Hu Azhen , Hu Zhengming , Yang Xiaoting , Bai Jianhua , Chen Xiaoyu , Li Bowei , Cheng Guanxun , Liu Li , Chen Yun , Sun Desheng , Shuai Xintao , Zheng Tingting
Published: February 2024

Correction for ‘MnO2/Ce6 microbubble-mediated hypoxia modulation for enhancing sono-photodynamic therapy against triple negative breast cancer’ by Ping Li et al., Biomater. Sci., 2024, https://doi.org/10.1039/d3bm00931a.
Visible light-driven cubic structured NiFe2O4@MWCNTs/TiO2 ternary nanocomposite for photocatalytic degradation of ciprofloxacin
Authors: Varghese Davis , S. Muthupandi , S. Arun , Francis Jijo , M. Joe Raja Ruban , P. Joselene Suzan Jennifer , D. Annie Canisius , J. Madhavan , M. Victor Antony Raj
Published: February 2024

Mechanism of photocatalysis under visible light irradiation with TiO2/NiFe2O4@MWCNTs as the photocatalyst.
Reversible and irreversible reaction mechanisms of Li–CO2 batteries
Authors: Zhang Xinxin , Wang Yu , Li Yafei
Published: February 2024

We disclose the rechargeable/reversible reaction mechanisms of Li–CO2 batteries by using state-of-the-art first-principles calculations.
Bio-inspired sustained entrainment in immiscible liquid–liquid systems for collecting floating oil
Authors: Cheng Ziyang , Shen Tao , Chen Shuaizhong , Yu Cunlong , Li Panhai , Tian Qirong , Li Chuxin , Jiang Lei , Dong Zhichao
Published: February 2024

Entrainment, where a solid object in a liquid bath moves towards the air phase, is common in industry and daily-life.
Structure tailoring and defect engineering of a highly thermally stable red emitting phosphor
Authors: Huo Xiaoxue , Wang Zhijun , Meng Xue , Zhang Jiawei , Wang Yu , Li Panlai
Published: February 2024

Gd3−yCay−0.02GaO6:0.02Eu2+ (y = 0.2) can produce 650 nm red light with a half-peak width of 68 nm, and its emission intensity can still maintain more than 95% of that at room temperature.
Interpolation of scheduled simulation results for real-time auralization of moving sources
Authors: Schäfer Philipp , Fatela João , Vorländer Michael
Published: February 2024

A central part of auralization is the consideration of realistic sound propagation effects. This can be achieved using computationally efficient physics-based simulations based on the principle geometrical acoustics. When considering complex effects, e.g. curved propagation due to atmospheric refraction, those simulations can be computationally demanding. This can become the bottleneck for real-time auralizations, as the run-time exceeds the duration of one audio block even for large block sizes. A solution is to schedule the simulations into a separate thread. However, this leads to an irregular update rate which is lower than the rate of the audio blocks. Consequently, the output signal can contain audible artifacts. This especially holds when considering the Doppler effect for dynamic scenarios with fast moving sources, like aircraft. This paper introduces a method for interpolating, and thereby upsampling, the results of scheduled simulations in an auralization context in order to avoid such artifacts. The method is applied to an aircraft flyover auralization considering curved sound propagation in an inhomogeneous, moving atmosphere. Using this method, it is possible to auralize such scenarios in real time.
The JLab 12 GeV Program
Authors: Napolitano Jim
Published: February 2024

We review results from the Jefferson Laboratory (JLab) program with the 12 GeV Upgrade of the CEBAF accelerator, with a particular emphasis on processes involving mesons. We include associated efforts in theory and phenomenology. We also discuss expected results from future analyses and data taking, including new instrumentation, in particular SoLID and the planned 22 GeV Upgrade of CEBAF.
Kaonic atoms with SIDDHARTA-2 at the DAΦNE collider
Authors: Sirghi F. , Abbene L. , Bazzi M. , Bosnar D. , Bragadireanu M. , Buttacavoli A. , Cargnelli M. , Carminati M. , Clozza A. , Deda G. , Del Grande R. , Dulski K. , De Paolis L. , Fabbietti L. , Fiorini C. , Friščić I. , Guaraldo C. , Iliescu M. , Iwasaki M. , Khreptak A. , Manti S. , Marton J. , Miliucci M. , Moskal P. , Napolitano F. , Sgaramella F. , Niedźwiecki S. , Ohnishi H. , Piscicchia K. , Sada Y. , Scordo A. , Silarski M. , Sirghi D. , Skurzok M. , Spallone A. , Toho K. , Tüchler M. , Yoshida C. , Zmeska J. , Curceanu C.
Published: February 2024

The most important information still missing in the field of the low-energy antikaon-nucleon inter actions studies is the experimental determination of the hadronic energy shift and width of kaonic deuterium. This measurement will be performed by the SIDDHARTA-2 experiment, installed at the DAΦNE collider and presently in data taking campaign. The precise measurement of the shift and width of the 1s level with respect to the purely electromagnetic calculated values, generated by the presence of the strong interaction, through the measurement of the X-ray transitions to this level, in kaonic hydrogen, was performed by the SIDDHARTA collaboration, the kaonic deuterium is underway by SIDDHARTA-2. These measurement will allow the first precise experimental extraction of the isospin dependent antikaon-nucleon scattering lengths, funda mental quantities for understanding low-energy QCD in the strangeness sector. The experimental challenge of the kaonic deuterium measurement is the very small X-rays yield, the even larger width (compared to kaonic hy drogen), and the difficulty to perform X-rays spectroscopy with weak signals in the high radiation environment of DAΦNE. It was, therefore, crucial to develop a new apparatus involving large-area X-rays detector system, to optimize the signal and to control and by improve the signal-to-background ratio by gaining in solid angle, increasing the timing capability, and as well implementing additional charge particle tracking veto systems.
Hadronic contribution to the Muon 𝑔 − 2 with emphasis on photon-photon fusion processes
Authors: Ren Xiu-Lei
Published: February 2024

The current status of muon 𝑔 − 2 is briefly reviewed, particularly for its hadronic contributions, hadronic vacuum polarization (HVP) and hadronic light-by-light (HLbL), using the data-driven and dispersive approach. As the subprocess of HLbL, the photon-photon fusion to hadrons, especially to π+π−π0 process, is studied in detail.
Helicity-flip transitions and the t-dependence of exclusive photoproduction of rho meson
Authors: Cisek Anna , Schäfer Wolfgang , Szczurek Antoni
Published: February 2024

We calculate the differential cross section dσ/dt for the diffractive photoproduction process γp → ρp and compare our results with experimental data. Our model is based on two-gluon exchange in the nonperturbative domain. We take into account both helicity conserving and often neglected helicity-flip amplitudes in the γ → V transition, which can contribute at finite t. The shape of the differential cross section as well as the role of helicity-flip processes is strongly related to the dependence of the unintegrated gluon distribution on transverse momenta in the nonperturbative region.
Decays of the tensor glueball in a chiral approach
Authors: Vereijken Arthur
Published: February 2024

Glueballs remain an experimentally undiscovered prediction of QCD. Lattice QCD predicts a spectrum of glueballs, with the tensor (JPC = 2++) glueball being the second lightest, behind the scalar glueball. From an effective hadronic model based on spontaneous and explicit chiral symmetry breaking, we compute decay ratios of the tensor glueball into various meson decay chan nels. We find the tensor glueball to primarily decay into 2 vector mesons, dom inated by ρρ and K* K*. These results are compared to experimental data of decay rates of spin 2 mesons. Based on this comparison we make statements on the eligibility of these mesons as potential tensor glueball candidates.
Insight into the light-flavour particle production mechanism from studies of the transverse spherocity dependence in pp collisions at √s =13 TeV with ALICE at the LHC
Authors: Rath Rutuparna
Published: February 2024

The Large Hadron Collider (LHC) Run 1 and Run 2 data revealed heavy-ion-like features such as enhanced strangeness production and long-range azimuthal correlation in high-multiplicity pp collisions paving the way to rethink particle production in small collision systems. Event shape observables like transverse spherocity are sensitive to isotropic and jet-like topologies, which are useful tools to distinguish the pp collisions dominated by soft or hard physics. The interplay between multiplicity and transverse spherocity on light-flavour particle production can be understood by comparing the results obtained by selecting multiplicity and/or transverse spherocity. This contribution presents recent results on light-flavour particle production (π, K, p, ф, K*0, K0s, Λ, ξ) at midrapidity obtained by the ALICE experiment in pp collisions at √s = 13 TeV as a function of event multiplicities and transverse spherocity. The results are even obtained by going to the most extreme selections such as the highest 0–1% in multiplicity and the highest 0–10% in transverse sphe rocity. The results include the transverse momentum spectra, yields, 〈pT〉 and their ratios. These measurements will be compared with the Monte Carlo (MC) predictions obtained from models such as PYTHIA8, EPOS and Herwig7.
Compositeness of near-threshold exotic hadrons with decay and coupled-channel effects
Authors: Kinugawa Tomona , Hyodo Tetsuo
Published: February 2024

Abstract. The near-threshold exotic hadrons such as Tcc and X(3872) are naively considered as the hadronic molecular state from the viewpoint of the low-energy universality. However, it is also known that the elementary dominant state is not completely excluded as the internal structure of the near-threshold states. Furthermore, the dominance of molecules is expected to be modified by the decay or coupled channels. We discuss these features of the near-threshold bound states by calculating the compositeness with the effective field theory.
Quark mass dependence of D*s0 (2317) and Ds1(2460) states
Authors: Gil Domínguez Fernando , Molina Raquel
Published: February 2024

Abstract. We investigate the dependence of both light and heavy quark masses on the properties of low-lying charmed mesons within the framework of one-loop HHX PT. Determination of the low energy constants is accomplished through an analysis of lattice data obtained from various Lattice Quantum Chro-modynamics (LQCD) simulations. Model selection tools are employed to identify the pertinent parameters needed to achieve higher precision alignment with the data. Our study extends to the analysis of HSC energy levels for DK scattering in I = 0, considering different boosts and two pion masses. A comprehensive global fit is performed, incorporating HSC energy levels along with those from DK and D* K scattering obtained from RQCD and Prelovsek et al. Finally, we extract the dependence of D*s0(2317) and Ds1(2460) resonances on the pion mass.
Test for Non-Relativistic QED in decays of positronium atoms
Authors: Sharma Sushil , Dulski Kamil , Moskal Pawel
Published: February 2024

Abstract. Positronium (Ps) is a bound state of electron and positron governed by electromagnetic interactions. Precise measurement of its decay rate is an important observational parameter to test theoretical predictions derived from Non-Relativistic Quantum Electrodynamics (NRQED). In this work, we present a new method for measuring the decay rate of Ps atoms, which has the potential to improve the precision and thus the description of the behavior of particles in bound states and to provide insight into the non-relativistic regime of QED.
Neutral meson production in Ag+Ag at √SNN = 2.55 GeV
Authors: Prozorov Alexandr
Published: February 2024

Abstract. Relativistic nucleus-nucleus collisions offer a unique possibility for studying nuclear matter under the influence of high temperature and pressure. During the collision a system of interacting nucleons, resonances, and mesons, called hadronic fireball, is created. HADES is a unique experiment capable of simultaneously measuring all three species of pions for this energy regime. Results on neutral pion production in Ag + Ag collisions at √SNN = 2.55 GeV (beam energy 1.58 A GeV) with 14 billion collected events will be presented. A measurement of a directed and elliptic flow, and yields of neutral pions corrected for detector acceptance and efficiency will be shown with respect to transverse momentum and rapidity for certain centrality classes; and further compared with the data, and charged pion data measured in the same experiment. In addition, the obtained results will be confronted with up-to-date model calculations.