Synthesis of Thiohydantoin Scaffolds on DNA for Focused DNA-Encoded Library Construction.

Thiohydantoin represents a significant class of biologically active privileged heterocyclic scaffolds. Herein, we present a convenient and robust DNA-compatible method for constructing a thiohydantoin-focused DNA-encoded library. This reaction can be applied to a wide variety of isothiocyanate partners, arylamine feedstocks, and diverse α-amine acid derivatives, exhibiting excellent conversions, high functional group tolerance, and preservation of DNA tag integrity. Our method allows for easy access to a valuable three-cycle thiohydantoin-focused DNA-encoded library.

Heterogeneous Photocatalytic Degradation of Selected Pharmaceuticals and Personal Care Products (PPCPs) Using Tungsten Doped TiO2: Effect of the Tungsten Precursors and Solvents.

Pharmaceuticals and personal care products (PPCPs) which include antibiotics such as tetracycline (TC) and ciprofloxacin (CIP), etc., have attracted increasing attention worldwide due to their potential threat to the aquatic environment and human health. In this work, a facile sol-gel method was developed to prepare tungsten-doped TiO2 with tunable W5+/W6+ ratio for the removal of PPCPs. The influence of solvents in the synthesis of the three different tungsten precursors doped TiO2 is also taken into account. WCl6, ammonium metatungstate (AMT), and Na2WO4●2H2O not only acted as the tungsten precursors but also controlled the tungsten ratio. The photocatalyst prepared by WCl6 as the tungsten precursor and ethanol as the solvent showed the highest photodegradation performance for ciprofloxacin (CIP) and tetracycline (TC), and the photodegradation performance for tetracycline (TC) was 2.3, 2.8, and 7.8 times that of AMT, Na2WO4●2H2O as the tungsten precursors and pristine TiO2, respectively. These results were attributed to the influence of the tungsten precursors and solvents on the W5+/W6+ ratio, sample crystallinity and surface properties. This study provides an effective method for the design of tungsten-doped TiO2 with tunable W5+/W6+ ratio, which has a profound impact on future studies in the field of photocatalytic degradation of PPCPs using an environmentally friendly approach.

Functional profiling of serine, threonine and tyrosine sites.

Systematic perturbation of amino acids at endogenous loci provides diverse insights into protein function. Here, we performed a genome-wide screen to globally assess the cell fitness dependency of serine, threonine and tyrosine residues. Using an adenine base editor, we designed a whole-genome library comprising 817,089 single guide RNAs to perturb 584,337 S, T and Y sites. We identified 3,467 functional substitutions affecting cell fitness and 677 of them involving phosphorylation, including numerous phosphorylation-mediated gain-of-function substitutions that regulate phosphorylation levels of itself or downstream factors. Furthermore, our findings highlight that specific substitution types, notably serine to proline, are crucial for maintaining domain structure broadly. Lastly, we demonstrate that 309 enriched hits capable of initiating cell overproliferation might be potential cancer driver mutations. This study represents an extensive functional profiling of S, T and Y residues and provides insights into the distinctive roles of these amino acids in biological mechanisms and tumor progression.

Ndufa8 promotes white fat Browning by improving mitochondrial respiratory chain complex I function to ameliorate obesity by in vitro and in vivo.

Obesity and its complications have become a global health problem that needs to be addressed urgently. White adipose tissue (WAT) browning contributes to consuming excess energy in WAT, which is important for improving obesity and maintaining a healthy energy homeostasis. Mitochondria, as the energy metabolism center of cells, are extensively involved in many metabolic processes, including the browning of WAT. NADH: Ubiquinone oxidoreductase subunit A8 (NDUFA8) is a constituent subunit of respiratory chain complex I (CI), which has been found to participate in a wide range of physiological processes by affecting the activity of respiratory CI. However, the regulatory effect of Ndufa8 on the browning of WAT has not been reported. Here, we used ß3-adrenergic agonis CL316, 243 to construct WAT browning models in vivo and in vitro to investigate the role and mechanism of Ndufa8 in the regulation of WAT browning. Briefly, Ndufa8 significantly increased CI activity and suppressed mitochondrial ROS levels in vitro, thereby improving mitochondrial function. Ndufa8 also increased the transcriptional levels and protein levels of UCP1 in vitro and in vivo, which promoted WAT browning. Our findings provide a new molecular approach for the research of browning of WAT in animals, as well as a new target for animal metabolism improvement and obesity treatments.

Dual-Pixel Raindrop Removal.

Removing raindrops in images has been addressed as a significant task for various computer vision applications. In this paper, we propose the first method using a dual-pixel (DP) sensor to better address raindrop removal. Our key observation is that raindrops attached to a glass window yield noticeable disparities in DP's left-half and right-half images, while almost no disparity exists for in-focus backgrounds. Therefore, the DP disparities can be utilized for robust raindrop detection. The DP disparities also bring the advantage that the occluded background regions by raindrops are slightly shifted between the left-half and the right-half images. Therefore, fusing the information from the left-half and the right-half images can lead to more accurate background texture recovery. Based on the above motivation, we propose a DP Raindrop Removal Network (DPRRN) consisting of DP raindrop detection and DP fused raindrop removal. To efficiently generate a large amount of training data, we also propose a novel pipeline to add synthetic raindrops to real-world background DP images. Experimental results on constructed synthetic and real-world datasets demonstrate that our DPRRN outperforms existing state-of-the-art methods, especially showing better robustness to real-world situations. Our source codes and datasets will be available at http://www.ok.sc.e.titech.ac.jp/res/SIR/dprrn/dprrn.html.

Preparation of oxygen-sensitive proteins for high-resolution cryoEM structure determination using (an)aerobic blot-free vitrification.

High-quality grid preparation for single-particle cryogenic electron microscopy (cryoEM) remains a bottleneck for routinely obtaining high-resolution structures. The issues that arise from traditional grid preparation workflows are particularly exacerbated for oxygen-sensitive proteins, including metalloproteins, whereby oxygen-induced damage and alteration of oxidation states can result in protein inactivation, denaturation, and/or aggregation. Indeed, 99% of the current structures in the EMBD were prepared aerobically and limited successes for anaerobic cryoEM grid preparation exist. Current practices for anaerobic grid preparation involve a vitrification device located in an anoxic chamber, which presents significant challenges including temperature and humidity control, optimization of freezing conditions, costs for purchase and operation, as well as accessibility. Here, we present a streamlined approach that allows for the (an)aerobic vitrification of oxygen-sensitive proteins using an automated aerobic blot-free grid vitrification device - the SPT Labtech chameleon. This robust workflow allows for high-resolution structure determination of dynamic, oxygen-sensitive proteins, of varying complexity and molecular weight.

Effect of Crevice Size on Crevice Corrosion of N80 Carbon Steel in CO2-Saturated NaCl-HAc Solution.

The effect of crevice size on the crevice corrosion of N80 carbon steel was investigated by electrochemical measurements and surface analysis in a CO2-saturated NaCl-HAc solution. The N80 carbon steel exhibits a high susceptibility to crevice corrosion in this environment, which can be initiated immediately without an induction period for specimens with crevice sizes of 100 µm, 300 µm, and 500 µm. Typically, crevice solutions become more acidic during crevice corrosion; however, in this study, the crevice solution became alkaline, resulting in galvanic corrosion between the inner and outer steel surfaces and leading to severe crevice corrosion. The pH levels of the crevice solution for specimens with 100 µm and 300 µm crevice sizes are similar, but both are notably higher than that of the specimen with a 500 µm crevice size. As a result, there is no significant difference in the crevice corrosion phenomenon between specimens with 100 µm and 300 µm crevice sizes, but it is more severe than in the specimen with a 500 µm crevice size.

Dynamic Human Gut Microbiome and Immune Shifts During an Immersive Psychosocial Therapeutic Program.

Background: Depression is a leading cause of disability worldwide yet its underlying factors, particularly microbial associations, are poorly understood. Methods: We examined the longitudinal interplay between the microbiome and immune system in the context of depression during an immersive psychosocial intervention. 142 multi-omics samples were collected from 52 well-characterized participants before, during, and three months after a nine-day inquiry-based stress reduction program. Results: We found that depression was associated with both an increased presence of putatively pathogenic bacteria and reduced microbial beta-diversity. Following the intervention, we observed reductions in neuroinflammatory cytokines and improvements in several mental health indicators. Interestingly, participants with a Prevotella-dominant microbiome showed milder symptoms when depressed, along with a more resilient microbiome and more favorable inflammatory cytokine profile, including reduced levels of CXCL-1. Conclusions: Our findings reveal a protective link between the Prevotella-dominant microbiome and depression, associated with a less inflammatory environment and moderated symptoms. These insights, coupled with observed improvements in neuroinflammatory markers and mental health from the intervention, highlight potential avenues for microbiome-targeted therapies in depression management.

Isothiocyanate intermediates facilitate divergent synthesis of N-heterocycles for DNA-encoded libraries.

The versatile reactivity of isothiocyanate intermediates enabled the diversity-oriented synthesis (DOS) of N-heterocycles in a DNA-compatible manner. We first reported a mild in situ conversion of DNA-conjugated amines to isothiocyanates. Subsequently, a set of diverse transformations was successfully developed to construct 2-thioxo-quinazolinones, 1,2,4-thiadiazoles, and 2-imino thiazolines. Finally, the feasibility of these approaches in constructing DELs was further demonstrated through enzymatic ligation and mock pool preparation. This study demonstrated the advantages of combining in situ conversion strategies with DOS, which effectively broadened the chemical and structural diversity of DELs.

A Polygenic Risk Analysis for Identifying Ulcerative Colitis Patients with European Ancestry.

The incidence of ulcerative colitis (UC) has increased globally. As a complex disease, the genetic predisposition for UC could be estimated by the polygenic risk score (PRS), which aggregates the effects of a large number of genetic variants in a single quantity and shows promise in identifying individuals at higher lifetime risk of UC. Here, based on a cohort of 2869 UC cases and 2900 controls with genotype array datasets, we used PRSice-2 to calculate PRS, and systematically analyzed factors that could affect the power of PRS, including GWAS summary statistics, population stratification, and impact of variants. After leveraging a stepwise condition analysis, we eventually established the best PRS model, achieving an AUC of 0.713. Meanwhile, samples in the top 20% of the PRS distribution had a risk of UC more than ten times higher than samples in the lowest 20% (OR = 10.435, 95% CI 8.571-12.703). Our analyses demonstrated that including population-enriched, more disease-associated SNPs and using GWAS summary statistics from similar ethnic background can improve the power of PRS. Strictly following the principle of focusing on one population in all aspects of generating PRS can be a cost-effective way to apply genotype-array-derived PRS to practical risk estimation.

Cognitive load in tele-robotic surgery: a comparison of eye tracker designs.

PURPOSE: Eye gaze tracking and pupillometry are evolving areas within the field of tele-robotic surgery, particularly in the context of estimating cognitive load (CL). However, this is a recent field, and current solutions for gaze and pupil tracking in robotic surgery require assessment. Considering the necessity of stable pupillometry signals for reliable cognitive load estimation, we compare the accuracy of three eye trackers, including head and console-mounted designs. METHODS: We conducted a user study with the da Vinci Research Kit (dVRK), to compare the three designs. We collected eye tracking and dVRK video data while participants observed nine markers distributed over the dVRK screen. We compute and analyze pupil detection stability and gaze prediction accuracy for the three designs. RESULTS: Head-worn devices present better stability and accuracy of gaze prediction and pupil detection compared to console-mounted systems. Tracking stability along the field of view varies between trackers, with gaze predictions detected at invalid zones of the image with high confidence. CONCLUSION: While head-worn solutions show benefits in confidence and stability, our results demonstrate the need to improve eye tacker performance regarding pupil detection, stability, and gaze accuracy in tele-robotic scenarios.

Using DNA-encoded libraries of fragments for hit discovery of challenging therapeutic targets.

INTRODUCTION: The effectiveness of Fragment-based drug design (FBDD) for targeting challenging therapeutic targets has been hindered by two factors: the small library size and the complexity of the fragment-to-hit optimization process. The DNA-encoded library (DEL) technology offers a compelling and robust high-throughput selection approach to potentially address these limitations. AREA COVERED: In this review, the authors propose the viewpoint that the DEL technology matches perfectly with the concept of FBDD to facilitate hit discovery. They begin by analyzing the technical limitations of FBDD from a medicinal chemistry perspective and explain why DEL may offer potential solutions to these limitations. Subsequently, they elaborate in detail on how the integration of DEL with FBDD works. In addition, they present case studies involving both de novo hit discovery and full ligand discovery, especially for challenging therapeutic targets harboring broad drug-target interfaces. EXPERT OPINION: The future of DEL-based fragment discovery may be promoted by both technical advances and application scopes. From the technical aspect, expanding the chemical diversity of DEL will be essential to achieve success in fragment-based drug discovery. From the application scope side, DEL-based fragment discovery holds promise for tackling a series of challenging targets.

Accelerated sonochemical fabrication of MIn2S4 (M = Zn, Mg, Ni, Co) for ultra-high photocatalytic hydrogen peroxide production.

Ternary metal sulfide (MIn2S4) by virtue of large extinction coefficient, suitable band gap and stability, has been proposed as a candidate for photocatalytic synthesis hydrogen peroxide (H2O2). However, MIn2S4 is conventionally synthesized by solvothermal method that is generally characterized by tedious operational steps and long reaction time. In this work, four sonoMIn2S4 (M = Zn, Mg, Ni, Co) were successfully prepared by sonochemical method within 2 h. These as-synthesized sonoMIn2S4 delivered much high-efficient photocatalytic H2O2 generation. Particularly, the sonoZnIn2S4 presented H2O2 production rate of 21295.5 µmol∙g-1∙h-1 in water/benzylalcohol system, which is 3.0 times that of ZnIn2S4 prepared by solvothermal method. The remarkably improved photocatalytic performance of sonoZnIn2S4 might be due to the multiple defects and fast electron-hole pair separation caused by ultrasound cavitation effect. Other metal sulfide photocatalysts with high performance were efficiently fabricated by facile sonochemical technology as well. The sonochemical method realized the rapid preparation of metal sulfide photocatalysts and efficient production of H2O2, which benefits to meet the United Nations Sustainable Development Goals (SDGs) including SDG-7 and SDG-12.

Intraoperative gaze guidance with mixed reality.

Efficient communication and collaboration are essential in the operating room for successful and safe surgery. While many technologies are improving various aspects of surgery, communication between attending surgeons, residents, and surgical teams is still limited to verbal interactions that are prone to misunderstandings. Novel modes of communication can increase speed and accuracy, and transform operating rooms. A mixed reality (MR) based gaze sharing application on Microsoft HoloLens 2 headset that can help expert surgeons indicate specific regions, communicate with decreased verbal effort, and guide novices throughout an operation is presented. The utility of the application is tested with a user study of endoscopic kidney stone localization completed by urology experts and novice surgeons. Improvement is observed in the NASA task load index surveys (up to 25.23%), in the success rate of the task (6.98% increase in localized stone percentage), and in gaze analyses (up to 31.99%). The proposed application shows promise in both operating room applications and surgical training tasks.

Effect of Tb3+ and Ce3+ Co-doping on the Structure and Photoluminescence Properties of Hexagonal Boron Nitride Phosphors.

In the paper, we have successfully prepared hexagonal boron nitride (h-BN:Tb3+, Ce3+) phosphors with melamine as the nitrogen source. The X-ray powder diffraction patterns confirm that the sample possesses a hexagonal crystal structure within the P 6 ¯ m2 space group. It is interesting that the co-doping combination of Tb3+ and Ce3+ can markedly enhance the threshold concentration of doped activators within the limited solid solution of h-BN phosphors. Under 302 nm excitation, the h-BN:Ce3+ phosphors exhibit broadband blue light emission at 406 nm. In h-BN:Tb3+, Ce3+ phosphors, the co-doping of Ce3+ not only ensures high phase purity but also results in strong green light emission. The energy transfer efficiency from Ce3+ to Tb3+ is about 55%. The fluorescence lifetime increases with the increase of Ce3+ and Tb3+ concentration, and the fluorescence lifetime of h-BN:0.025Tb3+, 0.05Ce3+ phosphor reached 2.087 ms. Additionally, the h-BN:0.025Tb3+, 0.05Ce3+ phosphor exhibits excellent thermal performance with an activation energy value of 0.2825 eV. Moreover, the photoluminescence quantum yield of the sample exceeds 52%. Therefore, the h-BN:Tb3+, Ce3+ samples can be used as green phosphors for solid state lighting and fluorescent labeling.

Protein-templated ligand discovery via the selection of DNA-encoded dynamic libraries.

DNA-encoded chemical libraries (DELs) have become a powerful technology platform in drug discovery. Dual-pharmacophore DELs display two sets of small molecules at the termini of DNA duplexes, thereby enabling the identification of synergistic binders against biological targets, and have been successfully applied in fragment-based ligand discovery and affinity maturation of known ligands. However, dual-pharmacophore DELs identify separate binders that require subsequent linking to obtain the full ligands, which is often challenging. Here we report a protein-templated DEL selection approach that can identify full ligand/inhibitor structures from DNA-encoded dynamic libraries (DEDLs) without the need for subsequent fragment linking. Our approach is based on dynamic DNA hybridization and target-templated in situ ligand synthesis, and it incorporates and encodes the linker structures in the library, along with the building blocks, to be sampled by the target protein. To demonstrate the performance of this method, 4.35-million- and 3.00-million-member DEDLs with different library architectures were prepared, and hit selection was achieved against four therapeutically relevant target proteins.

Unexpected Cyclization Product Discovery from the Photoinduced Bioconjugation Chemistry between Tetrazole and Amine.

Bioconjugation chemistry has emerged as a powerful tool for the modification of diverse biomolecules under mild conditions. Tetrazole, initially proposed as a bioorthogonal photoclick handle for 1,3-dipolar cyclization with alkenes, was later demonstrated to possess broader photoreactivity with carboxylic acids, serving as a versatile bioconjugation and photoaffinity labeling probe. In this study, we unexpectedly discovered and validated the photoreactivity between tetrazole and primary amine to afford a new 1,2,4-triazole cyclization product. Given the significance of functionalized N-heterocycles in medicinal chemistry, we successfully harnessed the serendipitously discovered reaction to synthesize both pharmacologically relevant DNA-encoded chemical libraries (DELs) and small molecule compounds bearing 1,2,4-triazole scaffolds. Furthermore, the mild reaction conditions and stable 1,2,4-triazole linkage found broad application in photoinduced bioconjugation scenarios, spanning from intramolecular peptide macrocyclization and templated DNA reaction cross-linking to intermolecular photoaffinity labeling of proteins. Triazole cross-linking products on lysine side chains were identified in tetrazole-labeled proteins, refining the comprehensive understanding of the photo-cross-linking profiles of tetrazole-based probes. Altogether, this tetrazole-amine bioconjugation expands the current bioconjugation toolbox and creates new possibilities at the interface of medicinal chemistry and chemical biology.

Synthesis of Diacylhydrazine Derivatives Based on Tetrazole-Focused DNA-Encoded Library.

Utilizing already existing DNA-encoded libraries (DELs) for the generation of a distinct DEL represents an expedited strategy for expanding the chemical space. Herein, we leverage the unique photoreactivity of tetrazoles to synthesize diacylhydrazines on DNA. Widely available carboxylic acids serving as building blocks were employed under the mild photomediated reaction conditions, affording diverse DNA-conjugated diacylhydrazines. This methodology also demonstrates robustness in DEL-compatible synthesis and facilitates the preparation of oligonucleotide-based chemical probes.

Association between metabolic dysfunction-associated fatty liver disease and abdominal aortic aneurysm.

BACKGROUND AND AIMS: Abdominal aortic aneurysm (AAA) is the second most common aortic pathological manifestation. Metabolic dysfunction-associated fatty liver disease (MAFLD) has a wide impact on the cardiovascular system and may be a risk factor for AAA. The aim of this study was to investigate whether MAFLD is associated with the risk of AAA. METHODS AND RESULTS: We used data from the prospective UK Biobank cohort study. MAFLD is defined as hepatic steatosis plus metabolic abnormality, type 2 diabetes, or overweight/obesity. AAA is collected by ICD-10 code. Cox regression was established to analyze the association between MAFLD and AAA. A total of 370203 participants were included; the average age of the participants was 56.7 ± 8.0 years, and 134649 (36.4 %) were diagnosed with MAFLD. During the 12.5 years of follow-up, 1561 (0.4 %) participants developed AAA. After fully adjusting for confounding factors, individuals with MAFLD had a significantly increased risk of AAA (HR 1.521, 95 % CI 1.351-1.712, p < 0.001). Importantly, the risk of AAA increases with the severity of MAFLD as assessed by fibrosis scores. These associations were consistent according to sex, weight, and alcohol consumption but weaker in elderly or diabetics (P for interaction <0.05). The association between the MAFLD phenotype and AAA was independent of the polygenic risk score. Additionally, MAFLD was not associated with thoracic aortic aneurysm or aortic dissection events. CONCLUSIONS: There was a significant relationship between MAFLD and AAA. These findings strongly recommend early prevention of AAA by intervening in MAFLD.

Attention-based deep clustering method for scRNA-seq cell type identification.

Single-cell sequencing (scRNA-seq) technology provides higher resolution of cellular differences than bulk RNA sequencing and reveals the heterogeneity in biological research. The analysis of scRNA-seq datasets is premised on the subpopulation assignment. When an appropriate reference is not available, such as specific marker genes and single-cell reference atlas, unsupervised clustering approaches become the predominant option. However, the inherent sparsity and high-dimensionality of scRNA-seq datasets pose specific analytical challenges to traditional clustering methods. Therefore, a various deep learning-based methods have been proposed to address these challenges. As each method improves partially, a comprehensive method needs to be proposed. In this article, we propose a novel scRNA-seq data clustering method named AttentionAE-sc (Attention fusion AutoEncoder for single-cell). Two different scRNA-seq clustering strategies are combined through an attention mechanism, that include zero-inflated negative binomial (ZINB)-based methods dealing with the impact of dropout events and graph autoencoder (GAE)-based methods relying on information from neighbors to guide the dimension reduction. Based on an iterative fusion between denoising and topological embeddings, AttentionAE-sc can easily acquire clustering-friendly cell representations that similar cells are closer in the hidden embedding. Compared with several state-of-art baseline methods, AttentionAE-sc demonstrated excellent clustering performance on 16 real scRNA-seq datasets without the need to specify the number of groups. Additionally, AttentionAE-sc learned improved cell representations and exhibited enhanced stability and robustness. Furthermore, AttentionAE-sc achieved remarkable identification in a breast cancer single-cell atlas dataset and provided valuable insights into the heterogeneity among different cell subtypes.