AI-driven antibody design with generative diffusion models: current insights and future directions.

Therapeutic antibodies are at the forefront of biotherapeutics, valued for their high target specificity and binding affinity. Despite their potential, optimizing antibodies for superior efficacy presents significant challenges in both monetary and time costs. Recent strides in computational and artificial intelligence (AI), especially generative diffusion models, have begun to address these challenges, offering novel approaches for antibody design. This review delves into specific diffusion-based generative methodologies tailored for antibody design tasks, de novo antibody design, and optimization of complementarity-determining region (CDR) loops, along with their evaluation metrics. We aim to provide an exhaustive overview of this burgeoning field, making it an essential resource for leveraging diffusion-based generative models in antibody design endeavors.

Three-directional digital shearography based on SLM using a honeycomb-like pattern.

The possibility of utilizing a honeycomb-like modulation pattern in a spatial light modulator (SLM) for multi-directional synchronous digital shearography measurements has been investigated. Each modulation pixel in the honeycomb-like pattern modulates the shearing amount in different directions, thus avoiding the resolution loss associated with previous methods where a single pixel could only modulate a specific shearing direction. It was demonstrated that high-quality phase maps for different shearing directions can be simultaneously obtained with a single exposure.

New Insights into the ORR Catalysis on Pt Alloy Nanoparticles from an Element Specific d-Band Analysis.

Bolstered by their unique atomic structures and tailored compositions, nanoalloys exhibit extraordinary properties making them ideal materials to solve challenges in energy storage and conversion catalysis. However, a quantitative description of the structure-property relationships using an accurate descriptor-based model for nanoalloys, ranging from bimetallic to multimetallic compositions, is needed to drive efficient material design toward high-performance catalysis. In this work, we highlight the electronic property and catalytic activity relationship from an element specific d-band analysis of Pt-based alloy catalysts using X-ray absorption near-edge spectroscopy (XANES). Using a series of L10-MPt/Pt (M = Fe, Co, Ni) core/shell alloy catalysts with well-defined atomic structures, we quantified subtle differences in the Pt d-electron states and correlated the Pt d-band structure to their superior catalytic activity toward the oxygen reduction reaction (ORR). Our analysis used the upper d-band edge position as a predictive descriptor for the mass activity toward the ORR instead of the commonly used d-band center position. Together with density functional theory calculations and Nørskov d-band theory, the upper d-band edge position for the Pt states, derived from experimental measurements, elucidates new physical insights into the ORR performance of the L10-MPt/Pt core/shell catalysts. An element specific Pt d-band analysis using XANES overcomes challenges in traditional X-ray photoelectron spectroscopy-based valence d-band analysis, which cannot distinguish signals from independent elements in nanoalloys. Thus, the insights from the element specific d-band analysis presented in this work are a promising approach to determine structure-property relationships in a variety of transition metal nanoalloys and will be useful in the design of future high-performance catalysts.

A Study on the Design of Knee Exoskeleton Rehabilitation Based on the RFPBS Model.

The gait rehabilitation knee exoskeleton is an advanced rehabilitative assistive device designed to help patients with knee joint dysfunction regain normal gait through training and activity support. This paper introduces a design framework based on the process knowledge representation method to optimize the design and control efficiency of the knee exoskeleton. This framework integrates knowledge of design objects and processes, specifically including requirements, functions, principle work areas, and the representation and multi-dimensional dynamic mapping of the Behavior-Structure (RFPBS) matrix, achieving multi-dimensional dynamic mapping of the knee exoskeleton. This method incorporates biomechanical and physiological knowledge from the rehabilitation process to more effectively simulate and support gait movements during rehabilitation. Research results indicate that the knee rehabilitation exoskeleton design, based on the RFPBS process knowledge representation model, accomplishes multi-dimensional dynamic mapping, providing a scientific basis and effective support for the rehabilitation of patients with knee joint dysfunction.

Flow and performance: a quantitative study of elicitation modeling in a piano performance perspective.

Introduction: Flow, defined as a heightened state of consciousness characterized by intense concentration during an activity, is influenced primarily by the perceived challenge and the dynamic equilibrium of skills. This investigation focuses on the patterns of flow state attainment and its elicitation mechanisms within the context of piano performance among Chinese music college students. Methods: Our study establishes a framework for accessing flow, utilizing quantitative data from music ontology to gauge the level of challenge and the level of music acquisition to assess skills. Additionally, we integrate external factors such as music culture heterogeneity and demographic variables to elucidate the causes and moderating effects of flow on piano performance. Results: The findings reveal a positive correlation between flow and performance, with the model of challenge and skill induction partially explaining these results. Notably, melodic Shannon Entropy emerges as a potential indicator of challenge, suggesting its relevance in future studies on flow. Discussion: This research provides multidimensional insights into the interplay between performance and flow in piano performance, guiding future investigations to explore the musical quantitative perspective more deeply.

Reducing language barriers, promoting information absorption, and communication using fanyi.

ABSTRACT: Interpreting genes of interest is essential for identifying molecular mechanisms, but acquiring such information typically involves tedious manual retrieval. To streamline this process, the fanyi package offers tools to retrieve gene information from sources like National Center for Biotechnology Information (NCBI), significantly enhancing accessibility. Additionally, understanding the latest research advancements and sharing achievements are crucial for junior researchers. However, language barriers often restrict knowledge absorption and career development. To address these challenges, we developed the fanyi package, which leverages artificial intelligence (AI)-driven online translation services to accurately translate among multiple languages. This dual functionality allows researchers to quickly capture and comprehend information, promotes a multilingual environment, and fosters innovation in academic community. Meanwhile, the translation functions are versatile and applicable beyond biomedicine research to other domains as well. The fanyi package is freely available at https://github.com/YuLab-SMU/fanyi .

Molecular basis for the activation of PAF receptor by PAF.

Platelet-activating factor (PAF) is a potent phospholipid mediator crucial in multiple inflammatory and immune responses through binding and activating the PAF receptor (PAFR). However, drug development targeting the PAFR has been limited, partly due to an incomplete understanding of its activation mechanism. Here, we present a 2.9-Å structure of the PAF-bound PAFR-Gi complex. Structural and mutagenesis analyses unveil a specific binding mode of PAF, with the choline head forming cation-π interactions within PAFR hydrophobic pocket, while the alkyl tail penetrates deeply into an aromatic cleft between TM4 and TM5. Binding of PAF modulates conformational changes in key motifs of PAFR, triggering the outward movement of TM6, TM7, and helix 8 for G protein coupling. Molecular dynamics simulation suggests a membrane-side pathway for PAF entry into PAFR via the TM4-TM5 cavity. By providing molecular insights into PAFR signaling, this work contributes a foundation for developing therapeutic interventions targeting PAF signal axis.

Cryo-EM structures of adenosine receptor A3AR bound to selective agonists.

The adenosine A3 receptor (A3AR), a key member of the G protein-coupled receptor family, is a promising therapeutic target for inflammatory and cancerous conditions. The selective A3AR agonists, CF101 and CF102, are clinically significant, yet their recognition mechanisms remained elusive. Here we report the cryogenic electron microscopy structures of the full-length human A3AR bound to CF101 and CF102 with heterotrimeric Gi protein in complex at 3.3-3.2 Å resolution. These agonists reside in the orthosteric pocket, forming conserved interactions via their adenine moieties, while their 3-iodobenzyl groups exhibit distinct orientations. Functional assays reveal the critical role of extracellular loop 3 in A3AR's ligand selectivity and receptor activation. Key mutations, including His3.37, Ser5.42, and Ser6.52, in a unique sub-pocket of A3AR, significantly impact receptor activation. Comparative analysis with the inactive A2AAR structure highlights a conserved receptor activation mechanism. Our findings provide comprehensive insights into the molecular recognition and signaling of A3AR, paving the way for designing subtype-selective adenosine receptor ligands.

High-temperature thermal disturbance elimination method based on multi-channel extraction and correction.

Digital image correlation (DIC) technology has been widely used in high-temperature measurement fields. However, due to the complexity of high-temperature environments, there are many interference factors that limit the development of high-temperature DIC technology, among which thermal disturbance is one of the most significant factors that severely affects the measurement accuracy of high-temperature DIC. In this paper, a multi-channel separation technique combined with a low-cost laser speckle device is proposed to eliminate thermal disturbance errors in high-temperature DIC measurements. First, a blue laser speckle generation system is independently designed to produce the most suitable speckle particles, and the best laser speckle is determined and projected onto the blue background white spot pattern. Then a green LED illuminates the sample to provide illumination for the sample's own grayscale characteristics. A color camera collects photos, and the obtained images are processed with channel separation to extract and calculate the displacement of different channels. Finally, the displacement fields of the green and blue channels are subtracted to separate the thermal disturbance error and correct the measurement values. In this paper, a laser speckle projection system is first assembled, followed by a comprehensive evaluation of the projected speckle and, finally, a DIC experimental system is constructed for verification experiments at both room temperature and high temperature, and the corrected values are compared with the true values. The results show that the corrected values are highly consistent with the true values, which verifies the reliability of the proposed method.

Inhibitory mechanism of quercetin on Alicyclobacillus acidoterrestris.

In this the antibacterial of quercetin against Alicyclobacillus acidoterrestris was evaluated by measuring the minimal inhibitory concentration (MIC) and minimal bactericidal concentration (MBC). Subsequently, the effect of quercetin on A. acidoterrestris cell membrane was evaluated through scanning electron microscopy (SEM), surface hydrophobicity determination, diacetate fluorescein staining and propidium iodide (PI) staining. Additionally, the effects of quercetin on intracellular macromolecules and cell metabolism were explored by measuring the culture medium protein, bacterial protein and intracellular sodium and potassium adenosine triphosphate (ATP) enzyme activity. The results revealed that quercetin exhibited the MIC and MBC values of 100 ug/mL and 400 ug/mL, respectively, against A. acidoterrestris. The SEM results revealed that quercetin could induce irreversible damage to the cell membrane effectively. Moreover, quercetin could enhance the surface hydrophobicity of A. acidoterrestris. The results of flow cytometry and fluorescence microscopy analyses revealed that quercetin could promote cell damage by altering the cell membrane permeability of A. acidoterrestris, inducing the release of nucleic acid substances from the cells. Furthermore, the determination of protein content in the culture medium, bacterial protein content, and the Na(+)/K(+)-ATPase activity demonstrated that quercetin could reduce the intracellular protein content and impedes protein expression and ATPase synthesis effectively, leading to apoptosis.

Molecular recognition of niacin and lipid-lowering drugs by the human hydroxycarboxylic acid receptor 2.

Niacin, an age-old lipid-lowering drug, acts through the hydroxycarboxylic acid receptor 2 (HCAR2), a G-protein-coupled receptor (GPCR). Yet, its use is hindered by side effects like skin flushing. To address this, specific HCAR2 agonists, like MK-6892 and GSK256073, with fewer adverse effects have been created. However, the activation mechanism of HCAR2 by niacin and these new agonists is not well understood. Here, we present three cryoelectron microscopy structures of Gi-coupled HCAR2 bound to niacin, MK-6892, and GSK256073. Our findings show that different ligands induce varying binding pockets in HCAR2, influenced by aromatic amino acid clusters (W91ECL1, H1614.59, W1885.38, H1895.39, and F1935.43) from receptors ECL1, TM4, and TM5. Additionally, conserved residues R1113.36 and Y2847.43, unique to the HCA receptor family, likely initiate activation signal propagation in HCAR2. This study provides insights into ligand recognition, receptor activation, and G protein coupling mediated by HCAR2, laying the groundwork for developing HCAR2-targeted drugs.

Rapid one-shot dual-shearing digital shearography using a spatial light modulator.

Digital shearography is a non-contact, whole-field, and high-accuracy laser-based optical interferometric method. It is widely used in the field of non-destructive testing and material evaluation. Dual-shearing DS, as the state-of-the-art method, can detect defects or measure the derivative of deformation in two sensitive directions. Most existing dual-shearing DS is realized with a bulky Michelson or Mach-Zehnder interferometer; recently, the usage of a spatial light modulator (SLM) in DS offers a new approach to designing a simple and light shearographic system. However, prior proposed SLM-based DS requires multiple shots for the phase map acquisition, with the classic temporal phase-shift (TPS) technique severely limiting its applications. This paper proposes a novel, to our best knowledge, one-shot dual-shearing DS by creating a dual-stripe pattern in the SLM. Two separate phase maps, with different sensitive directions, were acquired simultaneously via the spatial phase-shift technique. The measurement can be easily done within a single shot in its compact and light body. Moreover, the shearing amount of the two sensitive directions can be set independently and precisely. These advantages promote that the proposed system can be applied in various applications, especially for dynamic and complicated composite material testing. A detailed theory and experimental validation are described.

Identification of a drug binding pocket in TMEM16F calcium-activated ion channel and lipid scramblase.

The dual functions of TMEM16F as Ca2+-activated ion channel and lipid scramblase raise intriguing questions regarding their molecular basis. Intrigued by the ability of the FDA-approved drug niclosamide to inhibit TMEM16F-dependent syncytia formation induced by SARS-CoV-2, we examined cryo-EM structures of TMEM16F with or without bound niclosamide or 1PBC, a known blocker of TMEM16A Ca2+-activated Cl- channel. Here, we report evidence for a lipid scrambling pathway along a groove harboring a lipid trail outside the ion permeation pore. This groove contains the binding pocket for niclosamide and 1PBC. Mutations of two residues in this groove specifically affect lipid scrambling. Whereas mutations of some residues in the binding pocket of niclosamide and 1PBC reduce their inhibition of TMEM16F-mediated Ca2+ influx and PS exposure, other mutations preferentially affect the ability of niclosamide and/or 1PBC to inhibit TMEM16F-mediated PS exposure, providing further support for separate pathways for ion permeation and lipid scrambling.

GPCR activation and GRK2 assembly by a biased intracellular agonist.

Phosphorylation of G-protein-coupled receptors (GPCRs) by GPCR kinases (GRKs) desensitizes G-protein signalling and promotes arrestin signalling, which is also modulated by biased ligands1-6. The molecular assembly of GRKs on GPCRs and the basis of GRK-mediated biased signalling remain largely unknown owing to the weak GPCR-GRK interactions. Here we report the complex structure of neurotensin receptor 1 (NTSR1) bound to GRK2, Gαq and the arrestin-biased ligand SBI-5537. The density map reveals the arrangement of the intact GRK2 with the receptor, with the N-terminal helix of GRK2 docking into the open cytoplasmic pocket formed by the outward movement of the receptor transmembrane helix 6, analogous to the binding of the G protein to the receptor. SBI-553 binds at the interface between GRK2 and NTSR1 to enhance GRK2 binding. The binding mode of SBI-553 is compatible with arrestin binding but clashes with the binding of Gαq protein, thus providing a mechanism for its arrestin-biased signalling capability. In sum, our structure provides a rational model for understanding the details of GPCR-GRK interactions and GRK2-mediated biased signalling.

Conserved class B GPCR activation by a biased intracellular agonist.

Class B G-protein-coupled receptors (GPCRs), including glucagon-like peptide 1 receptor (GLP1R) and parathyroid hormone 1 receptor (PTH1R), are important drug targets1-5. Injectable peptide drugs targeting these receptors have been developed, but orally available small-molecule drugs remain under development6,7. Here we report the high-resolution structure of human PTH1R in complex with the stimulatory G protein (Gs) and a small-molecule agonist, PCO371, which reveals an unexpected binding mode of PCO371 at the cytoplasmic interface of PTH1R with Gs. The PCO371-binding site is totally different from all binding sites previously reported for small molecules or peptide ligands in GPCRs. The residues that make up the PCO371-binding pocket are conserved in class B GPCRs, and a single alteration in PTH2R and two residue alterations in GLP1R convert these receptors to respond to PCO371. Functional assays reveal that PCO371 is a G-protein-biased agonist that is defective in promoting PTH1R-mediated arrestin signalling. Together, these results uncover a distinct binding site for designing small-molecule agonists for PTH1R and possibly other members of the class B GPCRs and define a receptor conformation that is specific only for G-protein activation but not arrestin signalling. These insights should facilitate the design of distinct types of class B GPCR small-molecule agonist for various therapeutic indications.

Application of line-scan CMOS camera in multi-beam heterodyne differential laser Doppler vibration sensor.

The possibility of using a line-scan digital CMOS camera as a photodetector in a multi-beam heterodyne differential laser Doppler vibration sensor has been investigated. Application of the line-scan CMOS camera allows for selection of a different number of beams for a particular application in the sensor design, and for a compact design of the sensor. It was demonstrated that a limitation of the maximum measured velocity caused by the camera limited line rate can be overcome by selecting the beams separation on the object and the value of shear between images on the camera.

The ϕPA3 phage nucleus is enclosed by a self-assembling 2D crystalline lattice.

To protect themselves from host attack, numerous jumbo bacteriophages establish a phage nucleus-a micron-scale, proteinaceous structure encompassing the replicating phage DNA. Bacteriophage and host proteins associated with replication and transcription are concentrated inside the phage nucleus while other phage and host proteins are excluded, including CRISPR-Cas and restriction endonuclease host defense systems. Here, we show that nucleus fragments isolated from ϕPA3 infected Pseudomonas aeruginosa form a 2-dimensional lattice, having p2 or p4 symmetry. We further demonstrate that recombinantly purified primary Phage Nuclear Enclosure (PhuN) protein spontaneously assembles into similar 2D sheets with p2 and p4 symmetry. We resolve the dominant p2 symmetric state to 3.9 Šby cryo-EM. Our structure reveals a two-domain core, organized into quasi-symmetric tetramers. Flexible loops and termini mediate adaptable inter-tetramer contacts that drive subunit assembly into a lattice and enable the adoption of different symmetric states. While the interfaces between subunits are mostly well packed, two are open, forming channels that likely have functional implications for the transport of proteins, mRNA, and small molecules.

Neuroprotective effects of insulin-like growth factor-2 in 6-hydroxydopamine-induced cellular and mouse models of Parkinson's disease.

Skin-derived precursor Schwann cells have been reported to play a protective role in the central nervous system. The neuroprotective effects of skin-derived precursor Schwann cells may be attributable to the release of growth factors that nourish host cells. In this study, we first established a cellular model of Parkinson's disease using 6-hydroxydopamine. When SH-SY5Y cells were pretreated with conditioned medium from skin-derived precursor Schwann cells, their activity was greatly increased. The addition of insulin-like growth factor-2 neutralizing antibody markedly attenuated the neuroprotective effects of skin-derived precursor Schwann cells. We also found that insulin-like growth factor-2 levels in the peripheral blood were greatly increased in patients with Parkinson's disease and in a mouse model of Parkinson's disease. Next, we pretreated cell models of Parkinson's disease with insulin-like growth factor-2 and administered insulin-like growth factor-2 intranasally to a mouse model of Parkinson's disease induced by 6-hydroxydopamine and found that the level of tyrosine hydroxylase, a marker of dopamine neurons, was markedly restored, α-synuclein aggregation decreased, and insulin-like growth factor-2 receptor down-regulation was alleviated. Finally, in vitro experiments showed that insulin-like growth factor-2 activated the phosphatidylinositol 3 kinase (PI3K)/AKT pathway. These findings suggest that the neuroprotective effects of skin-derived precursor Schwann cells on the central nervous system were achieved through insulin-like growth factor-2, and that insulin-like growth factor-2 may play a neuroprotective role through the insulin-like growth factor-2 receptor/PI3K/AKT pathway. Therefore, insulin-like growth factor-2 may be an useful target for Parkinson's disease treatment.

Multi-beam heterodyne laser Doppler vibrometer based on a line-scan CMOS digital camera.

Multi-beam laser Doppler vibrometers (MB-LDVs) have an advantage over scanning single-beam laser Doppler vibrometers (LDVs) due to the reduction in measurement time and their ability to measure non-stationary and transient events. However, the number of simultaneously interrogated points in current MB-LDVs is limited due to the complexity of the electronic hardware, which increases with the number of measurement channels. Recent developments of high-speed line-scan CMOS cameras suggest that their use in MB-LDVs can reduce the hardware complexity and increase the number of measurement channels. We developed a MB-LDV based on a digital line-scan CMOS camera that simultaneously measures vibrations on a linear array of 99 points. The experimental setup and performance of the developed MB-LDV are discussed in this paper.

Focused Ultrasound Promotes the Delivery of Gastrodin and Enhances the Protective Effect on Dopaminergic Neurons in a Mouse Model of Parkinson's Disease.

Parkinson's disease (PD) is the second most common chronic neurodegenerative disease globally; however, it lacks effective treatment at present. Focused ultrasound (FUS) combined with microbubbles could increase the efficacy of drug delivery to specific brain regions and is becoming a promising technology for the treatment of central nervous system diseases. In this study, we explored the therapeutic potential of FUS-mediated blood-brain barrier (BBB) opening of the left striatum to deliver gastrodin (GAS) in a subacute PD mouse model induced by 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP). The concentration of GAS in the left hemisphere was detected by ultra-high performance liquid chromatography electrospray Q-Orbitrap mass spectrometry (UHPLC/ESI Q-Orbitrap) and the distribution of tyrosine hydroxylase (TH) neurons was detected by immunohistochemical staining. The expression of TH, Dopamine transporter (DAT), cleaved-caspase-3, B-cell lymphoma 2 (Bcl-2), brain-derived neurotrophic factor (BDNF), postsynaptic density protein 95 (PSD-95), and synaptophysin (SYN) protein were detected by western blotting. Analysis showed that the concentration of GAS in the left hemisphere of PD mice increased by approximately 1.8-fold after the BBB was opened. FUS-mediated GAS delivery provided optimal neuroprotective effects and was superior to the GAS or FUS control group. In addition, FUS enhanced GAS delivery significantly increased the expression of Bcl-2, BDNF, PSD-95, and SYN protein in the left striatum (P < 0.05) and reduced the levels of cleaved-caspase-3 remarkably (P = 0.001). In conclusion, the enhanced delivery by FUS effectively strengthened the protective effect of GAS on dopaminergic neurons which may be related to the reinforcement of the anti-apoptotic activity and the expression of synaptic-related proteins in the striatum. Data suggests that FUS-enhanced GAS delivery may represent a new strategy for PD treatment.