DeepBAM: a high-accuracy single-molecule CpG methylation detection tool for Oxford nanopore sequencing.

Recent nanopore sequencing system (R10.4) has enhanced base calling accuracy and is being increasingly utilized for detecting CpG methylation state. However, the robustness and universality of the methylation calling model in officially supplied Dorado remains poorly tested. In this study, we obtained heterogeneous datasets from human and plant sources to carry out comprehensive evaluations, which showed that Dorado performed significantly different across datasets. We therefore developed deep neural networks and implemented several optimizations in training a new model called DeepBAM. DeepBAM achieved superior and more stable performances compared with Dorado, including higher area under the ROC curves (98.47% on average and up to 7.36% improvement) and F1 scores (94.97% on average and up to 16.24% improvement) across the datasets. DeepBAM-based whole genome methylation frequencies have achieved >0.95 correlations with BS-seq on four of five datasets, outperforming Dorado in all instances. It enables unraveling allele-specific methylation patterns, including regions of transposable elements. The enhanced performance of DeepBAM paves the way for broader applications of nanopore sequencing in CpG methylation studies.

Suitability of R. pulmo Jellyfish-Collagen-Coated Well Plates for Cytocompatibility Analyses of Biomaterials.

Cytocompatibility analyses of new implant materials or biomaterials are not only prescribed by the Medical Device Regulation (MDR), as defined in the DIN ISO Norm 10993-5 and -12, but are also increasingly replacing animal testing. In this context, jellyfish collagen has already been established as an alternative to mammalian collagen in different cell culture conditions, but a lack of knowledge exists about its applicability for cytocompatibility analyses of biomaterials. Thus, the present study was conducted to compare well plates coated with collagen type 0 derived from Rhizostoma pulmo with plates coated with bovine and porcine collagen. The coated well plates were analysed in vitro for their cytocompatibility, according to EN ISO 10993-5/-12, using both L929 fibroblasts and MC3T3 pre-osteoblasts. Thereby, the coated well plates were compared, using established materials as positive controls and a cytotoxic material, RM-A, as a negative control. L929 cells exhibited a significantly higher viability (#### p < 0.0001), proliferation (## p < 0.01), and a lower cytotoxicity (## p < 0.01 and # p < 0.05)) in the Jellagen® group compared to the bovine and porcine collagen groups. MC3T3 cells showed similar viability and acceptable proliferation and cytotoxicity in all collagen groups. The results of the present study revealed that the coating of well plates with collagen Type 0 derived from R. pulmo leads to comparable results to the case of well plates coated with mammalian collagens. Therefore, it is fully suitable for the in vitro analyses of the cytocompatibility of biomaterials or medical devices.

Analyses of the Cellular Interactions between the Ossification of Collagen-Based Barrier Membranes and the Underlying Bone Defects.

Barrier membranes are an essential tool in guided bone Regeneration (GBR), which have been widely presumed to have a bioactive effect that is beyond their occluding and space maintenance functionalities. A standardized calvaria implantation model was applied for 2, 8, and 16 weeks on Wistar rats to test the interactions between the barrier membrane and the underlying bone defects which were filled with bovine bone substitute materials (BSM). In an effort to understand the barrier membrane's bioactivity, deeper histochemical analyses, as well as the immunohistochemical detection of macrophage subtypes (M1/M2) and vascular endothelial cells, were conducted and combined with histomorphometric and statistical approaches. The native collagen-based membrane was found to have ossified due to its potentially osteoconductive and osteogenic properties, forming a "bony shield" overlying the bone defects. Histomorphometrical evaluation revealed the resorption of the membranes and their substitution with bone matrix. The numbers of both M1- and M2-macrophages were significantly higher within the membrane compartments compared to the underlying bone defects. Thereby, M2-macrophages significantly dominated the tissue reaction within the membrane compartments. Statistically, a correlation between M2-macropahges and bone regeneration was only found at 2 weeks post implantationem, while the pro-inflammatory limb of the immune response correlated with the two processes at 8 weeks. Altogether, this study elaborates on the increasingly described correlations between barrier membranes and the underlying bone regeneration, which sheds a light on the understanding of the immunomodulatory features of biomaterials.

Exploring effective ways to increase reliable positive samples for machine learning-based urban waterlogging susceptibility assessments.

Machine learning (ML)-based urban waterlogging susceptibility studies suffer from class imbalance, as fewer positive samples are generally available than potential negative samples. Few studies have considered optimizing the results by improving the quality of training samples. To address this issue, we explored effective approaches to reliably increase the numbers of positive samples for such studies. The Synthetic Minority Over-Sampling Technique (SMOTE) and Optimized Seed Spread Algorithm (OSSA), representative of oversampling (synthesizing new samples based on the feature space) and physical (simulating potential inundated area based on the mechanisms of water flow) approaches, respectively, were employed to increase the number of positive samples. Waterlogging in Shenzhen was selected as a case study using eight selected spatial variables. An elaborate experiment was conducted to compare the quality of added samples based on the classifiers' performance and accuracy of waterlogging susceptibility maps (WSMs). The results indicated that (1) the performance of classifiers generated with SMOTE was worse than the original samples, while the use of OSSA improved the trained classifiers, and (2) the accuracy of WSMs was not improved with SMOTE but increased markedly with OSSA. These results may be driven by the diversity of information and features of the added samples. This study indicates the use of SMOTE fails to synthesize reliable samples when applied to waterlogging analysis in Shenzhen, whereas an effective solution for generating reliable positive samples is to use OSSA that simulates the potential submerged regions based on the mechanisms of disaster occurrence and spread.

Remote C-H Olefination of Heterocyclic Biaryls Enabled by Reversibly Bound Templates.

Remote C-H functionalization of heterocyclic biaryls will be of great importance in synthesis and medicinal chemistry. Through adjusting the geometric relationship of the directing atom and target C-H bonds, two new catalytic templates have been developed to enable the functionalization of the more hindered ortho-C-H bonds of heterobiaryls bearing directing heteroatom at the meta- or para-positions, affording unprecedented site-selectivity. The use of template chaperone also overcomes product inhibition and renders the directing templates catalytic. The utility of this protocol was demonstrated by olefination of heterocyclic biaryls with various substituents, overriding conventional steric and electronic effects. These ortho-C-H olefinated heterobiaryls are sterically hindered and can often be challenging to prepare through aryl-aryl coupling reactions.

The performance of an integrated model including retinal information in predicting childhood hypertension.

BACKGROUND: The objective of this study was to examine the association of an integrated model (composed of retinal arteriolar caliber, height, and sex) with blood pressure (BP) among a group of Chinese children, and assess the predictive value of the integrated model for childhood hypertension. METHODS: This study included 1460 candidates aged 12.634 ± 0.420 years. Height, weight, waist circumference, and BP were obtained and ophthalmological measurements were taken. The computer-imaging program (IVAN, University of Wisconsin, Madison, WI) was used to measure calibers of retinal vessels. Receiver-operating characteristic curve (ROC) analyses were performed to assess the accuracy of the integrated model as a diagnostic test of elevated BP in children. RESULTS: The accuracy of the integrated model (assessed by area under the curve) for identifying elevated BP was 0.777 (95% confidence interval: 0.742-0.812). The optimal threshold of the integrated model for defining hypertension was 0.153, and the calculation formula for the specific predictive risk was: Logit (p/1 - p) = -5.666 - 0.261 × retinal arteriolar caliber + 0.945 × sex + 0.438 × height. In identifying elevated BP, the sensitivity and specificity were 0.711 and 0.736, respectively. CONCLUSIONS: The model containing eye message is a comprehensive and relatively effective index to identify elevated BP in 12-year-old children, which can offer assistance to further understand childhood microcirculation disease. IMPACT: We firstly incorporated retinal vascular diameter, sex, and height into one integrated model to identify hypertension in 12-year-old children. The current discrimination of hypertension in children is difficult. There have been some studies to simplify the diagnosis of children's hypertension, but they were limited to anthropometric measurements. We proposed a composed model containing microcirculation information to predict childhood hypertension. Based on the knowledge that microcirculation is not only a means to study the manifestations but also early pathogenic correlates of hypertension, the combined model containing microcirculation message as a method may provide new insights into the diagnosis of childhood hypertension.

Barrier Membranes for Guided Bone Regeneration (GBR): A Focus on Recent Advances in Collagen Membranes.

Guided bone regeneration (GBR) has become a clinically standard modality for the treatment of localized jawbone defects. Barrier membranes play an important role in this process by preventing soft tissue invasion outgoing from the mucosa and creating an underlying space to support bone growth. Different membrane types provide different biological mechanisms due to their different origins, preparation methods and structures. Among them, collagen membranes have attracted great interest due to their excellent biological properties and desired bone regeneration results to non-absorbable membranes even without a second surgery for removal. This work provides a comparative summary of common barrier membranes used in GBR, focusing on recent advances in collagen membranes and their biological mechanisms. In conclusion, the review article highlights the biological and regenerative properties of currently available barrier membranes with a particular focus on bioresorbable collagen-based materials. In addition, the advantages and disadvantages of these biomaterials are highlighted, and possible improvements for future material developments are summarized.

In Vivo Analysis of the Regeneration Capacity and Immune Response to Xenogeneic and Synthetic Bone Substitute Materials.

Although various studies have investigated differences in the tissue reaction pattern to synthetic and xenogeneic bone substitute materials (BSMs), a lack of knowledge exists regarding the classification of both materials based on the DIN ISO 10993-6 scoring system, as well as the histomorphometrical measurement of macrophage subtypes within their implantation beds. Thus, the present study was conducted to analyze in vivo responses to both xenogeneic and synthetic bone substitute granules. A standardized calvaria implantation model in Wistar rats, in combination with established scoring, histological, histopathological, and histomorphometrical methods, was conducted to analyze the influence of both biomaterials on bone regeneration and the immune response. The results showed that the application of the synthetic BSM maxresorb® induced a higher pro-inflammatory tissue response, while the xenogeneic BSM cerabone® induced a higher anti-inflammatory reaction. Additionally, comparable bone regeneration amounts were found in both study groups. Histopathological scoring revealed that the synthetic BSM exhibited non-irritant scores at all timepoints using the xenogeneic BSM as control. Overall, the results demonstrated the biocompatibility of synthetic BSM maxresorb® and support the conclusion that this material class is a suitable alternative to natural BSM, such as the analyzed xenogeneic material cerabone®, for a broad range of indications.

The Upregulation of a Novel Long Noncoding RNA AK097647 Promotes Enterovirus 71 Replication and Decreases IFN-λ1 Secretion.

BACKGROUND: Enterovirus 71 (EV71) infects millions of children every year in China and has become a challenge to public health. However, there is no effective treatment for EV71 infection. Long noncoding RNAs (lncRNAs) have been found to play various roles in virus replication and infection. OBJECTIVE: We aimed to explore the role of a novel long noncoding RNA AK097647 (lncRNA-AK097647) during EV71 infection. METHODS: To assess the role of lncRNA-AK097647 during EV71 infection, siRNAs were used to silence lncRNA-K097647 expression. RT-qPCR assay and Western blotting were applied to measure the mRNA and protein levels of EV71 VP1 and the phosphorylation of NF-κB. ELISA was used to detect the level of IFN-λ1 expression. RESULTS: The novel lncRNA-AK097647 was upregulated in human rhabdomyosarcoma cells and the blood of hand, foot, and mouth disease patients infected with EV71, as demonstrated by RT-qPCR. Interestingly, RNAi-mediated knockdown of lncRNA-AK097647 dramatically increased the level of IFN-λ1 expression, resulting in the suppression of EV71 replication. In contrast, overexpression of lncRNA-AK097647 decreased the level of IFN-λ1 expression and resulted in increased EV71 replication. In addition, we found that lncRNA-AK097647 could inhibit the phosphorylation of NF-κB. CONCLUSION: These results suggest a novel mechanism by which EV71 evades the IFN-mediated host antiviral response by increasing lncRNA-AK097647 expression.

Two cases of refractory erythrodermic psoriasis effectively treated with secukinumab and a review of the literature.

Erythrodermic psoriasis (EP), which accounts for 1 to 2.25% of all psoriatic cases, typically occurs in patients with poor control of existing psoriasis. Secukinumab yields rapid and sustained improvements of signs and symptoms in patients with plaque psoriasis. Currently, clinical data on the treatment of EP with secukinumab are scarce. We describe two adult patients with severe EP, including one male and one female who were both ineligible for or resistant to acitretin or methotrexate treatment and had additional diseases. The patients underwent treatment with secukinumab using the standard regimen. After 4 weeks of treatment, a 75% reduction in the Psoriasis Area and Severity Index score (PASI 75) was achieved in both patients. Secukinumab was well tolerated and was continued for at least 32 weeks of treatment. We report the clinical use of secukinumab in the treatment of EP and review its potential role in the management of this severe condition.

Improved aging properties of bio-bitumen coating sheets by using modified lignin.

Papermaking waste liquid (black liquor) is a serious source of water pollution worldwide. The subsequent treatment of it is very difficult cause it contains a large amount of lignin, inorganic salts, organic matter, and pigments, which lead to serious water pollution. Lignin is the main by-product of the paper industry and is the only natural aromatic recyclable resource. Its effective utilization rate is currently less than 3%. Therefore, how to effectively recycle lignin in papermaking waste liquid and further synthesize industrialized products is of great significance to the sustainable development and environmental protection. Besides, based on the shortage of petroleum resources in recent years, the application of biomass resources instead of petroleum resources in the industry is also an important issue. In this article, we explored the best optimal conditions for the oxypropylation and esterification of lignin, and prepared bio-bitumen based on modified lignin, and then applied it to the waterproof coating sheets. FTIR and mechanical properties (softening point, low-temperature flexibility, peel strength, etc.) were tested on the obtained waterproof coating sheets. The results show that the addition of modified lignin reduced the softening point and peel strength of the coating sheets. Interestingly, both oxypropylated lignin (OL) and esterified lignin (OEL) were very beneficial to resist the decrease in peel strength during the aging process, showing a significant improvement in the performance of the coating sheets after aging compared to the control.

Biodegradation of low-density polyethylene by Microbulbifer hydrolyticus IRE-31.

Polyethylene (PE) is one of the most widespread plastic materials. Nevertheless, due to its recalcitrance against biological degradation and the presence of toxic additives, landfilled and carelessly disposed PE products have caused serious pollution in the natural environments. In this work, we aimed to investigate the growth characteristics of Microbulbifer hydrolyticus IRE-31 and its application in the biological degradation of low-density PE. The IRE-31 strain was isolated from marine pulp mill wastes rich in lignin which is a natural complex polymer containing also saturated carbon-carbon bonds like in PE. Following 30 days cultivation of the IRE-31 strain, the biodegradation of linear low-density PE particles was evidenced clearly by morphological changes of the polymer surface monitored by scanning electron microscopy and the formation of additional carbonyl groups in the polymer chains indicated by Fourier transform infrared spectroscopy.

Immobilized bacteria with pH-response hydrogel for self-healing of concrete.

Concrete is significant for construction. A problem in application is the appearance of cracks that will damage its strength. An autogenous crack-healing mechanism based on bacteria receives increasing attention in recent years. The bacteria are able to form calcium carbonate (CaCO3) precipitations in suitable conditions to protect and reinforce the concrete. However, a large number of spores are crushed in aged specimens, resulting in a loss of viability. A new kind of hydrogel crosslinked by alginate, chitosan and calcium ions was introduced in this study. It was observed that the addition of chitosan improved the swelling properties of calcium alginate. Opposite pH response to calcium alginate was observed when the chitosan content in the solution reached 1.0%. With an addition of 1.0% chitosan in hydrogel beads, 10.28% increase of compressive strength and 13.79% increase of flexural strength to the control were observed. The results reveal self-healing properties of concretes. A healing crack of 4 cm length and 1 mm width was observed when using cement PO325, with the addition of bacterial spores (2.54-3.07 × 105/cm3 concrete) encapsulated by hydrogel containing no chitosan.

meta-Selective C-H Arylation of Fluoroarenes and Simple Arenes.

Fluorine is known to promote ortho-C-H metalation. Based upon this reactivity, we employed an activated norbornene that traps the ortho-palladation intermediate and is then relayed to the meta position, leading to meta-selective C-H arylation of fluoroarenes. Deuterium experiment suggests that this meta-arylation is initiated by ortho C-H activation and the catalytic cycle is terminated by C-2 protonation. A dual-ligand system is crucial for the observed high reactivity and site selectivity. Applying this approach to simple benzene or other arenes also affords arylation products with good yield and site selectivity.

Ligand-Enabled ß-Methylene C(sp3 )-H Arylation of Masked Aliphatic Alcohols.

Despite recent advances, reactivity and site-selectivity remain significant obstacles for the practical application of C(sp3 )-H bond functionalization methods. Here, we describe a system that combines a salicylic-aldehyde-derived L,X-type directing group with an electron-deficient 2-pyridone ligand to enable the ß-methylene C(sp3 )-H arylation of aliphatic alcohols, which has not been possible previously. Notably, this protocol is compatible with heterocycles embedded in both alcohol substrates and aryl coupling partners. A site- and stereo-specific annulation of dihydrocholesterol and the synthesis of a key intermediate of englitazone illustrate the practicality of this method.

meta C-H Arylation of Electron-Rich Arenes: Reversing the Conventional Site Selectivity.

Controlling site selectivity of C-H activation without using a directing group remains a significant challenge. While Pd(II) catalysts modulated by a mutually repulsive pyridine-type ligand have been shown to favor the relatively electron-rich carbon centers of arenes, reversing the selectivity to favor palladation at the relatively electron-deficient positions has not been possible. Herein we report the first catalytic system that effectively performs meta C-H arylation of a variety of alkoxy aromatics including 2,3-dihydrobenzofuran and chromane with exclusive meta site selectivity, thus reversing the conventional site selectivity governed by native electronic effects. The identification of an effective ligand and modified norbornene (NBE-CO2Me), as well as taking advantage of the statistics, are essential for achieving the exclusive meta selectivity.

Chemoenzymatic Synthesis of Fragrance Compounds from Stearic Acid.

Fatty acids are versatile precursors for fuels, fine chemicals, polymers, perfumes, etc. The properties and applications of fatty acid derivatives depend on chain length and on functional groups and their positions. To tailor fatty acids for desired properties, an engineered P450 monooxygenase has been employed here for enhanced selective hydroxylation of fatty acids. After oxidation of the hydroxy groups to the corresponding ketones, Baeyer-Villiger oxidation could be applied to introduce an oxygen atom into the hydrocarbon chains to form esters, which were finally hydrolyzed to afford either hydroxylated fatty acids or dicarboxylic fatty acids. Using this strategy, we have demonstrated that the high-value-added flavors exaltolide and silvanone supra can be synthesized from stearic acid through a hydroxylation/carbonylation/esterification/hydrolysis/lactonization reaction sequence with isolated yields of about 36 % (for ω-1 hydroxylated stearic acid; 100, 60, 80, 75 % yields for the individual reactions, respectively) or 24 % (for ω-2 hydroxylated stearic acid). Ultimately, we obtained 7.91 mg of exaltolide and 13.71 mg of silvanone supra from 284.48 mg stearic acid.

Ligand-Promoted Non-Directed C-H Cyanation of Arenes.

This article reports the first example of a 2-pyridone accelerated non-directed C-H cyanation with an arene as the limiting reagent. This protocol is compatible with a broad scope of arenes, including advanced intermediates, drug molecules, and natural products. A kinetic isotope experiment (kH /kD =4.40) indicates that the C-H bond cleavage is the rate-limiting step. Also, the reaction is readily scalable, further showcasing the synthetic utility of this method.

Multi-omics metabolism analysis on irradiation-induced oxidative stress to Rhodotorula glutinis.

Oxidative stress is induced in many organisms by various natural abiotic factors including irradiation. It has been demonstrated that it significantly improves growth rate and lipid production of Rhodotorula glutinis. However, the specific mechanism of how irradiation influences the metabolism of R. glutinis remains still unavailable. To investigate and better understand the mechanisms involved in irradiation-induced stress resistance in R. glutinis, a multi-omics metabolism analysis was implemented. The results confirmed that irradiation indeed not only improved cell biomass but also accelerated the production of carotenoids and lipids, especially neutral lipid. Compared with the control, metabolome profiling in the group exposed to irradiation exhibited an obvious difference in the activation of the tricarboxylic acid cycle and triglyceride (TAG) production. The results of proteome analysis (data are available via ProteomeXchange with identifier PXD009678) showed that 423 proteins were changed significantly, and proteins associated with protein folding and transport, the Hsp40 and Sec12, were obviously upregulated, indicating that cells responded to irradiation by accelerating the protein folding and transport of correctly folded proteins as well as enhanced the degradation of misfolded proteins. A significant upregulation of the carotenoid biosynthetic pathway was observed which revealed that increased carotenoid content is a cellular defense mechanism against oxidative stress generated by irradiation. Therefore, the results of comprehensive omics analysis provide intensive insights on the response mechanism of R. glutinis to irradiation-induced oxidative stress which could be helpful for using irradiation as an effective strategy to enhance the joint production of the neutral lipid and carotene.