Iterative In Silico Screening for Optimizing Stable Conformation of Anti-SARS-CoV-2 Nanobodies.

Nanobodies (Nbs or VHHs) are single-domain antibodies (sdAbs) derived from camelid heavy-chain antibodies. Nbs have special and unique characteristics, such as small size, good tissue penetration, and cost-effective production, making Nbs a good candidate for the diagnosis and treatment of viruses and other pathologies. Identifying effective Nbs against COVID-19 would help us control this dangerous virus or other unknown variants in the future. Herein, we introduce an in silico screening strategy for optimizing stable conformation of anti-SARS-CoV-2 Nbs. Firstly, various complexes containing nanobodies were downloaded from the RCSB database, which were identified from immunized llamas. The primary docking between Nbs and the SARS-CoV-2 spike protein receptor-binding domain was performed through the ClusPro program, with the manual screening leaving the reasonable conformation to the next step. Then, the binding distances of atoms between the antigen-antibody interfaces were measured through the NeighborSearch algorithm. Finally, filtered nanobodies were acquired according to HADDOCK scores through HADDOCK docking the COVID-19 spike protein with nanobodies under restrictions of calculated molecular distance between active residues and antigenic epitopes less than 4.5 Å. In this way, those nanobodies with more reasonable conformation and stronger neutralizing efficacy were acquired. To validate the efficacy ranking of the nanobodies we obtained, we calculated the binding affinities (∆G) and dissociation constants (Kd) of all screened nanobodies using the PRODIGY web tool and predicted the stability changes induced by all possible point mutations in nanobodies using the MAESTROWeb server. Furthermore, we examined the performance of the relationship between nanobodies' ranking and their number of mutation-sensitive sites (Spearman correlation > 0.68); the results revealed a robust correlation, indicating that the superior nanobodies identified through our screening process exhibited fewer mutation hotspots and higher stability. This correlation analysis demonstrates the validity of our screening criteria, underscoring the suitability of these nanobodies for future development and practical implementation. In conclusion, this three-step screening strategy iteratively in silico greatly improved the accuracy of screening desired nanobodies compared to using only ClusPro docking or default HADDOCK docking settings. It provides new ideas for the screening of novel antibodies and computer-aided screening methods.

Novel Photocatalyst Based on Through-Space Charge Transfer Induced Intersystem Crossing Enables Rapid and Efficient Polymerization Under Low-Power Excitation Light.

Currently, most photoredox catalysis polymerization systems are limited by high excitation power, long polymerization time, or the requirement of electron donors due to the precise design of efficient photocatalysts still poses a great challenge. Herein, we propose a new approach: the creation of efficient photocatalysts having low ground state oxidation potentials and high excited state energy levels, along with through-space charge transfer (TSCT) induced intersystem crossing (ISC) properties. A cabazole-naphthalimide (NI) dyad (NI-1) characterized by long triplet excited state lifetime (τT=62 µs), satisfactory ISC efficiency (ΦΔ=54.3 %) and powerful reduction capacity [Singlet: E1/2 (PC+1/*PC)=-1.93 eV, Triplet: E1/2 (PC+1/*PC)=-0.84 eV] was obtained. An efficient and rapid polymerization (83 % conversion of 1 mM monomer in 30 s) was observed under the conditions of without electron donor, low excitation power (10 mW cm-2) and low catalyst (NI-1) loading (<50 µM). In contrast, the conversion rate was lower at 29 % when the reference catalyst (NI-4) was used for photopolymerization under the same conditions, demonstrating the advantage of the TSCT photocatalyst. Finally, the TSCT material was used as a photocatalyst in practical lithography for the first time, achieving pattern resolutions of up to 10 µm.

NanoBERTa-ASP: predicting nanobody paratope based on a pretrained RoBERTa model.

BACKGROUND: Nanobodies, also known as VHH or single-domain antibodies, are unique antibody fragments derived solely from heavy chains. They offer advantages of small molecules and conventional antibodies, making them promising therapeutics. The paratope is the specific region on an antibody that binds to an antigen. Paratope prediction involves the identification and characterization of the antigen-binding site on an antibody. This process is crucial for understanding the specificity and affinity of antibody-antigen interactions. Various computational methods and experimental approaches have been developed to predict and analyze paratopes, contributing to advancements in antibody engineering, drug development, and immunotherapy. However, existing predictive models trained on traditional antibodies may not be suitable for nanobodies. Additionally, the limited availability of nanobody datasets poses challenges in constructing accurate models. METHODS: To address these challenges, we have developed a novel nanobody prediction model, named NanoBERTa-ASP (Antibody Specificity Prediction), which is specifically designed for predicting nanobody-antigen binding sites. The model adopts a training strategy more suitable for nanobodies, based on an advanced natural language processing (NLP) model called BERT (Bidirectional Encoder Representations from Transformers). To be more specific, the model utilizes a masked language modeling approach named RoBERTa (Robustly Optimized BERT Pretraining Approach) to learn the contextual information of the nanobody sequence and predict its binding site. RESULTS: NanoBERTa-ASP achieved exceptional performance in predicting nanobody binding sites, outperforming existing methods, indicating its proficiency in capturing sequence information specific to nanobodies and accurately identifying their binding sites. Furthermore, NanoBERTa-ASP provides insights into the interaction mechanisms between nanobodies and antigens, contributing to a better understanding of nanobodies and facilitating the design and development of nanobodies with therapeutic potential. CONCLUSION: NanoBERTa-ASP represents a significant advancement in nanobody paratope prediction. Its superior performance highlights the potential of deep learning approaches in nanobody research. By leveraging the increasing volume of nanobody data, NanoBERTa-ASP can further refine its predictions, enhance its performance, and contribute to the development of novel nanobody-based therapeutics. Github repository: https://github.com/WangLabforComputationalBiology/NanoBERTa-ASP.

FASN-mediated fatty acid biosynthesis remodels immune environment in Clonorchis sinensis infection-related intrahepatic cholangiocarcinoma.

BACKGROUND & AIMS: Intrahepatic cholangiocarcinoma (ICC) is the second most common primary liver cancer with high lethality. Clonorchis sinensis (C. sinensis) infection is an important risk factor for ICC. Here we investigated the clinical impact and underlying molecular characteristics of C. sinensis-infected ICC. METHODS: We performed single-cell RNA sequencing, whole exome sequencing, RNA-sequencing, metabolomics and spatial transcriptomics in 251 ICC patients from three medical centers. The alterations of metabolic and immune microenvironment of C. sinensis-infected ICCs were validated through in vitro co-culture system and hydrodynamic injection ICC mouse model. RESULTS: We revealed that C. sinensis infection was significantly associated with ICC patients' overall survival and immunotherapy response. Fatty acid biosynthesis and the expression of FASN, a key enzyme catalyzing long-chain fatty acid synthesis, were significantly enriched in C. sinensis-infected ICCs. ICC cell lines treated with C. sinensis-produced excretory/secretory products (ESPs) displayed an elevation of FASN and free fatty acid. The metabolic alteration of tumor cells was closely correlated with the enrichment of tumor-associated macrophage-like (TAM-like) macrophages and the impairment function of T cells, which led to the immunosuppressive microenvironment formation and tumor progression. Spatial transcriptomics analysis revealed that malignant cells were in closer juxtaposition with TAM-like macrophages in C. sinensis-infected ICCs than non-C. sinensis-infected ICCs. Importantly, FASN inhibitor significantly reversed immunosuppressive microenvironment and enhanced anti-PD-1 efficacy in ICC mouse models treated with ESPs from C. sinensis. CONCLUSIONS: We uncover the metabolic signature and immune microenvironment of C. sinensis-infected ICCs and highlight the combination of FASN inhibitors with immunotherapy as a promising strategy for treating C. sinensis-infected ICCs. IMPACT AND IMPLICATIONS: C. sinensis-infected ICC patients have a poorer prognosis and worse response to immunotherapy than non-C. sinensis-infected ICCs. The underlying molecular characteristics of C. sinensis-infected ICCs remains unclear. Herein, we demonstrate that up-regulation of FASN and free fatty acids in C. sinensis-infected ICCs leads to immunosuppressive microenvironment formation and tumor progression. Thus, administration of FASN inhibitors could significantly reverse immunosuppressive environment and further enhance anti-PD-1 efficacy in combating C. sinensis-infected ICCs.

Th17 Cells Secrete TWEAK to Trigger Epithelial-Mesenchymal Transition and Promote Colorectal Cancer Liver Metastasis.

Liver metastasis is the leading cause of mortality in patients with colorectal cancer. Given the significance of both epithelial-mesenchymal transition (EMT) of tumor cells and the immune microenvironment in colorectal cancer liver metastasis (CRLM), the interplay between them could hold the key for developing improved treatment options. We employed multiomics analysis of 130 samples from 18 patients with synchronous CRLM integrated with external datasets to comprehensively evaluate the interaction between immune cells and EMT of tumor cells in liver metastasis. Single-cell RNA sequencing analysis revealed distinct distributions of nonmalignant cells between primary tumors from patients with metastatic colorectal cancer (mCRC) and non-metastatic colorectal cancer, showing that Th17 cells were predominantly enriched in the primary lesion of mCRC. TWEAK, a cytokine secreted by Th17 cells, promoted EMT by binding to receptor Fn14 on tumor cells, and the TWEAK-Fn14 interaction enhanced tumor migration and invasion. In mouse models, targeting Fn14 using CRISPR-induced knockout or lipid nanoparticle-encapsulated siRNA alleviated metastasis and prolonged survival. Mice lacking Il17a or Tnfsf12 (encoding TWEAK) exhibited fewer metastases compared with wild-type mice, while cotransfer of Th17 with tumor cells promoted liver metastasis. Higher TWEAK expression was associated with a worse prognosis in patients with colorectal cancer. In addition, CD163L1+ macrophages interacted with Th17 cells, recruiting Th17 via the CCL4-CCR5 axis. Collectively, this study unveils the role of immune cells in the EMT process and identifies TWEAK secreted by Th17 as a driver of CRLM. SIGNIFICANCE: TWEAK secreted by Th17 cells promotes EMT by binding to Fn14 on colorectal cancer cells, suggesting that blocking the TWEAK-Fn14 interaction may be a promising therapeutic approach to inhibit liver metastasis.

High-speed ADC based on photonic time-stretched technology with dispersion-tunable CFBG.

We propose a photonic time-stretched analog-to-digital converter (PTS-ADC) based on dispersion-tunable chirped fiber Bragg grating (CFBG), by demonstrating a economical ADC system with seven different stretch factors. The stretch factors are tunable by changing the dispersion of CFBG, in order to obtain different sampling points. Accordingly, the total sampling rate of the system can be improved. Only a single channel is required to increase the sampling rate and achieve the effect of multi-channel sampling. Finally, seven groups of different stretch factors ranging from 1.882 to 2.206 are obtained, which are equivalent to seven groups of different sampling points. We successfully recover the input radio frequency (RF) signals with frequencies from 2 GHz to 10 GHz. In addition, the sampling points are increased by 14.4 times and the equivalent sampling rate is increased to 288 GSa/s. The proposed scheme is suitable for commercial microwave radar systems, which can obtain a much higher sampling rate at a low cost.

Meta-analysis of the effectiveness of relapse prevention therapy for myelin-oligodendrocyte glycoprotein antibody-associated disease.

BACKGROUND: Approximately 40% of adults and 30% of children with Myelin-oligodendrocyte glycoprotein antibody-associated disease (MOGAD) experience a relapsing course, but the optimal relapse prevention therapy remains unclear. A meta- analysis was conducted to investigate the efficacy of azathioprine (AZA), mycophenolate mofetil (MMF), rituximab (RTX), maintenance intravenous immunoglobulin (IVIG), and tocilizumab (TCZ) in prevention of attacks in MOGAD. METHODS: English and Chinese-language articles published from January 2010 to May 2022 were searched in PubMed, Embase, Web of Science, Cochrane, Wanfang Data, China National Knowledge Infrastructure (CNKI), and China Science and Technology Journal Database (CQVIP). Studies with fewer than three cases were excluded. Meta-analysis of the relapse-free rate, the change of annualized relapse rate (ARR)and Expanded Disability Status Scale (EDSS) scores before and after treatment, and an age subgroup analysis was performed. RESULTS: A total of 41 studies were included. Three were prospective cohort studies, one was an ambispective cohort study, and 37 were retrospective cohort studies or case series. Eleven, eighteen, eighteen, eight, and two studies were included in the meta-analysis for relapse-free probability after AZA, MMF, RTX, IVIG, and TCZ therapy, respectively. The proportions of patients without relapse after AZA, MMF, RTX, IVIG, and TCZ were 65% [95% confidence interval (CI):49%-82%]), 73% (95%CI:62%-84%), 66% (95%CI:55%-77%), 79% (95%CI:66%-91%), and 93% (95%CI:54%-100%), respectively. The relapse-free rate did not significantly differ between the children and adults treated with each medication. Six, nine, ten, and three studies were included in the meta-analysis for the change of ARR before and after AZA, MMF, RTX, and IVIG therapy, respectively. ARR was significantly decreased after AZA, MMF, RTX, and IVIG therapy with a mean reduction of 1.58 (95%CI: [-2.29--0.87]), 1.32 (95%CI: [-1.57--1.07]), 1.01 (95%CI: [-1.34--0.67]), and 1.84 (95%CI: [-2.66--1.02]), respectively. The change in ARR did not significantly differ between children and adults. CONCLUSIONS: AZA, MMF, RTX, maintenance IVIG, and TCZ all reduce the risk of relapse in both pediatric and adult patients with MOGAD. The literatures included in the meta-analysis were mainly retrospective studies, so large randomized prospective clinical trials are needed to compare the efficacy of different treatments.

Multifunctional water-based metamaterial with polarization conversion and absorption.

A multifunctional metamaterial to realize broadband x-to-y cross-polarization conversion (CPC) and the absorption of electromagnetic waves is proposed in this paper. The presented multifunctional water-based metamaterial (MWM) consists of the top metallic dielectric substrate, the middle 3D printed container, and the bottom metal backplane. When the container is filled with water, the polarization conversion ratio (PCR) reaches more than 90% at 5.8-9.4 GHz, and the excellent absorption performance is achieved in the frequency band of 16.1-16.9 GHz. In addition, the CPC is achieved in two frequency bands (5.9-10.0 GHz and 14.3-16.4 GHz) without water injection. The unique properties of the proposed design are validated by experiments. As expected, the MWM simultaneously achieves polarization conversion and absorption functions, which is meaningful and consequential for multifunction and conformal stealth applications.

Accelerating the phase demodulation process for heterodyne Φ-OTDR using spatial phase shifting.

An effective orthogonal signal generation method for heterodyne-detection-based phase-sensitive optical time-domain reflectometer systems is proposed to accelerate the phase demodulation process. The demodulation principle is based on the spatial phase shifting technique. By exploiting the relative phase difference between adjacent spatial sampling channels, the orthogonal signal is easily obtained from basic algebra calculations. The simulation and experimental results showed that the proposed method achieved >100% computation speed improvement compared with the conventional methods, with a slight trade-off in phase demodulation performance. Therefore, the proposed method is potentially beneficial for the distributed acoustic sensing technology for reducing the computation complexity of phase demodulation procedures.

Efficacy of ketogenic diet in CDKL5-related epilepsy: a single arm meta-analysis.

BACKGROUND: Drug-resistant epilepsy is one of the most important features of cyclin-dependent kinase-like 5 (CDKL5) deficiency disorder. The ketogenic diet (KD) may be effective for patients with CDKL5-related epilepsy, but there is little high-quality evidence to confirm the efficacy. This meta-analysis investigated the efficacy and safety of KD in CDKL5-related epilepsy. METHODS: The PubMed, Embase, Web of Science, Cochrane Library, WanFang, CNKI and VIP databases were searched for relevant studies published up to January 1, 2022. Two reviewers independently screened the literature according to inclusion and exclusion criteria and evaluated the bias risk of the included studies. Meta-analysis was performed using Review Manager 5.3 software. RESULTS: A total of 12 retrospective studies involving 193 patients met the inclusion criteria. Meta-analysis revealed that the definite responder rate to KD in the treatment of CDKL5-related epilepsy was 18.0% [95% CI (0.07, 0.67)], with no statistical heterogeneity among studies (I2 = 0%, P = 0.45). The clinical responder rate was 50.5% [95% CI (0.75, 1.39)], and there was no statistical heterogeneity among all studies (I2 = 46%, P = 0.05). Subgroup analysis showed that there was no significant difference in the clinical responder rate between the two groups with seizure onset age before and after 1 month (P = 0.14). Only one study mentioned adverse reactions, and the incidence of adverse reactions was 78.3% (18/23). Constipation and vomiting were the main manifestations, implying a high incidence of gastrointestinal adverse reactions. CONCLUSIONS: The definite responder rate to KD in CDKL5-related epilepsy was 18%, and the gastrointestinal adverse reactions were probably common in these patients. All the studies included in the meta-analysis were retrospective, and most of them had small sample sizes. Additional high-quality studies are needed to confirm the efficacy and tolerance of KD in CDKL5-related epilepsy.

Evaluation of Statistical Process Control Techniques in Monitoring Weekly Body Condition Scores as an Early Warning System for Predicting Subclinical Ketosis in Dry Cows.

The management of body condition score (BCS) during the dry period is associated with the postpartum health outcomes of dairy cows. However, the difference between the actual BCS and the fixed ideal value is not able to accurately predict the occurrence of postpartum diseases. This study aimed to use statistical process control (SPC) technology to monitor the BCS of dry cows, to evaluate the effect of control charts on nutritional strategies, and to explore the utility of SPC in predicting the incidence of postpartum subclinical ketosis (SCK). The BCS and SCK data of 286 cows from the dry off period to 60 days postpartum were collected to set up the early warning function. Three control charts, including a control chart for the average BCS of the herds, for the BCS of each dry cow, and for individual BCS, were established. The early warning signs for postpartum SCK development were: (1) an individual BCS more than 3.5 that remained unchanged for six weeks; (2) a capability index (CPK), an SPC tool, greater than -0.52. Using these parameters, the early warning signs of SCK development were verified in 429 dry cows. The results showed that the accuracy of early warning signal was 0.64 and the precision was 0.26. The control chart showed that the average BCS of dry cows was consistently higher than the expected upper limit of BCS during the experimental period, and that the addition of new cows to the herds increased the average BCS. In summary, the application of SPC technology to monitor the BCS of dry cows was not a good tool for the prediction of postpartum SCK occurrence but was an appropriate tool for guiding positive nutrition strategies.

Synthesis and biological evaluation of novel hydroxybenzaldehyde-based kojic acid analogues as inhibitors of mushroom tyrosinase.

Two series of novel kojic acid analogues (4a-j) and (5a-d) were designed and synthesized, and their mushroom tyrosinase inhibitory activities was evaluated. The result indicated that all the synthesized derivatives exhibited excellent tyrosinase inhibitory properties having IC50 values in the range of 1.35±2.15-17.50±2.75µM, whereas standard inhibitor kojic acid have IC50 values 20.00±1.08µM. Specifically, 5-phenyl-3-[5-hydroxy-4-pyrone-2-yl-methylmercap-to]-4-(2,4-dihydroxyl-benzylamino)-1,2,4-triazole (4f) exhibited the most potent tyrosinase inhibitory activity with IC50 value of 1.35±2.15µM. The kinetic studies of the compound (4f) demonstrated that the inhibitory effects of the compound on the tyrosinase were belonging to competitive inhibitors. Meanwhile, the structure-activity relationship was discussed.