bluuebunny/crossref_metadata_2025 huggingface dataset:
Direct prediction of intrinsically disordered protein conformational properties from sequence
Authors: Lotthammer Jeffrey M. , Ginell Garrett M. , Griffith Daniel , Emenecker Ryan J. , Holehouse Alex S.
Published: January 2024

Intrinsically disordered regions (IDRs) are ubiquitous across all domains of life and play a range of functional roles. While folded domains are generally well described by a stable three-dimensional structure, IDRs exist in a collection of interconverting states known as an ensemble. This structural heterogeneity means that IDRs are largely absent from the Protein Data Bank, contributing to a lack of computational approaches to predict ensemble conformational properties from sequence. Here we combine rational sequence design, large-scale molecular simulations and deep learning to develop ALBATROSS, a deep-learning model for predicting ensemble dimensions of IDRs, including the radius of gyration, end-to-end distance, polymer-scaling exponent and ensemble asphericity, directly from sequences at a proteome-wide scale. ALBATROSS is lightweight, easy to use and accessible as both a locally installable software package and a point-and-click-style interface via Google Colab notebooks. We first demonstrate the applicability of our predictors by examining the generalizability of sequence–ensemble relationships in IDRs. Then, we leverage the high-throughput nature of ALBATROSS to characterize the sequence-specific biophysical behavior of IDRs within and between proteomes.
Tropomyosin 1-I/C coordinates kinesin-1 and dynein motors during oskar mRNA transport
Authors: Heber Simone , McClintock Mark A. , Simon Bernd , Mehtab Eve , Lapouge Karine , Hennig Janosch , Bullock Simon L. , Ephrussi Anne
Published: January 2024

Dynein and kinesin motors mediate long-range intracellular transport, translocating towards microtubule minus and plus ends, respectively. Cargoes often undergo bidirectional transport by binding to both motors simultaneously. However, it is not known how motor activities are coordinated in such circumstances. In theDrosophilafemale germline, sequential activities of the dynein–dynactin–BicD–Egalitarian (DDBE) complex and of kinesin-1 deliveroskarmessenger RNA from nurse cells to the oocyte, and within the oocyte to the posterior pole. We show through in vitro reconstitution that Tm1-I/C, a tropomyosin-1 isoform, links kinesin-1 in a strongly inhibited state to DDBE-associatedoskarmRNA. Nuclear magnetic resonance spectroscopy, small-angle X-ray scattering and structural modeling indicate that Tm1-I/C suppresses kinesin-1 activity by stabilizing its autoinhibited conformation, thus preventing competition with dynein until kinesin-1 is activated in the oocyte. Our work reveals a new strategy for ensuring sequential activity of microtubule motors.
MALDI-TOF as a powerful tool for identifying and differentiating closely related microorganisms: the strange case of three reference strains of Paenibacillus polymyxa
Authors: Lebano Ilaria , Fracchetti Fabio , Vigni Mario Li , Mejia Juan Fernando , Felis Giovanna , Lampis Silvia
Published: January 2024

Accurate identification and typing of microbes are crucial steps in gaining an awareness of the biological heterogeneity and reliability of microbial material within any proprietary or public collection.Paenibacillus polymyxais a bacterial species of great agricultural and industrial importance due to its plant growth-promoting activities and production of several relevant secondary metabolites. In recent years, matrix-assisted laser desorption ionisation time-of-flight mass spectrometry (MALDI-TOF MS) has been widely used as an alternative rapid tool for identifying, typing, and differentiating closely related strains. In this study, we investigated the diversity of threeP. polymyxastrains. The mass spectra of ATCC 842T, DSM 292, and DSM 365 were obtained, analysed, and compared to select discriminant peaks using ClinProTools software and generate classification models. MALDI-TOF MS analysis showed inconsistent results in identifying DSM 292 and DSM 365 as belonging toP. polimixaspecies, and comparative analysis of mass spectra revealed the presence of highly discriminatory biomarkers among the three strains. 16S rRNA sequencing and Average Nucleotide Identity (ANI) confirmed the discrepancies found in the proteomic analysis. The case study presented here suggests the enormous potential of the proteomic-based approach, combined with statistical tools, to predict and explore differences between closely related strains in large microbial datasets.
Research on improved black widow algorithm for medical image denoising
Authors: Qu Hepeng , Liu Kun , Zhang Lina
Published: January 2024

Improving the quality of medical images is crucial for accurate clinical diagnosis; however, medical images are often disrupted by various types of noise, posing challenges to the reliability and diagnostic accuracy of the images. This study aims to enhance the Black Widow optimization algorithm and apply it to the task of denoising medical images to improve both the quality of medical images and the accuracy of diagnostic results. By introducing Tent mapping, we refined the Black Widow optimization algorithm to better adapt to the complex features of medical images. The algorithm's denoising capabilities for various types of noise were enhanced through the combination of multiple filters, all without the need for training each time to achieve preset goals. Simulation results, based on processing a dataset containing 1588 images with Gaussian, salt-and-pepper, Poisson, and speckle noise, demonstrated a reduction in Mean Squared Error (MSE) by 0.439, an increase in Peak Signal-to-Noise Ratio (PSNR) by 4.315, an improvement in Structural Similarity Index (SSIM) by 0.132, an enhancement in Edge-to-Noise Ratio (ENL) by 0.402, and an increase in Edge Preservation Index (EPI) by 0.614. Simulation experiments verified that the proposed algorithm has a certain advantage in terms of computational efficiency. The improvement, incorporating Tent mapping and a combination of multiple filters, successfully elevated the performance of the Black Widow algorithm in medical image denoising, providing an effective solution for enhancing medical image quality and diagnostic accuracy.
National prevalence and trends in food labeling awareness, comprehension, usage, and COVID-19 pandemic-related factors in South Korea, 2014–2022
Authors: Choi Yujin , Kim Hyeon Jin , Park Jaeyu , Lee Seung Won , Rahmati Masoud , Koyanagi Ai , Smith Lee , Kim Min Seo , López Sánchez Guillermo F. , Dragioti Elena , Lee Jinseok , Rhee Sang Youl , Kim Sunyoung , Lim Hyunjung , Yon Dong Keon
Published: January 2024

Although food labeling on food packages is crucial for promoting a healthy diet, limited research has been conducted on how the COVID-19 pandemic (hereinafter “the pandemic”) has affected food labeling awareness. Therefore, this study aims to analyze the changes in trends in food labeling awareness, comprehension, and usage in South Korea during the pandemic. We utilized a nationwide, large-scale, and long-term dataset provided by the Korea Community Health Survey (KCHS) from 2014 to 2022 (total = 1,756,847 participants). This allowed the researchers to assess the long-term trends in the prevalence of food labeling awareness, comprehension, and usage. Furthermore, we investigated the factors associated with awareness specifically related to the pandemic. In total, 1,756,847 adults (54.19% women) participated in this study. The upward slope in overall food labeling awareness became less pronounced and even exhibited a downward slope during the pandemic (βdiff − 1.759; 95% CI − 1.874 to − 1.644). The upward slope in food labeling comprehension and usage became more pronounced during the pandemic (comprehension: βdiff 0.535; 95% CI 0.436–0.634; usage: βdiff 0.693; 95% CI 0.601–0.785). The vulnerability factors associated with lower food labeling awareness during the pandemic included older age, male, obesity, residing in rural areas, lower household income, lower educational level, smoking, and increased alcohol consumption. This study analyzed the 9-year trend in the prevalence of food labeling awareness, comprehension, and usage based on nationally representative data of adults in South Korea from 2014 to 2022. Our findings suggest that personalized nutrition strategies are needed to recognize vulnerable groups with risk factors and improve food labeling awareness among Korean adults during the pandemic.
Investigation of the emergency water supply schemes for youkou groundwater source field in Nanchang using a simulation–optimization model
Authors: Ma Qingshan , Wu Huijie , Ge Weiya , Zhang Jia
Published: January 2024

To enhance the resilience of Nanchang’s water supply system and ensure a dependable emergency water supply. Taking youkou emergency groundwater source field as an example, a flow simulation model was developed through an analysis of the hydrogeological conditions in the study area. Additionally, an optimization model based on the genetic algorithm (GA) technique was constructed and integrated into the flow simulation model. Subsequently, various water supply schemes were simulated with the minimum cost of groundwater extraction as the objective function. The results show that the values of the objective function were reduced by 4.92%, 15.67%, and 42.35% for the three different optimization schemes, namely pumping rates, joint pumping rates and the number of wells, and joint pumping rates, number of wells and well location. Ultimately, the optimal emergency water supply scheme was determined by considering a comprehensive range of factors. These factors encompassed considerations such as the area of the water level depression funnel, the dewatering thickness of the aquifer and the recovery of the groundwater level. The practice shows that the simulation–optimization model could effectively simulate complex groundwater flow systems, meeting the objective function and constraints toachieve the optimal exploitation scheme.
Temporal dynamics of the early immune response following Mycobacterium bovis infection of cattle
Authors: Holder Thomas , Srinivasan Sreenidhi , McGoldrick Adrian , Williams Gareth A. , Palmer Simonette , Clarke John , O’Brien Amanda , Conlan Andrew J. K. , Juleff Nick , Vordermeier H. Martin , Jones Gareth J. , Kapur Vivek
Published: January 2024

Bovine tuberculosis is an infectious disease of global significance that remains endemic in many countries. Mycobacterium bovis infection in cattle is characterized by a cell-mediated immune response (CMI) that precedes humoral responses, however the timing and trajectories of CMI and antibody responses determined by newer generation assays remain undefined. Here we used defined-antigen interferon-gamma release assays (IGRA) and an eleven-antigen multiplex ELISA (Enferplex TB test) alongside traditional tuberculin-based IGRA and IDEXX M. bovis antibody tests to assess immune trajectories following experimental M. bovis infection of cattle. The results show CMI responses developed as early as two-weeks post-infection, with all infected cattle testing positive three weeks post-infection. Interestingly, 6 of 8 infected animals were serologically positive with the Enferplex TB assay as early as 4 weeks post-infection. As expected, application of the tuberculin skin test enhanced subsequent serological reactivity. Infrequent M. bovis faecal shedding was observed but was uncorrelated with observed immune trajectories. Together, the results show that early antibody responses to M. bovis infection are detectable in some individuals and highlight an urgent need to identify biomarkers that better predict infection outcomes, particularly for application in low-and-middle income countries where test-and-slaughter based control methods are largely unfeasible.
Facial and genital color ornamentation, testosterone, and reproductive output in high-ranking male rhesus macaques
Authors: Sobral Gisela , Dubuc Constance , Winters Sandra , Ruiz‑Lambides Angelina , Emery Thompson Melissa , Maestripieri Dario , Milich Krista M.
Published: January 2024

Males in many vertebrate species have colorful ornaments that evolved by sexual selection. The role of androgens in the genesis and maintenance of these signals is unclear. We studied 21 adult high-ranking male rhesus macaques from nine social groups in the free-ranging population on Cayo Santiago, Puerto Rico, and analyzed facial and genital skin luminance and redness, fecal androgens, rates of mating behaviors, and offspring sired. Facial and genital coloration varied in relation to age, mating behavior, reproductive success, and testosterone concentration. Our results indicate that skin coloration in high-ranking male rhesus macaques is a sexually-selected trait mediated by androgens. These results add to the growing literature on the proximate and ultimate causes of male sexual signals and highlight the need to examine how these characteristics change with age in other species.
Automated deep learning model for estimating intraoperative blood loss using gauze images
Authors: Yoon Dan , Yoo Mira , Kim Byeong Soo , Kim Young Gyun , Lee Jong Hyeon , Lee Eunju , Min Guan Hong , Hwang Du-Yeong , Baek Changhoon , Cho Minwoo , Suh Yun-Suhk , Kim Sungwan
Published: January 2024

The intraoperative estimated blood loss (EBL), an essential parameter for perioperative management, has been evaluated by manually weighing blood in gauze and suction bottles, a process both time-consuming and labor-intensive. As the novel EBL prediction platform, we developed an automated deep learning EBL prediction model, utilizing the patch-wise crumpled state (P-W CS) of gauze images with texture analysis. The proposed algorithm was developed using animal data obtained from a porcine experiment and validated on human intraoperative data prospectively collected from 102 laparoscopic gastric cancer surgeries. The EBL prediction model involves gauze area detection and subsequent EBL regression based on the detected areas, with each stage optimized through comparative model performance evaluations. The selected gauze detection model demonstrated a sensitivity of 96.5% and a specificity of 98.0%. Based on this detection model, the performance of EBL regression stage models was compared. Comparative evaluations revealed that our P-W CS-based model outperforms others, including one reliant on convolutional neural networks and another analyzing the gauze’s overall crumpled state. The P-W CS-based model achieved a mean absolute error (MAE) of 0.25 g and a mean absolute percentage error (MAPE) of 7.26% in EBL regression. Additionally, per-patient assessment yielded an MAE of 0.58 g, indicating errors < 1 g/patient. In conclusion, our algorithm provides an objective standard and streamlined approach for EBL estimation during surgery without the need for perioperative approximation and additional tasks by humans. The robust performance of the model across varied surgical conditions emphasizes its clinical potential for real-world application.
Analysis of related factors of plasma antibody levels in patients with severe and critical COVID-19
Authors: Xie Yudi , Xia Yang , Xu Haixia , Wang Jue , Zhang Wei , Li Ling , Liu Zhong
Published: January 2024

Coronavirus disease 2019 (COVID-19) continues to impact global public health. The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has become less virulent as it mutates, prompting China to ease restrictions at the end of 2022. With the complete reopening, a surge in COVID-19 cases has ensued. Therefore, we conducted a study to explore the correlation between plasma antibody levels and baseline conditions or clinical outcomes in severe and critical patients. We collected the basic information of 79 included patients. Enzyme-linked immunosorbent assay (ELISA) tests were performed on plasma samples. The receptor-binding domain (RBD) IgG antibody level of the mild group was significantly higher than that of the severe/critical group (P = 0.00049). And in the severe/critical group, there existed an association between plasma antibody levels and age (P < 0.001, r = − 0.471), as well as plasma antibody levels and vaccination status (P = 0.00147, eta2 = 0.211). Besides, the level of plasma antibody seemed to be moderately correlated with the age, indicating the need for heightened attention to infections in the elderly. And plasma antibody levels were strongly associated with vaccination status in the severe/critical patients.
Evidence that recent climatic changes have expanded the potential geographical range of the Mediterranean fruit fly
Authors: Szyniszewska Anna M. , Bieszczak Hanna , Kozyra Karol , Papadopoulos Nikos T. , De Meyer Marc , Nowosad Jakub , Ota Noboru , Kriticos Darren J.
Published: January 2024

The species distributions migration poleward and into higher altitudes in a warming climate is especially concerning for economically important insect pest species, as their introduction can potentially occur in places previously considered unsuitable for year-round survival. We explore the expansion of the climatically suitable areas for a horticultural pest, the Mediterranean fruit fly (medfly) Ceratitis capitata (Diptera, Tephritidae), with an emphasis on Europe and California. We reviewed and refined a published CLIMEX model for C. capitata, taking into consideration new records in marginal locations, with a particular focus on Europe. To assess the model fit and to aid in interpreting the meaning of the new European distribution records, we used a time series climate dataset to explore the temporal patterns of climate suitability for C. capitata from 1970 to 2019. At selected bellwether sites in Europe, we found statistically significant trends in increasing climate suitability, as well as a substantial northward expansion in the modelled potential range. In California, we also found a significant trend of northward and altitudinal expansion of areas suitable for C. capitata establishment. These results provide further evidence of climate change impacts on species distributions and the need for innovative responses to increased invasion threats.
Modeling mutation-specific arrhythmogenic phenotypes in isogenic human iPSC-derived cardiac tissues
Authors: Maurissen Thomas L. , Kawatou Masahide , López-Dávila Víctor , Minatoya Kenji , Yamashita Jun K. , Woltjen Knut
Published: January 2024

Disease modeling using human induced pluripotent stem cells (hiPSCs) from patients with genetic disease is a powerful approach for dissecting pathophysiology and drug discovery. Nevertheless, isogenic controls are required to precisely compare phenotypic outcomes from presumed causative mutations rather than differences in genetic backgrounds. Moreover, 2D cellular models often fail to exhibit authentic disease phenotypes resulting in poor validation in vitro. Here we show that a combination of precision gene editing and bioengineered 3D tissue models can establish advanced isogenic hiPSC-derived cardiac disease models, overcoming these drawbacks. To model inherited cardiac arrhythmias we selected representative N588D and N588K missense mutations affecting the same codon in the hERG potassium channel gene KCNH2, which are reported to cause long (LQTS) and short (SQTS) QT syndromes, respectively. We generated compound heterozygous variants in normal hiPSCs, and differentiated cardiomyocytes (CMs) and mesenchymal cells (MCs) to form 3D cardiac tissue sheets (CTSs). In hiPSC-derived CM monolayers and 3D CTSs, electrophysiological analysis with multielectrode arrays showed prolonged and shortened repolarization, respectively, compared to the isogenic controls. When pharmacologically inhibiting the hERG channels, mutant 3D CTSs were differentially susceptible to arrhythmic events than the isogenic controls. Thus, this strategy offers advanced disease models that can reproduce clinically relevant phenotypes and provide solid validation of gene mutations in vitro.
Olfactory system structure and function in newly hatched and adult locusts
Authors: Sun Kui , Ray Subhasis , Gupta Nitin , Aldworth Zane , Stopfer Mark
Published: January 2024

An important question in neuroscience is how sensory systems change as animals grow and interact with the environment. Exploring sensory systems in animals as they develop can reveal how networks of neurons process information as the neurons themselves grow and the needs of the animal change. Here we compared the structure and function of peripheral parts of the olfactory pathway in newly hatched and adult locusts. We found that populations of olfactory sensory neurons (OSNs) in hatchlings and adults responded with similar tunings to a panel of odors. The morphologies of local neurons (LNs) and projection neurons (PNs) in the antennal lobes (ALs) were very similar in both age groups, though they were smaller in hatchlings, they were proportional to overall brain size. The odor evoked responses of LNs and PNs were also very similar in both age groups, characterized by complex patterns of activity including oscillatory synchronization. Notably, in hatchlings, spontaneous and odor-evoked firing rates of PNs were lower, and LFP oscillations were lower in frequency, than in the adult. Hatchlings have smaller antennae with fewer OSNs; removing antennal segments from adults also reduced LFP oscillation frequency. Thus, consistent with earlier computational models, the developmental increase in frequency is due to increasing intensity of input to the oscillation circuitry. Overall, our results show that locusts hatch with a fully formed olfactory system that structurally and functionally matches that of the adult, despite its small size and lack of prior experience with olfactory stimuli.
Aerosolized delivery of ESKAPE pathogens for murine pneumonia models
Authors: Rox Katharina , Medina Eva
Published: January 2024

Murine pneumonia models for ESKAPE pathogens serve to evaluate novel antibacterials or to investigate immunological responses. The majority of published models uses intranasal or to a limited extent the intratracheal instillation to challenge animals. In this study, we propose the aerosol delivery of pathogens using a nebulizer. Aerosol delivery typically results in homogeneous distribution of the inoculum in the lungs because of lower particle size. This is of particular importance when compounds are assessed for their pharmacokinetic and pharmacodynamic (PK/PD) relationships as it allows to conduct several analysis with the same sample material. Moreover, aerosol delivery has the advantage that it mimics the ‘natural route’ of respiratory infection. In this short and concise study, we show that aerosol delivery of pathogens resulted in a sustained bacterial burden in the neutropenic lung infection model for five pathogens tested, whereas it gave a similar result in immunocompetent mice for three out of five pathogens. Moreover, a substantial bacterial burden in the lungs was already achieved 2 h post inhalation. Hence, this study constitutes a viable alternative for intranasal administration and a refinement of murine pneumonia models for PK/PD assessments of novel antibacterial compounds allowing to study multiple readouts with the same sample material.
Time–frequency analysis of gustatory event related potentials (gERP) in taste disorders
Authors: Mastinu Mariano , Grzeschuchna Lisa Sophie , Mignot Coralie , Guducu Cagdas , Bogdanov Vasyl , Hummel Thomas
Published: January 2024

In taste disorders, the key to a correct diagnosis and an adequate treatment is an objective assessment. Compared to psychophysical tests, EEG-derived gustatory event-related potentials (gERP) could be used as a less biased measure. However, the responses identified using conventional time-domain averaging show a low signal-to-noise ratio. This study included 44 patients with dysgeusia and 59 healthy participants, who underwent a comprehensive clinical examination of gustatory function. gERPs were recorded in response to stimulation with two concentrations of salty solutions, which were applied with a high precision gustometer. Group differences were examined using gERP analyzed in the canonical time domain and with Time–Frequency Analyses (TFA). Dysgeusic patients showed significantly lower scores for gustatory chemical and electrical stimuli. gERPs failed to show significant differences in amplitudes or latencies between groups. However, TFA showed that gustatory activations were characterized by a stronger power in controls than in patients in the low frequencies (0.1–4 Hz), and a higher desynchronization in the alpha-band (8–12 Hz). Hence, gERPs reflect the altered taste sensation in patients with dysgeusia. TFA appears to enhance the signal-to-noise ratio commonly present when using conventional time-domain averaging, and might be of assistance for the diagnosis of dysgeusia.
Downregulation of Roundabout guidance receptor 2 suppresses hepatocellular carcinoma progression by interacting with Y-box binding protein 1
Authors: Liu Ting , Zhai Congjie , Tian Bo , Li Chao , Han Shuangshuang , Wang Shihui , Xuan Mingda , Liu Dehua , Zhao Yunxia , Zhao Hongyan , Yu Weifang , Wang Jia
Published: January 2024

Roundabout guidance receptor 2 (Robo2) is closely related to malignant tumors such as pancreatic cancer and liver fibrosis, but there is no relevant research on the role of Robo2 in HCC. The study will further explore the function and mechanism of Robo2 and its downstream target genes in HCC. Firstly, Robo2 protein levels in human HCC tissues and paired adjacent normal liver tissues were detected. Then we established HepG2 and Huh7 hepatoma cell lines with knock-down Robo2 by transfection with lentiviral vectors, and examined the occurrence of EMT, proliferation and apoptosis abilities in HCC cells by western blot, flow cytometry, wound healing assay and TUNEL staining. Then we verified the interaction between Robo2 and its target gene by Co-IP and immunofluorescence co-staining, and further explored the mechanism of Robo2 and YB-1 by rescue study. The protein expression level of Robo2 in HCC was considerably higher than that in the normal liver tissues. After successfully constructing hepatoma cells with knock-down Robo2, it was confirmed that down-regulated Robo2 suppressed EMT and proliferation of hepatoma cells, and accelerated the cell apoptosis. High-throughput sequencing and validation experiments verified that YB-1 was the downstream target gene of Robo2, and over-expression of YB-1 could reverse the apoptosis induced by Robo2 down-regulation and its inhibitory effect on EMT and proliferation. Robo2 deficiency inhibits EMT and proliferation of hepatoma cells and augments the cell apoptosis by regulating YB-1, thus inhibits the occurrence of HCC and provides a new strategy for the treatment of HCC.
False-positive results of galactomannan assays in patients administered glucose-containing solutions
Authors: Shin Dong Woo , Cho Jungwon , Choi Kyung Suk , Lee Jungwha , Choi Yunsang , Choi Seong Jin , Kim Sang-A , Moon Song Mi , Kim Eu Suk , Kim Hong Bin , Park Kyoung Un , Hong Yun Ji , Song Kyoung-Ho
Published: January 2024

Galactomannan (GM) is a polysaccharide cell wall component released by Aspergillus spp., and an immunoenzymatic GM assay is used for the diagnosis of invasive pulmonary aspergillosis. We evaluated the cause of strong positivity for GM in patients with no typical signs of aspergillosis. Repeat assays were performed using different instruments and reagent lots, but there were no differences in results among the assays. Patients with strongly positive GM results were investigated. Medication histories revealed that 14 of 23 patients had been administered total parenteral nutrition solution from one manufacturer and 4 patients had been administered dextrose solution from a different manufacturer before being tested. The results of GM assays conducted on samples of dextrose solution and the glucose fraction of the total parenteral nutrition solution were strongly positive, confirming the causes of the false-positive reactions. We hypothesize that a trace amount of GM was introduced into the glucose-containing solutions because glucoamylase, which is necessary for the saccharification step of glucose synthesis, was derived from Aspergillus niger. To enhance patient care and prevent unnecessary antifungal prescriptions, healthcare providers and manufacturers of healthcare products need to be aware of the possibility of false-positive reactions for GM.
Dose-dependent exposure to indoxyl sulfate alters AHR signaling, sirtuins gene expression, oxidative DNA damage, and bone mineral status in rats
Authors: Karbowska Malgorzata , Pawlak Krystyna , Sieklucka Beata , Domaniewski Tomasz , Lebkowska Urszula , Zawadzki Radoslaw , Pawlak Dariusz
Published: January 2024

Indoxyl sulfate (IS), an agonist of aryl hydrocarbon receptors (AhR), can accumulate in patients with chronic kidney disease, but its direct effect on bone is not clear. The present study investigated the effect of chronic exposure to low (100 mg/kg b.w.; 100 IS) and high (200 mg/kg b.w.; 200 IS) dose of IS on bone AhR pathway, sirtuins (SIRTs) expression, oxidative DNA damage and bone mineral status in Wistar rats. The accumulation of IS was observed only in trabecular bone tissue in both doses. The differences were observed in the bone parameters, depending on the applied IS dose. The exposure to 100 IS increased AhR repressor (AhRR)-CYP1A2 gene expression, which was associated with SIRT-1, SIRT-3 and SIRT-7 expression. At the low dose group, the oxidative DNA damage marker was unchanged in the bone samples, and it was inversely related to the abovementioned SIRTs expression. In contrast, the exposure to 200 IS reduced the expression of AhRR, CYP1A, SIRT-3 and SIRT-7 genes compared to 100 IS. The level of oxidative DNA damage was higher in trabecular bone in 200 IS group. Femoral bone mineral density was decreased, and inverse relations were noticed between the level of trabecular oxidative DNA damage and parameters of bone mineral status. In conclusion, IS modulates AhR-depending signaling affecting SIRTs expression, oxidative DNA damage and bone mineral status in a dose dependent manner.
Far-reaching effects of tyrosine64 phosphorylation on Ras revealed with BeF3– complexes
Authors: Baumann Patrick , Jin Yi
Published: January 2024

Tyrosine phosphorylation on Ras by Src kinase is known to uncouple Ras from upstream regulation and downstream communication. However, the mechanisms by which phosphorylation modulates these interactions have not been detailed. Here, the major mono-phosphorylation level on tyrosine64 is quantified by 31P NMR and mutagenesis. Crystal structures of unphosphorylated and tyrosine64-phosphorylated Ras in complex with a BeF3− ground state analogue reveal “closed” Ras conformations very different from those of the “open” conformations previously observed for non-hydrolysable GTP analogue structures of Ras. They deliver new mechanistic and conformational insights into intrinsic GTP hydrolysis. Phosphorylation of tyrosine64 delivers conformational changes distant from the active site, showing why phosphorylated Ras has reduced affinity to its downstream effector Raf. 19F NMR provides evidence for changes in the intrinsic GTPase and nucleotide exchange rate and identifies the concurrent presence of a major “closed” conformation alongside a minor yet functionally important “open” conformation at the ground state of Ras. This study expands the application of metal fluoride complexes in revealing major and minor conformational changes of dynamic and modified Ras proteins.
Rapid screening of bacteriostatic and bactericidal antimicrobial agents against Escherichia coli by combining machine learning (artificial intelligence) and UV-VIS spectroscopy
Authors: Orrell-Trigg R. , Awad M. , Gangadoo S. , Cheeseman S. , Shaw Z. L. , Truong V. K. , Cozzolino D. , Chapman J.
Published: January 2024

A standard UV-Vis spectrophotometer, chemometrics, and machine learning algorithms enables faster identification of bacteriostatic and bactericidal mechanisms. Compared to traditional methods, this approach accelerates the evaluation of tetracycline and amoxicillin on E. coli.
Which nets are the most common? Reticular chemistry and information entropy
Authors: Krivovichev Sergey V.
Published: January 2024

The information-entropy measures of the complexity of 3D nets indicate that the most common nets in metal–organic frameworks (MOFs) are usually the simplest and highest-entropy nets within the respective category.
Oxygen vacancy-enriched Zn2SnO4 for aliphatic alcohol sensing and enhanced selectivity towards n-butanol
Authors: Parayil Reshmi Thekke , Bhagat B. , Gupta Santosh K. , Mukherjee K. , Mohapatra Manoj
Published: January 2024

This work highlights the potential of oxygen vacancies enriched in high-temperature-annealed zinc stannate towards the selective gas sensing of n-butanol.
Beyond the electrical double layer model: ion-dependent effects in nanoscale solvent organization
Authors: Souna Amanda J. , Motevaselian Mohammad H. , Polster Jake W. , Tran Jason D. , Siwy Zuzanna S. , Aluru Narayana R. , Fourkas John T.
Published: January 2024

Electrochemical measurements, nonlinear spectroscopy, and MD simulations are used to explore how the sizes and identities of ions influence their non-uniform distribution in acetonitrile that is highly organized due to proximity to a polar interface.
Competitive adsorption mechanisms of Cd(ii), Cu(ii) and Pb(ii) on bioinspired mesoporous silica revealed by complementary adsorption/isothermal titration calorimetry studies
Authors: Gourmand Cléophée , Bertagnolli Caroline , Prelot Bénédicte , Boos Anne , Hubscher-Bruder Véronique , Brandel Jérémy
Published: January 2024

This work presents an original adsorption/isothermal titration calorimetry (ITC) study that allowed highlighting the competitive adsorption mechanisms of Cd(ii), Cu(ii) and Pb(ii) on bioinspired mesoporous silica.
Nano-mineral assemblages in mercury- and silver-contaminated soils: records of sequestration, transformation, and release of mercury- and silver-bearing nanoparticles
Authors: Schindler Michael , Loria Ainsleigh , Ramos-Arroyo Yann Rene , Wang Feiyue
Published: January 2024

In mercury-contaminated soils, mercury sulfides (HgS) occur as nanoparticles in mineral surface coatings. The coatings are composed of ferrihydrite and its replacement by goethite results in the release of the HgS nanoparticles.
Analysis of design criteria for biological post-treatment of ozonated wastewater treatment plant effluent
Authors: Sauter Daniel , Gnirss Regina , Wintgens Thomas
Published: January 2024

This study provides a science-based approach for the design of biological post-treatment of ozonated wastewater treatment plant effluent and compares it with common practice.
On-chip droplet analysis and cell spheroid screening by capillary wrapping enabled shape-adaptive ferrofluid transporters
Authors: Wang Xuejiao , Li Xin , Pu Aoyang , Shun Ho Bak , Chen Cien , Ai Liqing , Tan Zhaoling , Zhang Jilin , Liu Kai , Gao Jun , Ban Kiwon , Yao Xi
Published: January 2024

We propose a ferrofluid transporter for digital droplet manipulation in an additive-free and lossless manner. The transporter shows high reliability with an on-chip design for droplet-based bioanalysis and high throughput cell spheroid screening.
Exploring pristine and transition metal doped SiP2 monolayer as a promising anode material for metal (Li, Na, Mg) ion battery
Authors: Sahoo Shubham , Kumari Puja , Ray Soumya Jyoti
Published: January 2024

We investigate the structural and electronic properties of pristine 2D SiP2 monolayers, and upon doping with a transition metal (Cr, Mn, Co, Ni). Further, we show the potential application as an anode material in metal ion batteries.
Porous single crystal microcubes of niobium nitride for highly efficient electrocatalysis
Authors: Li Xuehua , Luo Cong , Lin Guoming , Xi Shaobo , Xie Kui
Published: January 2024

This study successfully prepared porous single crystal niobium nitride microcubes with abundant active sites, which greatly enhances the catalytic activity and stability of the electrode.
Highly dispersed Pd nanoparticles on a SiO2 support for dehydrogenation of dodecahydro-N-ethylcarbazole
Authors: Shi Monan , Zhang Chunying , Ma Mengnan , Zhang Chen , Huang Long
Published: January 2024

Highly dispersed Pd catalysts for dehydrogenation of dodecahydro-N-ethylcarbazole were prepared using an amino modification method. The kinetic model and Pd particle size effect on dehydrogenation reactivity were studied.
A copper–palladium/reduced graphene oxide composite as a catalyst for the oxygen reduction reaction
Authors: Brusko Vasiliy , Prytkova Anna , Kirsanova Maria , Vakhitov Iskander , Sabirova Aigul , Tayurskii Dmitrii , Kadirov Marsil , Dimiev Ayrat M.
Published: January 2024

Replacing expensive platinum in electrocatalytic materials by cheaper and readily available alternatives is a paramount task in hydrogen-based energetics.
Reversible optical control of magnetism in engineered artificial multiferroics
Authors: Ochoa Diego A. , Menéndez Enric , López-Sánchez Jesús , Del Campo Adolfo , Ma Zheng , Spasojević Irena , Fina Ignasi , Fernández José F. , Rubio-Marcos Fernando , Sort Jordi , García José E.
Published: January 2024

Reversible modulation of magnetism in Fe75Al25/BaTiO3 multiferroic heterostructures using low-intensity visible-light at room temperature is demonstrated, which constitutes an innovative approach to wireless control of magnetism in multiferroics.
A doping strategy to regulate the adsorption energy of Li2S4 and Li2S to promote sulfur reduction on Chevrel phase Mo6Se8 in lithium–sulfur batteries
Authors: Duan Tengfei , Fan Dong , Ma Zhongyun , Pei Yong
Published: January 2024

The reaction mechanism of sulfur reduction reaction on metal doped Mo6Se8 system and the linear relationship between the overpotential and adsorption energy of Li2S and Li2S4 were studied.
A silver-mediated radical process of β-keto sulfones for the synthesis of 2,3-diacyl furans
Authors: Fan Jian , Zu Yanhong , Zheng Zhimin , Song Lulu , Wang Yating , Zhou Zhou , Liu Yujun , Xu Shuwen
Published: January 2024

A concise synthesis of 2,3-diacyl furans through the intermolecular reaction of β-keto sulfones with their own three components is developed.
(NH4)2S2O8 promoted tandem radical cyclization of quinazolin-4(3H)-ones with oxamic acids for the construction of fused quinazolinones under metal-free conditions
Authors: Gao Shenyuan , Cai Menglu , Xu Gang , Jin Qiaolin , Wang Xiaozhong , Xu Linze , Wang Lixiang , Dai Liyan
Published: January 2024

A novel cascade radical addition/cyclization reaction of non-activated olefins and oxamic acids has been proposed.
Ti3AlC2 MXene nanosheets as a novel corrosion inhibitor for carbon steel in 0.5 M sulfuric acid solution
Authors: Min Xuehong , Ma Shiquan , Zhou Zongyi , Wu Dequan , Liao Bokai
Published: January 2024

Herein, anti-corrosion behavior and mechanism of Ti3AlC2 MXene nanosheets were firstly studied, which formed the protective film on metal surface due to its high adsorption capacity.
A study on the bio-based surfactant sodium cocoyl alaninate as a foaming agent for enhanced oil recovery in high-salt oil reservoirs
Authors: Hao Hongda , Wu Hongze , Diao Haoyu , Zhang Yixin , Yang Shuo , Deng Song , Li Qiu , Yan Xiaopeng , Peng Mingguo , Qu Ming , Li Xinyu , Xu Jiaming , Yang Erlong
Published: January 2024

A bio-based surfactant of SCA is proposed as a foaming agent, which has better foaming ability, stability, and anti-salt ability compared to OP-10 and SDS. It can enhance oil recovery by more than 15% after primary waterflooding.
A study of the capacity fade of a LiCoO2/graphite battery during the temperature storage process at 45 °C under different SOCs
Authors: Liu Weigang , Fan Xinming , Zheng Jingqiang , Zhang Zhi , Peng Erke , Li Zhaoyang , Chen Zhiyong , Jiang Hao , Tong Yan , Hong Bo , Li Jie
Published: January 2024

This study investigates the impact of commercial battery storage on electrochemical performance and elucidates the underlying causes of the associated capacity degradation.
Detoxification of corn stover prehydrolysate by different biochars and its effect on lactic acid fermentation
Authors: Wang Chun , Shan Yu , Shen Yuli , Fu Weng , Li Jing , Blersch David , Wu Wei , Shi Suan , Han Lujia
Published: January 2024

During the utilization of lignocellulosic biomass such as corn stover, many by-products are produced in the pretreatment process that can severely inhibit the activity of microbes in the fermentation step.
The intricate link between membrane lipid structure and composition and membrane structural properties in bacterial membranes
Authors: Lee Tzong-Hsien , Charchar Patrick , Separovic Frances , Reid Gavin E. , Yarovsky Irene , Aguilar Marie-Isabel
Published: January 2024

The dynamic nature of bacterial lipid diversity and membrane properties in response to stress conditions is discussed. This emerging area has implications for a range of cellular processes and drug design for selective cell targeting.
Stabilized four-electron aqueous zinc–iodine batteries by quaternary ammonium complexation
Authors: Jiang Pengjie , Du Qijun , Lei Chengjun , Xu Chen , Liu Tingting , He Xin , Liang Xiao
Published: January 2024

The complexation between quaternary ammonium salts and I+ species results in a solid compound that neither solubilizes nor hydrolyzes in a dilute ZnSO4 aqueous electrolyte, paving the way for the creation of four-electron Zn–I2 aqueous batteries.
Precisely modulating the chromatin tracker via substituent engineering: reporting pathological oxidative stress during mitosis
Authors: Li Jinsong , Ni Yingyong , Wang Junjun , Zhu Yicai , Wang Aidong , Zhu Xiaojiao , Sun Xianshun , Wang Sen , Li Dandan , Zhou Hongping
Published: January 2024

An in-depth understanding of cancer-cell mitosis presents unprecedented advantages for solving metastasis and proliferation of tumors, which has aroused great interest in visualizing the behavior via a luminescence tool.
The glass phase in the grain boundary of Na3Zr2Si2PO12, created by gallium modulation
Authors: Lou Chenjie , Zhang Wenda , Liu Jie , Gao Yanan , Sun Xuan , Fu Jipeng , Shi Yongchao , Xu Ligang , Luo Huajie , Chen Yongjin , Gao Xiang , Kuang Xiaojun , Su Lei , Tang Mingxue
Published: January 2024

A glass phase grain boundary was constructed by introducing Ga ions into a traditional NASICON electrolyte, successfully improving electrochemical performance. The overall activation energy of the whole pellet is reduced due to the enhanced connection by the filled glass phase.
Modulation of the electrostatic potential around α-lactalbumin using oligoelectrolyte chains, pH and salt concentration
Authors: Torres Paola B. , Baldor Sofia , Quiroga Evelina , Ramirez-Pastor Antonio Jose , Spelzini Dario , Boeris Valeria , Narambuena Claudio F.
Published: January 2024

We studied how α-lactalbumin interacts with strong negatively charged oligoelectrolyte chains, looking at the electrostatic potential profile as pH and salt concentration change.
Trapping and manipulation of bubbles with holographic optical tweezers
Authors: Molina-Jiménez Juan Manuel , Morales-Cruzado Beatriz , Briceño-Ahumada Zenaida , Carrasco-Fadanelli Virginia , Sarmiento-Gómez Erick
Published: January 2024

A robust methodology for trapping low-index objects is introduced, employing holographical optical tweezers with a ray-tracing theoretical framework. This enables a one-time trap stiffness calibration.
Photochemical transformation of a perylene diimide derivative beneficial for thein situformation of a molecular photocatalyst of the hydrogen evolution reaction
Authors: Hoffman Estera , Kozakiewicz Karol , Rybczyńska Małgorzata , Mońka Michał , Grzywacz Daria , Liberek Beata , Bojarski Piotr , Serdiuk Illia E.
Published: January 2024

Photochemical cleavage of amide bonds of the perylene diimide derivative in the presence of Pt2+cations affords HER-active photocatalyst, whose efficiency is the highest in the micellar nanoparticle form.
Reinforcing hydrogen and carbon nanotube co-production via Cr–O–Ni catalyzed methane decomposition
Authors: Sun Zhao , Gong Yunhan , Cheng Dongfang , Sun Zhiqiang
Published: January 2024

Schematic illustration of Cr–O–Ni catalyzed methane decomposition into high-quality hydrogen and single-walled carbon nanotubes.
A synthetic strategy towards single crystals of Zr6 cluster and phosphonate-based metal–organic frameworks
Authors: Xie Haomiao , Kirlikovali Kent O. , Chen Zhijie , Idrees Karam B. , Islamoglu Timur , Farha Omar K.
Published: January 2024

We developed a strategy for synthesizing single-crystal Zr-phosphonate MOFs, retaining parent topology via post-synthesis. SALE and post-synthetic oxidation enable linker modification, enhancing hydrophilicity and Brønsted acidity.
Designing one-dimensional covalent organic frameworks: novel post-synthetic modification on hydroxyl groups and ratiometric detection of chemical warfare agent mimics
Authors: Shen Xiaoqin , Yan Bing
Published: January 2024

A post-synthetic modification based on substitution reaction of the hydroxyl group in COFs is utilized to construct a dual-emission hybrid material for real-time detection of 2-chloroethyl ethyl sulfide (2-CEES) and diethyl cyanophosphonate (DCNP), mimics of chemical warfare agents.
Channel confinement and separation properties in an adaptive supramolecular framework using an adamantane tecton
Authors: Lutz Nicholas , Bicknell Josephine , Loya Jesus Daniel , Reinheimer Eric W. , Campillo-Alvarado Gonzalo
Published: January 2024

A supramolecular framework with adaptive channels based on an adamantane tecton enables confinement and separation of small molecules and petrochemicals.
A molecular container providing supramolecular protection against acetylcholine hydrolysis
Authors: Lu Yi-Long , Su Jing , Li Jian-Wei , Xu Wen-Rong
Published: January 2024

Utilizing confinement effects, TBTQ-C6 safeguards acetylcholine and butyrylcholine from enzymatic breakdown by AChE and BChE through host–guest interactions.
Development and Validation of an Efficient and Safe Loud Music Exposure Paradigm
Authors: Iliadou Eleftheria , Pastiadis Konstantinos , Dimitriadis Dimitrios , Plack Christopher J. , Bibas Athanasios
Published: January 2024

Purpose:

The purpose of this study was to develop a time-efficient music exposure and testing paradigm that safely creates temporary cochlear dysfunction that could be used in future temporary threshold shift (TTS) studies.

Method:

A 30-min audio compilation of pop rock music tracks was created. Adult volunteers with normal hearing were then exposed to this music material monaurally through headphones for 30 min at 97 dBA or 15 min at 100 dBA. Levels were measured from the ear of a manikin and are considered to provide an equivalent daily noise dose based on a 3-dB exchange. We assessed the changes in their hearing, by means of distortion product otoacoustic emission (DPOAE) testing, and standard and extended high-frequency pure-tone audiometry before and after exposure. There were 17 volunteers in total. In the first trial, eight volunteers (four females;
Mdn
age
= 31 years [interquartile range, IQR = 4.25]) were included. Although TTS was observed in all eight participants for at least one frequency, a large variation in affected frequencies was observed. To address this issue, the audio material was further remastered to adjust levels across the different frequency bands. Fourteen adults (nine newly recruited and five from the first trial; seven females;
Mdn
age
= 31 years [IQR = 5]) were exposed to the new material.

Results:

All but two of 17 participants presented clinically significant TTS or decrease in DPOAE amplitude in at least one frequency. Statistically significant average TTS of 7.43 dB was observed at 6 kHz. There were statistically significant average DPOAE amplitude shifts of −2.55 dB at 4 kHz, −4.97 dB at 6 kHz, and −3.14 dB at 8 kHz. No participant presented permanent threshold shift.

Conclusions:

A monaural music paradigm was developed and shown to induce statistically significant TTS and DPOAE amplitude shifts, without evidence of permanent loss. This realistic and time-efficient paradigm may be considered a viable option for experimental studies of temporary music-induced hearing loss.

Supplemental Material:

https://doi.org/10.23641/asha.25016471