Thermochemical Transformation of Calcium during Biomass Burning and the Effects on Postfire Aqueous Dissolution of Macronutrients.

Calcium is commonly the most abundant element in fire residues and its speciation largely determines the geochemical properties of fire residues and their effects on postfire soil chemistry. To explore the effects of biomass composition and fire conditions on ash Ca speciation, this study characterizes the speciation of Ca in charcoal and ash samples that were derived from different plant compartments and thermal conditions, using Ca K-edge X-ray absorption near edge spectroscopy. Results showed that biomass contains abundant organic Ca complexes, which were mineralized into fairchildite and calcite after heating at 450 to 600 °C and then CaO, as temperature increased to 750 °C. Apatite could be an abundant Ca species in fire residues if the Ca/P molar ratio of the biomass is small (<2). The mineralization of organic Ca to the identified Ca minerals during burning was negligibly affected by the oxygen level. Calcium speciation in prescribed fire residues resembled that of biomass ash burned at 550 °C with similar Ca/P molar ratios. Batch experiments showed that macronutrients (Ca, Mg, K, and P) were differentially released, as a result of different solubility of minerals in ashes and reprecipitation of minerals. The aqueous solubility of Ca, Mg, and P decreased as pH increased from 5 to 9, while K showed no pH dependency and was almost completely soluble. Results from this study improve our understanding of the chemistry of fire residues and their geochemical behaviors, which can help evaluate the impact of fire on postfire soil properties and macronutrient cycling.

Re-examination of the Claimed Isolation of Stable Noncyclic 1,2-Disulfoxides.

Re-examination of the claimed isolation and X-ray characterization of di-p-tolyl and dimesityl 1,2-disulfoxides from thermolysis of the corresponding aryl sulfinimines and thiosulfinates showed that the isolated disulfide dioxides are instead the well-known isomeric thiosulfonates, as confirmed by XAS, DART-MS, X-ray, IR and NMR methods. Concerns with the original X-ray structures are addressed. Our results agree with the DFT prediction of very weak diaryl 1,2-disulfoxide S-S bond dissociation enthalpies. For now, room-temperature-stable noncyclic 1,2-disulfoxides remain unknown.

Confined Flash Printing and Synthesis of Stable Perovskite Nanofilms under Ambient Conditions.

The fabrication of stable perovskite nanofilm patterns is important for the development of functional optical devices. However, current production approaches are limited by the requirement for strict inert gas protection and long processing times. Here, a confined flash printing synthesis method is presented to generate perovskite nanofilms under ambient conditions, combining precursor transfer, perovskite synthesis, crystallization, and polymer protection in a single step within milliseconds. A laser simultaneously prints and induces the flash synthesis, confined in a polymer nanofilm, under normal ambient conditions. Due to its simplicity and flexibility, the method enables the combination and screening of many different perovskite precursor materials on various substrates. Besides for the development of novel perovskite materials and devices, the nanofilms can be applied for biodetection. The unique H2O2-responsive property of the ultrathin perovskite quantum dot film is applied for biomolecule detection based on oxidase-catalyzed enzymatic reactions.

Beyond smoothness: A general optimization framework for graph neural networks with negative Laplacian regularization.

Graph Neural Networks (GNNs) have drawn great attention in handling graph-structured data. To characterize the message-passing mechanism of GNNs, recent studies have established a unified framework that models the graph convolution operation as a graph signal denoising problem. While increasing interpretability, this framework often performs poorly on heterophilic graphs and also leads to shallow and fragile GNNs in practice. The key reason is that it encourages feature smoothness, but ignores the high-frequency information of node features. To address this issue, we propose a general framework for GNNs via relaxation of the smoothness regularization. In particular, it employs an information aggregation mechanism to learn the low- and high-frequency components adaptively from data, offering more flexible graph convolution operators compared to the smoothness-promoted framework. Theoretical analyses demonstrate that our framework can capture both low- and high-frequency information of node features, effectively. Experiments on nine benchmark datasets show that our framework achieves the state-of-the-art performance in most cases. Furthermore, it can be used to handle deep models and adversarial attacks.

Telling Data Stories with the Hero's Journey: Design Guidance for Creating Data Videos.

Data videos increasingly becoming a popular data storytelling form represented by visual and audio integration. In recent years, more and more researchers have explored many narrative structures for effective and attractive data storytelling. Meanwhile, the Hero's Journey provides a classic narrative framework specific to the Hero's story that has been adopted by various mediums. There are continuous discussions about applying Hero's Journey to data stories. However, so far, little systematic and practical guidance on how to create a data video for a specific story type like the Hero's Journey, as well as how to manipulate its sound and visual designs simultaneously. To fulfill this gap, we first identified 48 data videos aligned with the Hero's Journey as the common storytelling from 109 high-quality data videos. Then, we examined how existing practices apply Hero's Journey for creating data videos. We coded the 48 data videos in terms of the narrative stages, sound design, and visual design according to the Hero's Journey structure. Based on our findings, we proposed a design space to provide practical guidance on the narrative, visual, and sound custom design for different narrative segments of the hero's journey (i.e., Departure, Initiation, Return) through data video creation. To validate our proposed design space, we conducted a user study where 20 participants were invited to design data videos with and without our design space guidance, which was evaluated by two experts. Results show that our design space provides useful and practical guidance for data storytellers effectively creating data videos with the Hero's Journey.

Multichannel Lanthanide-Doped Nanoprobes for Serodiagnosis and Therapy.

In this account, we will highlight recent progress in the development of multichannel lanthanide-doped (MC-Ln) nanoprobes for highly efficient serodiagnosis and therapy, with a particular focus on our own work. First, we first provide a classification of the types of MC-Ln nanoprobes based on the contained type and number of signals. The merits of different types of nanoprobes and the reason using lanthanides are elucidated. Then, we provide an overview of the current uses of MC-Ln nanoprobes in serodiagnosis and therapy, focusing on the strategic exploration to improve the diagnostic and therapeutic performance from different perspectives. Finally, we present a prospective outlook on the future development and potential issues of next-generation MC-Ln nanoprobes. We hope that this timely account will update our understanding of MC-Ln and similar nanoprobes for bioapplications and provide helpful references for the state-of-the-art tools for serodiagnosis and therapy.

A unique trimeric triphenylene radical cation: stacking aggregation, bonding, and stability.

A new and unique π-stacking triphenylene trimer cation radical unit appears in the crystal structure of a newly synthesized salt with an oligomeric gallium(iii) chloride, [(C18H12)3]˙+(Ga3Cl10)-, which is the first triphenylene aggregate observed. The structure is attributed to a shared electron distributed over the trimer displaying π-stacking pancake bonding. Computational modeling rationalizes the appearance of a "chain-shaped" rather than a "star-shaped" gallium chloride anion as well as the reasons why the trimer, rather than a radical cation aggregate of different size, is preferred in this system. Moreover, the calculations allowed evaluation of larger cationic triphenylene radical π-stacked aggregates. Additional stabilization due to the shared single unpaired electron is calculated to remain significant at 5-7 kcal mol-1 for aggregates as large as 5-6 units.

[Application of ARHGAP8 in Predicting the Efficacy of Neoadjuvant Chemotherapy for Locally Advanced Mid-Low Rectal Cancer].

Objective To analyze the sensitivity of ARHGAP8 in predicting the efficacy of neoadjuvant chemotherapy in the patients with locally advanced mid-low colorectal cancer and provide accurate evidence for the treatment of advanced colorectal cancer. Methods The differentially expressed gene ARHGAP8 was screened out by bioinformatics analysis.Cancer tissue and rectal tissue of 68 patients with primary rectal cancer were selected.The rectal cancer tissue samples and the rectal tissue samples were collected for clinical validation of ARHGAP8 expression by quantitative real-time PCR,Western blotting,and immunohistochemistry.The clinical and pathological features such as gender,age,tumor stage,differentiation degree,and pathological type of the patients were collected for functional validation.Forty-four patients with locally advanced mid-low rectal cancer who received neoadjuvant chemotherapy were selected for immunohistochemical examination of ARHGAP8 expression.The expression level of ARHGAP8 was compared between before and after chemotherapy and among different efficacy groups. Results The bioinformatics analysis revealed differences in the expression level of ARHGAP8 between the cancer tissue and rectal tissue (P<0.001).The expression level of ARHGAP8 was correlated with tumor stage (P=0.024),lymph node metastasis (P=0.007),and age (P=0.005).Quantitative real-time PCR results showed that the mRNA level of ARHGAP8 in the cancer tissue was higher than that in the rectal tissue (P<0.001).Western blotting and immunohistochemistry results demonstrated that the protein level of ARHGAP8 in the cancer tissue was higher than that in the rectal tissue (P=0.011).The expression of ARHGAP8 was correlated with tumor size (P=0.010) and pathological stage (P=0.005),while it showed no significant association with tumor differentiation degree,lymph node metastasis,liver metastasis,Ki-67,or microsatellite instability expression level.The 44 patients receiving neoadjuvant chemotherapy included 13,8,8,and 15 patients of tumor regression grades 0,1,2,and 3,respectively.Among them,65.91% (29/44) patients showed responses to the treatment.After neoadjuvant chemotherapy,the expression of ARHGAP8 in the cancer tissue was down-regulated in the patients who responded to the chemotherapy (P<0.001).The response rate in the patients with low protein level of ARHGAP8 was 92.86%,which was higher than that (53.33%) in the patients with high protein level of ARHGAP8 (P=0.033). Conclusion ARHGAP8 is highly expressed in the rectal cancer tissue.The patients with locally advanced mid-low rectal cancer and low ARHGAP8 expression are more sensitive to neoadjuvant chemotherapy with the XELOX protocol.ARHGAP8 can serve as a potential biomarker for the occurrence and development of rectal cancer and an important index for evaluating the efficacy of neoadjuvant chemotherapy with the XELOX protocol in the patients with locally advanced mid-low rectal cancer.

Performance in the Fundamentals of Laparoscopic Surgery: Does it reflect global rating scales in the Objective Structured Assessment of Technical Skills in porcine laparoscopic surgery?

Objective: To correlate the utility of the Fundamentals of Laparoscopic Surgery (FLS) manual skills program with the Objective Structured Assessment of Technical Skills (OSATS) global rating scale in evaluating operative performance. Methods: The Asian Urological Surgery Training and Educational Group (AUSTEG) Laparoscopic Upper Tract Surgery Course implemented and validated the FLS program for its usage in laparoscopic surgical training. Delegates' basic laparoscopic skills were assessed using three different training models (peg transfer, precision cutting, and intra-corporeal suturing). They also performed live porcine laparoscopic surgery at the same workshop. Live surgery skills were assessed by blinded faculty using the OSATS rating scale. Results: From March 2016 to March 2019, a total of 81 certified urologists participated in the course, with a median of 5 years of post-residency experience. Although differences in task time did not reach statistical significance, those with more surgical experience were visibly faster at completing the peg transfer and intra-corporeal suturing FLS tasks. However, they took longer to complete the precision cutting task than participants with less experience. Overall OSATS scores correlated weakly with all three FLS tasks (peg transfer time: r=-0.331, r 2=0.110; precision cutting time: r=-0.240, r 2=0.058; suturing with intra-corporeal knot time: r=-0.451, r 2=0.203). Conclusion: FLS task parameters did not correlate strongly with OSATS globing rating scale performance. Although FLS task models demonstrated strong validity, it is important to assimilate the inconsistencies when benchmarking technical proficiency against real-life operative competence, as evaluated by FLS and OSATS, respectively.

Chemical reduction of π-expanded functionalized pentacene: cooperation of side group in alkali metal binding.

Chemical reduction of a vertically expanded pentacene, TIPS-peri-pentacenopentacene (TIPS-PPP), with sodium metal in THF readily afforded a doubly-reduced product isolated as [{Na+(THF)3}2(TIPS-PPP2-)]. Single-crystal X-ray diffraction revealed the formation of a π-complex of TIPS-PPP2- with two {Na+(THF)3} moieties. The sodium ion is coordinated to three C-atoms at the most negatively charged edge sites and at the lateral ethynyl group. The delocalisation of the charge on the ethynyl function is accompanied by its notable elongation (Δ = 0.015 Å) coupled with the contraction of the adjacent single C-C bond (Δ = 0.033 Å). Bond length analysis supported by Harmonic Aromaticity Oscillator Model (HOMA) shows that the dianion can be written with four aromatic sextets in agreement with the Clar representation. Although TIPS-PPP2- has 36 π-electrons (4n), it does not show a global magnetic paratropic response. The rings with the most negative charge density have a very low paratropic response, while the other rings have a low diatropic response. Overall, the dianion is a non-aromatic molecule.

Two polymorph modifications of tris(hexafluoroacetylacetonato)iron(III) revealed: is that common for other trivalent metals?

A long-standing issue about the correct identification of an important starting reagent, iron(III) hexafluoroacetylacetonate, Fe(hfac)3 (1), has been resolved. The tris-chelated mononuclear complex was found to crystallize in two polymorph modifications which can be assigned as the low-temperature (1-L) monoclinic P21/n and the high-temperature (1-H) trigonal P-3. Low-temperature polymorph 1-L was found to transform to 1-H upon sublimation at 44 °C. Two modifications are clearly distinguished by powder X-ray diffraction (PXRD), single-crystal X-ray diffraction, differential scanning calorimetry (DSC), and melting-point measurements. On the other hand, the two forms share similar characteristics in direct analysis in real-time mass spectrometry (DART-MS), attenuated total reflection (ATR) spectroscopy, and some physical properties, such as color, volatility, sensitivity, and solubility. Analysis of the literature and some of our preliminary data strongly suggest that the appearance of two polymorph modifications for trivalent metal (both transition and main group) hexafluoroacetylacetonates is a common case for several largely used complexes not yet accounted for in the crystallographic databases.

Decoding the Molecular Mechanisms of BRAF V600E-Induced Nevi Formation.

Melanocytes derived from neural crest cells harbor the BRAF V600E mutation, which is the predominant driver of nevus formation in humans. This mutation leads to malignant cell proliferation and subsequent cell cycle arrest, culminating in oncogene-induced senescence and nevus development. Nevertheless, emerging evidence has highlighted the heterogeneity of cellular senescence markers in BRAF V600E-induced senescent melanocytes. Moreover, the capacity of melanocytes within nevi to regain their proliferative ability raises questions about the molecular mechanisms by which BRAF V600E, via the mitogen-activated protein kinase signaling pathway, triggers nevus formation. This study provides an overview and discussion of the molecular mechanisms underpinning BRAF V600E-induced melanocyte nevus formation and the relevant animal models employed for their elucidation. It also highlights the significance of elucidating dynamic changes in cytoplasmic and nuclear substrates that interact with phosphorylated extracellular signal-regulated protein kinases 1 and 2 and underscores the value of using targeted BRAF V600E animal models created through gene editing technologies.

Phytochemical components analysis and hypolipidemic effect on hyperlipidemia mice of the aerial parts from Allium sativum.

Background: The bulbs of Allium sativum are widely used as food or seasoning (garlic), while they have also been utilized as a famous traditional medicine since ancient eras for the treatment of scabies, tuberculosis, pertussis, diarrhea and dysentery, etc. However, very few studies focus on their abundant aerial parts, which are normally discarded during the harvest season. Methods: The hyperlipidemic mice model has been used to study the lipid-lowering effect of the aerial parts in this article. 180 mice were randomly divided into 18 groups, including blank control (BC), model (Mod), positive control (PC), and low-, medium-, and high-dose groups of the crude extract, petroleum ether, ethyl acetate, n-butanol, and residual water extracts (corresponding to CE, PEE, EAE, NBE, WE), with 10 mice in each group. The preventive effects of the extracts on hyperlipidemic mice lasted for four weeks. Ultra performance liquid chromatography quadrupole time-of-flight mass spectrometry (UPLC-Q/TOF-MS) and gas chromatography tandem mass spectrometry (GC-MS/MS) were used to analyze the chemical components of NBE and PEE respectively. Results: The results of the mice experiment showed that n-butanol extract (NBE) and petroleum ether extract (PEE) from the aerial parts could significantly reduce the contents of total cholesterol (TC), triglycerides (TG), low density lipoprotein cholesterol (LDL-C), alanine transaminase (ALT) and aspartate transaminase (AST) in serum of hyperlipidemic mice, and increase the contents of high density lipoprotein cholesterol (HDL-C). They could enhance the activity of superoxide dismutase (SOD) in liver and reduce the level of malondialdehyde (MDA). At the same time, they could improve steatosis and inflammation of liver cells. The results of phytochemical components analysis showed that NBE was rich in organic acids, flavonoids and nitrogen-containing constituents, while PEE contained organic sulfur compounds, aliphatic acids and derivatives, alkaloids, phytosterols, etc. Conclusion: These results support that the aerial parts of A. sativum are an interesting source of bioactive ingredients that may be useful in the prevention and treatment of hyperlipidemia.

Development and Evaluation of DOTA-FAPI-Maleimide as a Novel Radiotracer for Tumor Theranostic with Extended Circulation.

This study aimed to evaluate a novel albumin-binding strategy for addressing the challenge of insufficient tumor retention of fibroblast activation protein inhibitors (FAPIs). Maleimide, a molecule capable of covalent binding to free thiol groups, was modified to conjugate with FAPI-04 in order to enhance its binding to endogenous albumin, resulting in an extended blood circulation half-life and increased tumor uptake. DOTA-FAPI-maleimide was prepared and radiolabeled with Ga-68 and Lu-177, followed by cellular assays, pharmacokinetic analysis, PET/CT, and SPECT/CT imaging to assess the probe distribution in various tumor-bearing models. Radiolabeling of the modified probe was successfully achieved with a radiochemical yield of over 99% and remained stable for 144 h. Cellular assays showed that the ligand concentration required for 50% inhibition of the probe was 1.20 ± 0.31 nM, and the Kd was 0.70 ± 0.07 nM with a Bmax of 7.94 ± 0.16 fmol/cell, indicative of higher specificity and affinity of DOTA-FAPI-maleimide compared to other FAPI-04 variants. In addition, DOTA-FAPI-maleimide exhibited a persistent blood clearance half-life of 7.11 ± 0.34 h. PET/CT images showed a tumor uptake of 2.20 ± 0.44%ID/g at 0.5 h p.i., with a tumor/muscle ratio of 5.64 in HT-1080-FAP tumor-bearing models. SPECT/CT images demonstrated long-lasting tumor retention. At 24 h p.i., the tumor uptake of [177Lu]Lu-DOTA-FAPI-maleimide reached 5.04 ± 1.67%ID/g, with stable tumor retention of 3.40 ± 1.95%ID/g after 4 days p.i. In conclusion, we developed and evaluated the thiol group-attaching strategy, which significantly extended the circulation and tumor retention of the adapted FAPI tracer. We envision its potential application for clinical cancer theranostics.

The "appearing" and "disappearing" ascites in the treatment of colorectal cancer: a case report.

Background: Colorectal cancer (CRC) is one of the most common cancers worldwide. In the treatment of patients with CRC, oxaliplatin plays a pivotal role, with moderate side effects. Neurotoxicity, myelosuppression, ototoxicity, delayed hypersensitivity reactions, and rhabdomyolysis induced by oxaliplatin have been reported individually. However, the occurrence of oxaliplatin-induced ascites has not been reported previously. The objectives of this case report were to elaborate on the rare occurrence of ascites in a patient with CRC after oxaliplatin therapy and to explore its characteristics and causes. Case description: We report on a case of upper rectal cancer seen in a 65-year-old man who underwent robotic-assisted laparoscopic anterior rectal resection. The patient developed ascites during postoperative adjuvant therapy with oxaliplatin and capecitabine. We ruled out tumor recurrence by laparoscopy, intraoperative biopsy, and biochemistry of the ascites. The patient did not experience a recurrence of ascites after discontinuation of chemotherapy. Conclusion: This case suggests that chemotherapy with oxaliplatin might cause ascites. The mechanism of the oxaliplatin-induced liver injury was further discussed, which might have been the cause of ascite formation. When patients with CRC who underwent chemotherapy with oxaliplatin develop ascites, surgeons should actively determine whether this is a side effect of chemotherapy or is due to tumor recurrence in order to avoid unnecessary surgery.

Progress and Outlook on Electrochemical Sensing of Lung Cancer Biomarkers.

Electrochemical biosensors have emerged as powerful tools for the ultrasensitive detection of lung cancer biomarkers like carcinoembryonic antigen (CEA), neuron-specific enolase (NSE), and alpha fetoprotein (AFP). This review comprehensively discusses the progress and potential of nanocomposite-based electrochemical biosensors for early lung cancer diagnosis and prognosis. By integrating nanomaterials like graphene, metal nanoparticles, and conducting polymers, these sensors have achieved clinically relevant detection limits in the fg/mL to pg/mL range. We highlight the key role of nanomaterial functionalization in enhancing sensitivity, specificity, and antifouling properties. This review also examines challenges related to reproducibility and clinical translation, emphasizing the need for standardization of fabrication protocols and robust validation studies. With the rapid growth in understanding lung cancer biomarkers and innovations in sensor design, nanocomposite electrochemical biosensors hold immense potential for point-of-care lung cancer screening and personalized therapy guidance. Realizing this goal will require strategic collaboration among material scientists, engineers, and clinicians to address technical and practical hurdles. Overall, this work provides valuable insight for developing next-generation smart diagnostic devices to combat the high mortality of lung cancer.

Icanbelimod (CBP-307), a next-generation Sphingosine-1-phosphate receptor modulator, in healthy men: pharmacokinetics, pharmacodynamics, safety, and tolerability in a randomized trial in Australia.

Background: Icanbelimod (formerly CBP-307) is a next-generation S1PR modulator, targeting S1PR1. In this first-in-human study, icanbelimod was investigated in healthy men in Australia. Methods: Participants were randomized 3:1, double-blind, to icanbelimod or placebo in four single-dose cohorts (0.1 mg, 0.25 mg, 0.5 mg [n=8 per cohort], 2.5 mg [n=4]) or for 28-days once-daily treatment in two cohorts (0.15 mg, 0.25 mg [n=8 per cohort]). Participants in the 0.25-mg cohort received 0.1 mg on Day 1. Treatments were administered orally after fasting; following one-week washout, icanbelimod was administered after breakfast in the 0.5-mg cohort. Results: Icanbelimod exposure increased rapidly and dose-dependently with single and multiple dosing (Tmax 4-7 hours). Lymphocyte counts decreased rapidly after single (-11%, 0.1 mg; -40%, 0.25 mg; -71%, 0.5 mg; -77%, 2.5 mg) and multiple doses (-49%, 0.15 mg; -75%, 0.25 mg), and recovered quickly, 7 days after dosing. After single-dose 0.5 mg, although a high-fat breakfast versus fasting did not affect maximal decrease, lymphocyte counts tended to be lower after breakfast across most timepoints up to 72 hours. Twenty-eight participants (63.6%) experienced mainly mild treatment-emergent adverse events (TEAEs). After single-dose icanbelimod, the most common TEAEs were headache (28.6%, n=6) and dizziness (19.0%, n=4). Three participants experienced transient bradycardia, with one serious, following single-dose 2.5 mg icanbelimod. After multiple-dose icanbelimod, the most common TEAEs were headache (50.0%, n=6) and lymphopenia (41.7%, n=5), and two participants withdrew due to non-serious TEAEs. Up-titration attenuated heart rate reductions. Conclusion: Icanbelimod was well-tolerated up to 0.5 mg and effectively reduced lymphocyte counts. Clinical trial registration: ClinicalTrials.gov, identifier NCT02280434.b.

Bio-electrocatalytic alkene reduction using ene-reductases with methyl viologen as electron mediator.

Asymmetric hydrogenation of alkene moieties is important for the synthesis of chiral molecules, but achieving high stereoselectivity remains a challenge. Biocatalysis using ene-reductases (EReds) offers a viable solution. However, the need for NAD(P)H cofactors limits large-scale applications. Here, we explored an electrochemical alternative for recycling flavin-containing EReds using methyl viologen as a mediator. For this, we built a bio-electrocatalytic setup with an H-type glass reactor cell, proton exchange membrane, and carbon cloth electrode. Experimental results confirm the mediator's electrochemical reduction and enzymatic consumption. Optimization showed increased product concentration at longer reaction times with better reproducibility within 4-6 h. We tested two enzymes, Pentaerythritol Tetranitrate Reductase (PETNR) and the Thermostable Old Yellow Enzyme (TOYE), using different alkene substrates. TOYE showed higher productivity for the reduction of 2-cyclohexen-1-one (1.20 mM h-1), 2-methyl-2-cyclohexen-1-one (1.40 mM h-1) and 2-methyl-2-pentanal (0.40 mM h-1), with enantiomeric excesses ranging from 11% to 99%. PETNR outperformed TOYE in terms of enantioselectivity for the reduction of 2-methyl-2-pentanal (ee 59±7% (S)). Notably, TOYE achieved promising results also in reducing ketoisophorone, a challenging substrate, with similar enantiomeric excess compared to published values using NADH.

Unveil cis-acting combinatorial mRNA motifs by interpreting deep neural network.

SUMMARY: Cis-acting mRNA elements play a key role in the regulation of mRNA stability and translation efficiency. Revealing the interactions of these elements and their impact plays a crucial role in understanding the regulation of the mRNA translation process, which supports the development of mRNA-based medicine or vaccines. Deep neural networks (DNN) can learn complex cis-regulatory codes from RNA sequences. However, extracting these cis-regulatory codes efficiently from DNN remains a significant challenge. Here, we propose a method based on our toolkit NeuronMotif and motif mutagenesis, which not only enables the discovery of diverse and high-quality motifs but also efficiently reveals motif interactions. By interpreting deep-learning models, we have discovered several crucial motifs that impact mRNA translation efficiency and stability, as well as some unknown motifs or motif syntax, offering novel insights for biologists. Furthermore, we note that it is challenging to enrich motif syntax in datasets composed of randomly generated sequences, and they may not contain sufficient biological signals. AVAILABILITY AND IMPLEMENTATION: The source code and data used to produce the results and analyses presented in this manuscript are available from GitHub (https://github.com/WangLabTHU/combmotif).