bluuebunny/crossref_metadata_2025 huggingface dataset:
Optimized purification methods for metallic contaminant removal from directly recycled Li-ion battery cathodes
Authors: Fink Kae , Gasper Paul , Major Joshua , Brow Ryan , Schulze Maxwell C. , Colclasure Andrew M. , Keyser Matthew A.
Published: February 2023

Metallic contaminants pose a significant challenge to the viability of directly recycling Li-ion batteries. To date, few strategies exist to selectively remove metallic impurities from mixtures of shredded end-of-life material (black mass; BM) without concurrently damaging the structure and electrochemical performance of the target active material. We herein present tailored methods to selectively ionize two major contaminants—Al and Cu—while retaining a representative cathode (LiNi0.33Mn0.33Co0.33O2; NMC-111) intact. This BM purification process is conducted at moderate temperatures in a KOH-based solution matrix. We rationally evaluate approaches to increase both the kinetic corrosion rate and the thermodynamic solubility of Al0 and Cu0, and evaluate the impact of these treatment conditions on the structure, chemistry, and electrochemical performance of NMC. Specifically, we explore the impacts of chloride-based salts, a strong chelating agent, elevated temperature, and sonication on the rate and extent of contaminant corrosion, while concurrently evaluating the effects on NMC. The reported BM purification process is then demonstrated on samples of “simulated BM” containing a practically relevant 1 wt% concentration of Al or Cu. Increasing the kinetic energy of the purifying solution matrix through elevated temperature and sonication accelerates the corrosion of metallic Al and Cu, such that ∼100% corrosion of 75 μm Al and Cu particles is achieved within 2.5 hr. Further, we determine that effective mass transport of ionized species critically impacts the efficacy of Cu corrosion, and that saturated Cl– hinders rather than accelerates Cu corrosion by increasing solution viscosity and introducing competitive pathways for Cu surface passivation. The purification conditions do not induce bulk structural damage to NMC, and electrochemical capacity is maintained in half-cell format. Testing in full cells suggests that a limited quantity of residual surface species are present after treatment, which initially disrupt electrochemical behavior at the graphite anode but are subsequently consumed. Process demonstration on simulated BM suggests that contaminated samples—which prior to treatment show catastrophic electrochemical performance—can be recovered to pristine electrochemical capacity. The reported BM purification method offers a compelling and commercially viable solution to address contamination, particularly in the “fine” fraction of BM where contaminant sizes are on the same order of magnitude as NMC and where traditional separation approaches are unfeasible. Thus, this optimized BM purification technique offers a pathway towards viable direct recycling of BM feedstocks that would otherwise be unusable.
Systematic analysis of lysine crotonylation in human macrophages responding to MRSA infection
Authors: Zhang Hao , Ma Wei , Liu Haoru , Tang Wanqi , Shu Junjie , Zhou Jianping , Zheng Hongsheng , Xiao Hongyan , Yang Xue , Liu Daoyan , Liang Huaping , Yang Xia
Published: February 2023

Methicillin-resistant Staphylococcus aureus (MRSA) is one of the most commonly encountered bacteria found in healthcare clinics and has been ranked a priority 2 pathogen. Research is urgently needed to develop new therapeutic approaches to combat the pathogen. Variations in the pattern of protein posttranslational modifications (PTMs) of host cells affect physiological and pathological events, as well as therapeutic effectiveness. However, the role of crotonylation in MRSA-infected THP1 cells remains unknown. In this study, we found that crotonylation profiles of THP1 cells were altered after MRSA infection. It was then confirmed that lysine crotonylation profiles of THP1 cells and bacteria were different; MRSA infection inhibited global lysine crotonylation (Kcro) modification but partially elevated Kcro of host proteins. We obtained a proteome-wide crotonylation profile of THP1 cells infected by MRSA further treated by vancomycin, leading to the identification of 899 proteins, 1384 sites of which were down-regulated, and 160 proteins with 193 sites up-regulated. The crotonylated down-regulated proteins were mainly located in cytoplasm and were enriched in spliceosome, RNA degradation, protein posttranslational modification, and metabolism. However, the crotonylated up-regulated proteins were mainly located in nucleus and significantly involved in nuclear body, chromosome, ribonucleoprotein complex, and RNA processing. The domains of these proteins were significantly enriched on RNA recognition motif, and linker histone H1 and H5 families. Some proteins related to protecting against bacterial infection were also found to be targets of crotonylation. The present findings point to a comprehensive understanding of the biological functions of lysine crotonylation in human macrophages, thereby providing a certain research basis for the mechanism and targeted therapy on the immune response of host cells against MRSA infection.
Porcine fungal mock community analyses: Implications for mycobiome investigations
Authors: Arfken Ann M. , Frey Juli Foster , Carrillo Nora Isabel , Dike Nneka Ijeoma , Onyeachonamm Ogechukwu , Rivera Daniela Nieves , Davies Cary Pirone , Summers Katie Lynn
Published: February 2023

Introduction

The gut microbiome is an integral partner in host health and plays a role in immune development, altered nutrition, and pathogen prevention. The mycobiome (fungal microbiome) is considered part of the rare biosphere but is still a critical component in health. Next generation sequencing has improved our understanding of fungi in the gut, but methodological challenges remain. Biases are introduced during DNA isolation, primer design and choice, polymerase selection, sequencing platform selection, and data analyses, as fungal reference databases are often incomplete or contain erroneous sequences.

Methods

Here, we compared the accuracy of taxonomic identifications and abundances from mycobiome analyses which vary among three commonly selected target gene regions (18S, ITS1, or ITS2) and the reference database (UNITE - ITS1, ITS2 and SILVA - 18S). We analyze multiple communities including individual fungal isolates, a mixed mock community created from five common fungal isolates found in weanling piglet feces, a purchased commercial fungal mock community, and piglet fecal samples. In addition, we calculated gene copy numbers for the 18S, ITS1, and ITS2 regions of each of the five isolates from the piglet fecal mock community to determine whether copy number affects abundance estimates. Finally, we determined the abundance of taxa from several iterations of our in-house fecal community to assess the effects of community composition on taxon abundance.

Results

Overall, no marker-database combination consistently outperformed the others. Internal transcribed space markers were slightly superior to 18S in the identification of species in tested communities, but Lichtheimia corymbifera, a common member of piglet gut communities, was not amplified by ITS1 and ITS2 primers. Thus, ITS based abundance estimates of taxa in piglet mock communities were skewed while 18S marker profiles were more accurate. Kazachstania slooffiae displayed the most stable copy numbers (83-85) while L. corymbifera displayed significant variability (90-144) across gene regions.

Discussion

This study underscores the importance of preliminary studies to assess primer combinations and database choice for the mycobiome sample of interest and raises questions regarding the validity of fungal abundance estimates.
A pilot study on the availability and reception of audio description in the Chinese mainland
Authors: Yang Hui , Shen Weiju , Liu Bo , Wang Yi
Published: February 2023

Introduction

Audio description (AD) is in its infancy in the Chinese mainland, both in terms of the provision of the service and as an academic object of study. In order to learn about the availability of AD and target audiences' reception of existing AD services in the Chinese mainland, we designed and carried out this study.

Methods

This paper first provides a brief overview of the availability of AD in the Chinese mainland and analyses difficulties encountered in its development. Then, it conducts a face-to-face questionnaire-based study on the reception of AD through a survey of 26 visually impaired persons.

Results and discussion

AD service in the Chinese mainland is only limited to movies and there is a big gap between supply and demand. AD practice is facing many difficulties such as copyright constraints, low quality of AD services, lack of professionals and insufficient theoretical research. Our empirical research shows that the participants are quite satisfied with the quality of existing AD services, although they do not have a high level of comprehension of movies. Over interpretation, revealing the plot, subjective speculations are common practices in AD services in the Chinese mainland but are applauded by the participants for which helps them to understand the film.
The U-shaped association of non-high-density lipoprotein cholesterol with all-cause and cardiovascular mortality in general adult population
Authors: Huang Yu , Yan Meng Qi , Zhou Dan , Chen Chao Lei , Feng Ying Qing
Published: February 2023

Background

Non-high-density lipoprotein cholesterol (non-HDL-C) has been associated with atherosclerosis. However, the association between non-HDL-C and mortality in adult population remains unclear. We intended to investigate the association of non-HDL-C with cardiovascular and all-cause mortality using national representative data.

Methods

The study included 32,405 participants from the National Health and Nutrition Examination Survey (1999–2014). Mortality outcomes were ascertained by linkage to National Death Index records through December 31, 2015. Multivariable-adjusted Cox regression models were used to evaluate hazard ratio (HR) and 95% confidence interval (CI) of non-HDL-C concentrations in quintiles. Two-piecewise linear regression and restricted cubic spline analyzes were performed to test dose–response associations.

Results

After a median follow-up of 98.40  months, 2,859 (8.82%) all-cause and 551 (1.70%) cardiovascular deaths occurred. Compared with the highest group, the multivariable-adjusted hazard ratio (HR) of the first quintile for all-cause mortality was 1.53 (95%CI, 1.35–1.74). Higher non-HDL-C above a cutoff value of 4.9 mmol/L was related with cardiovascular mortality (HR = 1.33, 95%CI, 1.13–1.57). A U-shaped relationship between non-HDL-C and all-cause mortality was found in spline analysis with a cutoff value around 4 mmol/L. Similar results in subgroups analyzes were found among male, non-white population, participants who were not taking lipid-lowering drugs, and with body mass index (BMI) <25 kg/m2.

Conclusion

Our findings suggest a U-shaped association between non-HDL-C and mortality among adult population.
Patient-specific, echocardiography compatible flow loop model of aortic valve regurgitation in the setting of a mechanical assist device
Authors: Kassi Mahwash , Filippini Stefano , Avenatti Eleonora , Xu Susan , El-Tallawi Kinan Carlos , Angulo Clara I. , Vukicevic Marija , Little Stephen H.
Published: February 2023

Background

Aortic regurgitation (AR) occurs commonly in patients with continuous-flow left ventricular assist devices (LVAD). No gold standard is available to assess AR severity in this setting. Aim of this study was to create a patient-specific model of AR-LVAD with tailored AR flow assessed by Doppler echocardiography.

Methods

An echo-compatible flow loop incorporating a 3D printed left heart of a Heart Mate II (HMII) recipient with known significant AR was created. Forward flow and LVAD flow at different LVAD speed were directly measured and AR regurgitant volume (RegVol) obtained by subtraction. Doppler parameters of AR were simultaneously measured at each LVAD speed.

Results

We reproduced hemodynamics in a LVAD recipient with AR. AR in the model replicated accurately the AR in the index patient by comparable Color Doppler assessment. Forward flow increased from 4.09 to 5.61 L/min with LVAD speed increasing from 8,800 to 11,000 RPM while RegVol increased by 0.5 L/min (2.01 to 2.5 L/min).

Conclusions

Our circulatory flow loop was able to accurately replicate AR severity and flow hemodynamics in an LVAD recipient. This model can be reliably used to study echo parameters and aid clinical management of patients with LVAD.
Fabrication, property and performance evaluation of Stainless Steel 430L as porous supports for metal supported solid oxide fuel cells
Authors: Fu Shengjie , Zhang Jinqiu , Xu Kai , Yang Jun , Zhu Liangzhu
Published: February 2023

Metal-supported solid oxide fuel cells (MS-SOFCs) have attracted increasing attention due to their superior mechanical strength, relatively low material cost, and capability of fast thermal cycling, as compared to the conventional all-ceramic solid oxide fuel cell. However, fabrication of MS-SOFCs still remains challenging. This study reports a cost-effective powder metallurgical manufacturing route for producing MS-SOFCs. Stainless steel 430L (SS430L) powder is selected for producing the metal support due to its relatively low cost and good thermal expansion compatibility. MS-SOFC button cells with the SS430L/YSZ|Ni/YSZ|YSZ|LSCF structure were successfully prepared by co-sintering and ultrasonic pyrolytic spraying. We found that the trace oxygen level in the dilute H2/Ar gas mixture could play a drastic role in laboratory sintering of the SS430L support; local oxygen control is essential, particularly to avoid Cr oxidation. The addition of no more than 10% YSZ as a second phase to SS430L substantially minimized over-sintering of the SS430L support, leading to a more porous metallic-type substrate, while the electrical conductivity and thermal expansion were not much affected. The fabricated MS-SOFC button cells with the SS430L/YSZ|Ni/YSZ|YSZ|LSCF structure delivered a maximum power density of 180 mW cm-2 at 800°C with an open-circuit voltage of 1.13 V, using dry hydrogen as the fuel and ambient air as an oxidant. A cell tested at 750°C showed relatively good stability for a period of 140 h. While the performance still needs further optimization, the high OCV and good stability indicated that the reported powder metallurgy route is a promising method, and the relevant experimental details, particularly on producing metallic and oxidation-free porous supports, are critical for the preparation of MS-SOFCs.
Ichthyoplankton and plastic waste drift in a river in the Amazon Basin, Brazil
Authors: Oliveira Lucas S. , Oliveira-Junior José M. B. , Cajado Ruineris A. , Silva Fabíola K. S. , Zacardi Diego M.
Published: February 2023

Egg and larvae drift is a key mechanism for early fish stages to colonize nursery and growth areas and provides insights into ichthyofauna spawning times and spawning locations—crucial information for understanding fish biology. In the Tapajós River, Amazon Basin, no study has investigated the drift of ichthyoplankton along the hydrological phases nor the occurrence and dispersion of plastic waste associated with plankton. Thus, we aimed to present an overview of the spatio-temporal drift of ichthyoplankton and plastic waste in this river. Temporal sampling was carried out along a spatial gradient of approximately 300 km, covering different sectors of the river. Ichthyoplankton and plastic waste were captured through horizontal trawls on the subsurface of the water column for 10 min. Fish larvae belonging to 10 taxonomic orders and with an average size of 4.98 mm ± 3.14 mm were captured. Clupeiformes larvae occurred in all hydrological phases and reproductive peaks for other orders were recorded. Plastic waste was classified into 20 types according to color and shape and an average size of 1.55 mm ± 1.27 mm. Green fragments and blue filaments were the most abundant. We found the highest density of fish eggs and larvae drifting during the drought phase in stretches with greater environmental structure, whereas plastics were more abundant during the receding water phase in more turbulent stretches that have impacts from illegal mining. Simultaneous drift of ichthyoplankton and plastic waste was recorded in all hydrological phases and sampled sectors. This is worrying because, although we did not analyze the ingestion of plastics by fish larvae, plastic waste can enter the nursery areas of the Tapajós River and reduce the function of these areas for fish. Here we discover through the high densities of fish eggs and larvae deriving that the Tapajós River is an important reproduction site for ichthyofauna and that the presence of different landscape configurations prove to be a key factor in the dispersion, retention and development of ichthyoplankton and plastic waste.
Improving the heavy rainfall forecasting using a weighted deep learning model
Authors: Chen Yutong , Huang Gang , Wang Ya , Tao Weichen , Tian Qun , Yang Kai , Zheng Jiangshan , He Hubin
Published: February 2023

Weather forecasting has been playing an important role in socio-economics. However, operational numerical weather prediction (NWP) is insufficiently accurate in terms of precipitation forecasting, especially for heavy rainfalls. Previous works on NWP bias correction utilizing deep learning (DL) methods mostly focused on a local region, and the China-wide precipitation forecast correction had not been attempted. Meanwhile, earlier studies imposed no particular focus on strong rainfalls despite their severe catastrophic impacts. In this study, we propose a DL model called weighted U-Net (WU-Net) that incorporates sample weights for various precipitation events to improve the forecasts of intensive precipitation in China. It is found that WU-Net can further improve the forecasting skill of heaviest rainfall comparing with the ordinary U-Net and ECMWF-IFS. Further analysis shows that this improvement increases with growing lead time, and distributes mainly in the eastern parts of China. This study suggests that a DL model considering the imbalance of the meteorological data could further improve the precipitation forecasting generated by numerical weather prediction.
Development of embodied capital: Diet composition, foraging skills, and botanical knowledge of forager children in the Congo Basin
Authors: Veen Jorin , Jang Haneul , Raubenheimer David , van Pinxteren Bryndan O. C. M. , Kandza Vidrige , Meirmans Patrick G. , van Dam Nicole M. , Dunker Susanne , Hoffmann Petra , Worrich Anja , Janmaat Karline R. L.
Published: February 2023

The embodied capital theory states that the extended juvenile period has enabled human foragers to acquire the complex foraging skills and knowledge needed to obtain food. Yet we lack detailed data on how forager children develop these skills and knowledge. Here, we examine the seasonal diet composition, foraging behavior, and botanical knowledge of Mbendjele BaYaka forager children in the Republic of the Congo. Our data, acquired through long-term observations involving full-day focal follows, show a high level of seasonal fluctuation in diet and foraging activities of BaYaka children, in response to the seasonal availability of their food sources. BaYaka children foraged more than half of the time independent from adults, predominantly collecting and eating fruits, tubers, and seeds. For these most-consumed food types, we found an early onset of specialization of foraging skills in children, similar to the gendered division in foraging in adults. Specifically, children were more likely to eat fruit and seed species when there were more boys and men in the group, and girls were more likely than boys to collect tuber species. In a botanical knowledge test, children were more accurate at identifying plant food species with increasing age, and they used fruits and trunks for species identification, more so than using leaves and barks. These results show how the foraging activities of BaYaka children may facilitate the acquisition of foraging skills and botanical knowledge and provide insights into the development of embodied capital. Additionally, BaYaka children consumed agricultural foods more than forest foods, probably reflecting BaYaka’s transition into a horticultural lifestyle. This change in diet composition may have significant consequences for the cognitive development of BaYaka children.
RF_phage virion: Classification of phage virion proteins with a random forest model
Authors: Zhang Yanqin , Li Zhiyuan
Published: February 2023

Introduction: Phages play essential roles in biological procession, and the virion proteins encoded by the phage genome constitute critical elements of the assembled phage particle.

Methods: This study uses machine learning methods to classify phage virion proteins. We proposed a novel approach, RF_phage virion, for the effective classification of the virion and non-virion proteins. The model uses four protein sequence coding methods as features, and the random forest algorithm was employed to solve the classification problem.

Results: The performance of the RF_phage virion model was analyzed by comparing the performance of this algorithm with that of classical machine learning methods. The proposed method achieved a specificity (Sp) of 93.37%%, sensitivity (Sn) of 90.30%, accuracy (Acc) of 91.84%, Matthews correlation coefficient (MCC) of .8371, and an F1 score of .9196.
GPR30-mediated non-classic estrogen pathway in mast cells participates in endometriosis pain via the production of FGF2
Authors: Xu Xinxin , Wang Jianzhang , Guo Xinyue , Chen Yichen , Ding Shaojie , Zou Gen , Zhu Libo , Li Tiantian , Zhang Xinmei
Published: February 2023

Pain is one of the main clinical symptoms of endometriosis, but its underlying mechanism is still not clear. Recent studies have shown that the secretory mediators of mast cells activated by estrogen are involved in the pathogenesis of endometriosis-related pain, but how estrogen-induced mast cell mediators are involved in endometriosis-related pain remains unclear. Here, mast cells were found to be increased in the ovarian endometriotic lesions of patients. They were also closely located closely to the nerve fibers in the ovarian endometriotic lesions from of patients with pain symptoms. Moreover, fibroblast growth factor 2 (FGF2)-positive mast cells were upregulated in endometriotic lesions. The concentration of FGF2 in ascites and the protein level of fibroblast growth factor receptor 1 (FGFR1) were higher in patients with endometriosis than in those without endometriosis, and they were correlated with pain symptoms. In vitro, estrogen could promote the secretion of FGF2 through G-protein-coupled estrogen receptor 30 (GPR30) via the MEK/ERK pathway in rodent mast cells. Estrogen-stimulated mast cells enhanced the concentration of FGF2 in endometriotic lesions and aggravated endometriosis-related pain in vivo. Targeted inhibition of the FGF2 receptor significantly restrained the neurite outgrowth and calcium influx in dorsal root ganglion (DRG) cells. Administration of FGFR1 inhibitor remarkably elevated the mechanical pain threshold (MPT) and prolonged the heat source latency (HSL) in a rat model of endometriosis. These results suggested that the up-regulated production of FGF2 by mast cells through non-classic estrogen receptor GPR30 plays a vital role in the pathogenesis of endometriosis-related pain.
Engineered NF-κB siRNA-encapsulating exosomes as a modality for therapy of skin lesions
Authors: Lu Wei , Zhang Jinzhong , Wu Yungang , Sun Wenxue , Jiang Zipei , Luo Xu
Published: February 2023

Introduction

Despite the protection and management of skin has been paid more and more attention, effective countermeasures are still lacking for patients suffering from UV or chemotherapy with damaged skin. Recently, gene therapy by small interfering RNA (siRNA) has emerged as a new therapeutic strategy for skin lesions. However, siRNA therapy has not been applied to skin therapy due to lack of effective delivery vector.

Methods

Here, we develop a synthetic biology strategy that integrates the exosomes with artificial genetic circuits to reprogram the adipose mesenchymal stem cell to express and assemble siRNAs into exosomes and facilitate in vivo delivery siRNAs for therapy of mouse models of skin lesions.

Results

Particularly, siRNA enriched exosomes (si-ADMSC-EXOs) could be directly taken up by the skin cells to inhibit the expression of skin injury related genes. When mice with skin lesions were smeared with si-ADMSC-EXOs, the repair of lesioned skin became faster and the expression of inflammatory cytokines were decreased.

Discussion

Overall, this study establishes a feasible therapeutic strategy for skin injury, which may offer an alternative to conventional biological therapies requiring two or more independent compounds.
Immunity of turbot Induced by inactivated vaccine of Aeromonas salmonicida from the perspective of DNA methylation
Authors: Li Yingrui , Su Lin , Liu Xiaofei , Guo Huimin , Zhou Shun , Xiu Yunji
Published: February 2023

Introduction

DNA methylation was one of the most important modification in epigenetics and played an important role in immune response. Since the introduction of Scophthalmus maximus, the scale of breeding has continued to expand, during which diseases caused by various bacteria, viruses and parasites have become increasingly serious. Therefore, the inactivated vaccines have been widely researched and used in the field of aquatic products with its unique advantages. However, the immune mechanism that occurred in turbot after immunization with inactivated vaccine of Aeromonas salmonicida was not clear.

Methods

In this study, differentially methylated regions (DMRs) were screened by Whole Genome Bisulfite Sequencing (WGBS) and significantly differentially expressed genes (DEGs) were screened by Transcriptome sequencing. Double luciferase report assay and DNA pull-down assay were further verified the DNA methylation state of the gene promoter region affected genes transcriptional activity after immunization with inactivated vaccine of Aeromonas salmonicida.

Results

A total of 8149 differentially methylated regions (DMRs) were screened, in which there were many immune-related genes with altered DNA methylation status. Meanwhile, 386 significantly differentially expressed genes (DEGs) were identified, many of which were significantly enriched in Toll-like receptor signaling pathway, NOD-like receptor signaling pathway and C-type lectin receptor signaling pathway. Combined analysis of WGBS results and RNA-seq results, a total of 9 DMRs of negatively regulated genes are located in the promoter region, including 2 hypermethylated genes with lower expression and 7 hypomethylated genes with higher expression. Then, two immune-related genes C5a anaphylatoxin chemotactic receptor 1-like (C5ar1-Like) and Eosinophil peroxidase-like (EPX-Like), were screened to explore the regulation mechanism of DNA methylation modification on their expression level. Moreover, the DNA methylation state of the gene promoter region affected genes transcriptional activity by inhibiting the binding of transcription factors, which lead to changes in the expression level of the gene.

Discussion

We jointly analyzed WGBS and RNA-seq results and revealed the immune mechanism that occurred in turbot after immunized with inactivated vaccine of A. salmonicida from the perspective of DNA methylation.
Fast underwater image enhancement based on a generative adversarial framework
Authors: Guan Yang , Liu Xiaoyan , Yu Zhibin , Wang Yubo , Zheng Xingyu , Zhang Shaoda , Zheng Bing
Published: February 2023

Underwater image enhancement is a fundamental requirement in the field of underwater vision. Along with the development of deep learning, underwater image enhancement has made remarkable progress. However, most deep learning-based enhancement methods are computationally expensive, restricting their application in real-time large-size underwater image processing. Furthermore, GAN-based methods tend to generate spatially inconsistent styles that decrease the enhanced image quality. We propose a novel efficiency model, FSpiral-GAN, based on a generative adversarial framework for large-size underwater image enhancement to solve these problems. We design our model with equal upsampling blocks (EUBs), equal downsampling blocks (EDBs) and lightweight residual channel attention blocks (RCABs), effectively simplifying the network structure and solving the spatial inconsistency problem. Enhancement experiments on many real underwater datasets demonstrate our model's advanced performance and improved efficiency.
YKL-40 as a possible marker of neutrophilic asthma
Authors: Specjalski Krzysztof , Romantowski Jan , Niedoszytko Marek
Published: February 2023

Asthma is a heterogeneous chronic disorder of the airways, with inflammation and bronchial hyperresponsiveness as its major underlying phenomena. Asthmatics vary in terms of inflammation pattern, concomitant pathologies, and factors aggravating the course of the disease. As a result, there is a need for sensitive and specific biomarkers that could facilitate diagnosing asthma as well as phenotyping in everyday practice. Chitinases and chitinase-like proteins (CLPs) seem promising in this field. Chitinases are evolutionarily conserved hydrolases that degrade chitin. In contrast, CLPs bind chitin but do not have degrading activity. Mammalian chitinases and CLPs are produced by neutrophils, monocytes, and macrophages in response to parasitic or fungal infections. Recently, several questions have been raised about their role in chronic airway inflammation. Several studies demonstrated that overexpression of CLP YKL-40 was associated with asthma. Moreover, it correlated with exacerbation rate, therapy resistance, poor control of symptoms, and, inversely, with FEV1. YKL-40 facilitated allergen sensitization and IgE production. Its concentration was elevated in bronchoalveolar lavage fluid after an allergen challenge. It was also found to promote the proliferation of bronchial smooth muscle cells and correlate with subepithelial membrane thickness. Thus, it may be involved in bronchial remodeling. Associations between YKL-40 and particular asthma phenotypes remain unclear. Some studies showed that YKL-40 correlates with blood eosinophilia and FeNO, suggesting a role in T2-high inflammation. Quite the opposite, cluster analyses revealed the highest upregulation in severe neutrophilic asthma and obesity-associated asthma. The main limitation in the practical application of YKL-40 as a biomarker is its low specificity. High serum levels of YKL-40 were also found in COPD and several malignancies, in addition to infectious and autoimmune diseases. To conclude, the level of YKL-40 correlates with asthma and some clinical features in the whole asthmatic population. The highest levels are found in neutrophilic and obesity-related phenotypes. However, due to its low specificity, the practical application of YKL-40 remains uncertain but could be useful in phenotyping, especially when combined with other biomarkers.
From prediction to function: Current practices and challenges towards the functional characterization of type III effectors
Authors: De Ryck Joren , Van Damme Petra , Goormachtig Sofie
Published: February 2023

The type III secretion system (T3SS) is a well-studied pathogenicity determinant of many bacteria through which effectors (T3Es) are translocated into the host cell, where they exercise a wide range of functions to deceive the host cell’s immunity and to establish a niche. Here we look at the different approaches that are used to functionally characterize a T3E. Such approaches include host localization studies, virulence screenings, biochemical activity assays, and large-scale omics, such as transcriptomics, interactomics, and metabolomics, among others. By means of the phytopathogenic Ralstonia solanacearum species complex (RSSC) as a case study, the current advances of these methods will be explored, alongside the progress made in understanding effector biology. Data obtained by such complementary methods provide crucial information to comprehend the entire function of the effectome and will eventually lead to a better understanding of the phytopathogen, opening opportunities to tackle it.
Nitrate as an alternative electron acceptor destabilizes the mineral associated organic carbon in moisturized deep soil depths
Authors: Song Wei , Hu Chunsheng , Luo Yu , Clough Tim J. , Wrage-Mönnig Nicole , Ge Tida , Luo Jiafa , Zhou Shungui , Qin Shuping
Published: February 2023

Numerous studies have investigated the effects of nitrogen (N) addition on soil organic carbon (SOC) decomposition. However, most studies have focused on the shallow top soils <0.2 m (surface soil), with a few studies also examining the deeper soil depths of 0.5–1.0 m (subsoil). Studies investigating the effects of N addition on SOC decomposition in soil >1.0 m deep (deep soil) are rare. Here, we investigated the effects and the underlying mechanisms of nitrate addition on SOC stability in soil depths deeper than 1.0 m. The results showed that nitrate addition promoted deep soil respiration if the stoichiometric mole ratio of nitrate to O2 exceeded the threshold of 6:1, at which nitrate can be used as an alternative acceptor to O2 for microbial respiration. In addition, the mole ratio of the produced CO2 to N2O was 2.57:1, which is close to the theoretical ratio of 2:1 expected when nitrate is used as an electron acceptor for microbial respiration. These results demonstrated that nitrate, as an alternative acceptor to O2, promoted microbial carbon decomposition in deep soil. Furthermore, our results showed that nitrate addition increased the abundance of SOC decomposers and the expressions of their functional genes, and concurrently decreased MAOC, and the ratio of MAOC/SOC decreased from 20% before incubation to 4% at the end of incubation. Thus, nitrate can destabilize the MAOC in deep soils by stimulating microbial utilization of MAOC. Our results imply a new mechanism on how above-ground anthropogenic N inputs affect MAOC stability in deep soil. Mitigation of nitrate leaching is expected to benefit the conservation of MAOC in deep soil depths.
Translation of in vitro-transcribed RNA therapeutics
Authors: von der Haar Tobias , Mulroney Thomas E. , Hedayioglu Fabio , Kurusamy Sathishkumar , Rust Maria , Lilley Kathryn S. , Thaventhiran James E. , Willis Anne E. , Smales C. Mark
Published: February 2023

In vitro transcribed, modified messenger RNAs (IVTmRNAs) have been used to vaccinate billions of individuals against the SARS-CoV-2 virus, and are currently being developed for many additional therapeutic applications. IVTmRNAs must be translated into proteins with therapeutic activity by the same cellular machinery that also translates native endogenous transcripts. However, different genesis pathways and routes of entry into target cells as well as the presence of modified nucleotides mean that the way in which IVTmRNAs engage with the translational machinery, and the efficiency with which they are being translated, differs from native mRNAs. This review summarises our current knowledge of commonalities and differences in translation between IVTmRNAs and cellular mRNAs, which is key for the development of future design strategies that can generate IVTmRNAs with improved activity in therapeutic applications.
Analysis of risk factors for severe acute kidney injury in patients with acute myocardial infarction: A retrospective study
Authors: Nong Yuxin , Wei Xuebiao , Qiu Hongrui , Yang Honghao , Yang Jiale , Lu Junquan , Cao Jianfeng , Fu Yanbin , Yu Danqing
Published: February 2023

Background

Patients with acute myocardial infarction (AMI) complicated by acute kidney injury (AKI) tend to have a poor prognosis. However, the exact mechanism of the co‐occurrence of the two diseases is unknown. Therefore, this study aims to determine the risk factors for severe AKI in patients with AMI.

Methods

A total of 2022 patients were included in the Medical Information Mart for Intensive Care. Variables were identified via univariate logistic regression, and the variables were corrected via multivariate logistic regression. Restricted cubic splines were used to examine the risks associated with the variables. The Kaplan–Meier method was used to compare the risk of severe AKI among the patients.

Results

Patients with severe AKI had a higher in‐hospital mortality rate (28.6% vs. 9.0%, P < 0.001) and a longer duration of intensive care (6.5 days vs. 2.9 days, P < 0.001). In patients with AMI, the mean systolic blood pressure (SBP); international normalized ratio (INR); the levels of blood urea nitrogen (BUN), glucose, and calcium; and a history of liver disease were found to be the independent risk factors for developing severe AKI after their admission. Increased levels of BUN and blood glucose and a high INR increased the risk of severe AKI; however, increased levels of calcium decreased the risk; SBP presented a U‐shaped curve relationship.

Conclusions

Patients with severe AKI have a poor prognosis following an episode of AMI. Furthermore, in patients with AMI, SBP; INR; a history of liver disease; and the levels of BUN, glucose, and calcium are the independent risk factors for developing severe AKI after their admission.
Case report: Multiple brain metastases of atrial myxoma: Clinical experience and literature review
Authors: Ma Kang , Zhao Dawei , Li Xuegang , Duan Haijun , Yan Chaojun , Wang Shi , Zeng Lan , Xu Kai , Lai Ying , Chen Beike , Mu Ning , Yang Chuanyan , Quan Yulian , Li Zhengyang , Wang Xiaoming , Feng Hua , Li Fei
Published: February 2023

Myxoma is the most common type of benign cardiac tumor in adults, and it has a strong tendency to embolize or metastasize to distant organs. Patients with multiple brain metastases have rarely been seen in clinics; hence, standard treatment protocols for multimyxoma metastasis in the brain have not been established. We present the case of a 47-year-old female who had convulsions in the right hand and repeated seizures. Computed tomography revealed multiple tumor sites in her brain. Craniotomy was conducted to remove the tumor sites. However, recurrent brain tumors and unexpected cerebral infarctions occurred frequently shortly after the treatment because the cardiac myxoma had not been treated due to the patient's personal concerns. The myxoma was resected by gamma knife radiosurgery, and temozolomide was given prior to cardiac surgery. There has been no evidence of tumor recurrence from the 2 years following the surgery until the present. This case highlights the importance of prioritizing cardiac lesions over cerebral lesions; if a cerebral metastasis has been found, it is likely that the cardiac myxoma is already unstable, with high rates of spread and metastasis. Therefore, it is unwise to treat metastasis sites before the cardiac myxoma. Additionally, the case suggests that gamma knife radiosurgery combined with temozolomide is effective as treatment for multiple myxoma metastasis in the brain. Compared with conventional cerebral surgery, gamma knife radiosurgery is safer, causes less bleeding, and requires a shorter time for recovery.
Decreased synaptic vesicle glycoprotein 2A binding in a rodent model of familial Alzheimer's disease detected by [18F]SDM-16
Authors: Zheng Chao , Toyonaga Takuya , Chen Baosheng , Nicholson LaShae , Mennie William , Liu Michael , Spurrier Joshua , Deluca Kristin , Strittmatter Stephen M. , Carson Richard E. , Huang Yiyun , Cai Zhengxin
Published: February 2023

Introduction

Synapse loss is one of the hallmarks of Alzheimer's disease (AD) and is associated with cognitive decline. In this study, we tested [18F]SDM-16, a novel metabolically stable SV2A PET imaging probe, in the transgenic APPswe/PS1dE9 (APP/PS1) mouse model of AD and age-matched wild-type (WT) mice at 12 months of age.

Methods

Based on previous preclinical PET imaging studies using [11C]UCB-J and [18F]SynVesT-1 in the same strain animals, we used the simplified reference tissue model (SRTM), with brain stem as the pseudo reference region to calculate distribution volume ratios (DVRs).

Results

To simplify and streamline the quantitative analysis, we compared the standardized uptake value ratios (SUVRs) from different imaging windows to DVRs and found that the averaged SUVRs from 60–90 min post-injection (p.i.) are most consistent with the DVRs. Thus, we used averaged SUVRs from 60–90 min for group comparisons and found statistically significant differences in the tracer uptake in different brain regions, e.g., hippocampus (p = 0.001), striatum (p = 0.002), thalamus (p = 0.003), and cingulate cortex (p = 0.0003).

Conclusions

In conclusion, [18F]SDM-16 was used to detect decreased SV2A levels in the brain of APP/PS1 AD mouse model at one year old. Our data suggest that [18F]SDM-16 has similar statistical power in detecting the synapse loss in APP/PS1 mice as [11C]UCB-J and [18F]SynVesT-1, albeit later imaging window (60–90 min p.i.) is needed when SUVR is used as a surrogate for DVR for [18F]SDM-16 due to its slower brain kinetics.
Diagnostic performance of CSF biomarkers in a well-characterized Australian cohort of sporadic Creutzfeldt-Jakob disease
Authors: Senesi Matteo , Lewis Victoria , Varghese Shiji , Stehmann Christiane , McGlade Amelia , Doecke James D. , Ellett Laura , Sarros Shannon , Fowler Christopher J. , Masters Colin L. , Li Qiao-Xin , Collins Steven J.
Published: February 2023

The most frequently utilized biomarkers to support a pre-mortem clinical diagnosis of sporadic Creutzfeldt–Jakob disease (sCJD) include concentrations of the 14-3-3 and total tau (T-tau) proteins, as well as the application of protein amplification techniques, such as the real time quaking-induced conversion (RT-QuIC) assay, in cerebrospinal fluid (CSF). Utilizing CSF from a cohort of neuropathologically confirmed (definite) sCJD (n = 50) and non-CJD controls (n = 48), we established the optimal cutpoints for the fully automated Roche Elecsys® immunoassay for T-tau and the CircuLexTM 14-3-3 Gamma ELISA and compared these to T-tau protein measured using a commercially available assay (INNOTEST hTAU Ag) and 14-3-3 protein detection by western immunoblot (WB). These CSF specimens were also assessed for presence of misfolded prion protein using the RT-QuIC assay. T-tau showed similar diagnostic performance irrespective of the assay utilized, with ~90% sensitivity and specificity. The 14-3-3 protein detection by western blot (WB) has 87.5% sensitivity and 66.7% specificity. The 14-3-3 ELISA demonstrated 81.3% sensitivity and 84.4% specificity. RT-QuIC was the single best performing assay, with a sensitivity of 92.7% and 100% specificity. Our study indicates that a combination of all three CSF biomarkers increases sensitivity and offers the best chance of case detection pre-mortem. Only a single sCJD case in our cohort was negative across the three biomarkers, emphasizing the value of autopsy brain examination on all suspected CJD cases to ensure maximal case ascertainment.
Predicting transient ischemic attack risk in patients with mild carotid stenosis using machine learning and CT radiomics
Authors: Xia Hai , Yuan Lei , Zhao Wei , Zhang Chenglei , Zhao Lingfeng , Hou Jialin , Luan Yancheng , Bi Yuxin , Feng Yaoyu
Published: February 2023

Objective

This study aims to establish a radiomics-based machine learning model that predicts the risk of transient ischemic attack in patients with mild carotid stenosis (30–50% North American Symptomatic Carotid Endarterectomy Trial) using extracted computed tomography radiomics features and clinical information.

Methods

A total of 179 patients underwent carotid computed tomography angiography (CTA), and 219 carotid arteries with a plaque at the carotid bifurcation or proximal to the internal carotid artery were selected. The patients were divided into two groups; patients with symptoms of transient ischemic attack after CTA and patients without symptoms of transient ischemic attack after CTA. Then we performed random sampling methods stratified by the predictive outcome to obtain the training set (N = 165) and testing set (N = 66). 3D Slicer was employed to select the site of plaque on the computed tomography image as the volume of interest. An open-source package PyRadiomics in Python was used to extract radiomics features from the volume of interests. The random forest and logistic regression models were used to screen feature variables, and five classification algorithms were used, including random forest, eXtreme Gradient Boosting, logistic regression, support vector machine, and k-nearest neighbors. Data on radiomic feature information, clinical information, and the combination of these pieces of information were used to generate the model that predicts the risk of transient ischemic attack in patients with mild carotid artery stenosis (30–50% North American Symptomatic Carotid Endarterectomy Trial).

Results

The random forest model that was built based on the radiomics and clinical feature information had the highest accuracy (area under curve = 0.879; 95% confidence interval, 0.787–0.979). The combined model outperformed the clinical model, whereas the combined model showed no significant difference from the radiomics model.

Conclusion

The random forest model constructed with both radiomics and clinical information can accurately predict and improve discriminative power of computed tomography angiography in identifying ischemic symptoms in patients with carotid atherosclerosis. This model can aid in guiding the follow-up treatment of patients at high risk.
Enhancing the depth perception of DSA images with 2D–3D registration
Authors: Zhang Xiaofeng , Deng Yongzhi , Tian Congyu , Chen Shu , Wang Yuanqing , Zhang Meng , Wang Qiong , Liao Xiangyun , Si Weixin
Published: February 2023

Objective

Today, cerebrovascular disease has become an important health hazard. Therefore, it is necessary to perform a more accurate and less time-consuming registration of preoperative three-dimensional (3D) images and intraoperative two-dimensional (2D) projection images which is very important for conducting cerebrovascular disease interventions. The 2D–3D registration method proposed in this study is designed to solve the problems of long registration time and large registration errors in 3D computed tomography angiography (CTA) images and 2D digital subtraction angiography (DSA) images.

Methods

To make a more comprehensive and active diagnosis, treatment and surgery plan for patients with cerebrovascular diseases, we propose a weighted similarity measure function, the normalized mutual information-gradient difference (NMG), which can evaluate the 2D–3D registration results. Then, using a multi-resolution fusion optimization strategy, the multi-resolution fused regular step gradient descent optimization (MR-RSGD) method is presented to attain the optimal value of the registration results in the process of the optimization algorithm.

Result

In this study, we adopt two datasets of the brain vessels to validate and obtain similarity metric values which are 0.0037 and 0.0003, respectively. Using the registration method proposed in this study, the time taken for the experiment was calculated to be 56.55s and 50.8070s, respectively, for the two sets of data. The results show that the registration methods proposed in this study are both better than the Normalized Mutual (NM) and Normalized Mutual Information (NMI).

Conclusion

The experimental results in this study show that in the 2D–3D registration process, to evaluate the registration results more accurately, we can use the similarity metric function containing the image gray information and spatial information. To improve the efficiency of the registration process, we can choose the algorithm with gradient optimization strategy. Our method has great potential to be applied in practical interventional treatment for intuitive 3D navigation.