Single-Cell Analyses Inform Mechanisms of Myeloid-Targeted Therapies in Colon Cancer.

Single-cell RNA sequencing (scRNA-seq) is a powerful tool for defining cellular diversity in tumors, but its application toward dissecting mechanisms underlying immune-modulating therapies is scarce. We performed scRNA-seq analyses on immune and stromal populations from colorectal cancer patients, identifying specific macrophage and conventional dendritic cell (cDC) subsets as key mediators of cellular cross-talk in the tumor microenvironment. Defining comparable myeloid populations in mouse tumors enabled characterization of their response to myeloid-targeted immunotherapy. Treatment with anti-CSF1R preferentially depleted macrophages with an inflammatory signature but spared macrophage populations that in mouse and human expresses pro-angiogenic/tumorigenic genes. Treatment with a CD40 agonist antibody preferentially activated a cDC population and increased Bhlhe40+ Th1-like cells and CD8+ memory T cells. Our comprehensive analysis of key myeloid subsets in human and mouse identifies critical cellular interactions regulating tumor immunity and defines mechanisms underlying myeloid-targeted immunotherapies currently undergoing clinical testing.

scATAC-Ref: a reference of scATAC-seq with known cell labels in multiple species.

Chromatin accessibility profiles at single cell resolution can reveal cell type-specific regulatory programs, help dissect highly specialized cell functions and trace cell origin and evolution. Accurate cell type assignment is critical for effectively gaining biological and pathological insights, but is difficult in scATAC-seq. Hence, by extensively reviewing the literature, we designed scATAC-Ref (https://bio.liclab.net/scATAC-Ref/), a manually curated scATAC-seq database aimed at providing a comprehensive, high-quality source of chromatin accessibility profiles with known cell labels across broad cell types. Currently, scATAC-Ref comprises 1 694 372 cells with known cell labels, across various biological conditions, >400 cell/tissue types and five species. We used uniform system environment and software parameters to perform comprehensive downstream analysis on these chromatin accessibility profiles with known labels, including gene activity score, TF enrichment score, differential chromatin accessibility regions, pathway/GO term enrichment analysis and co-accessibility interactions. The scATAC-Ref also provided a user-friendly interface to query, browse and visualize cell types of interest, thereby providing a valuable resource for exploring epigenetic regulation in different tissues and cell types.

SpatialRef: a reference of spatial omics with known spot annotation.

Spatial omics technologies have enabled the creation of intricate spatial maps that capture molecular features and tissue morphology, providing valuable insights into the spatial associations and functional organization of tissues. Accurate annotation of spot or domain types is essential for downstream spatial omics analyses, but this remains challenging. Therefore, this study aimed to develop a manually curated spatial omics database (SpatialRef, https://bio.liclab.net/spatialref/), to provide comprehensive and high-quality spatial omics data with known spot labels across multiple species. The current version of SpatialRef aggregates >9 million manually annotated spots across 17 Human, Mouse and Drosophila tissue types through extensive review and strict quality control, covering multiple spatial sequencing technologies and >400 spot/domain types from original studies. Furthermore, SpatialRef supports various spatial omics analyses about known spot types, including differentially expressed genes, spatially variable genes, Gene Ontology (GO)/KEGG annotation, spatial communication and spatial trajectories. With a user-friendly interface, SpatialRef facilitates querying, browsing and visualizing, thereby aiding in elucidating the functional relevance of spatial domains within the tissue and uncovering potential biological effects.

Lineage tracking reveals dynamic relationships of T cells in colorectal cancer.

T cells are key elements of cancer immunotherapy1 but certain fundamental properties, such as the development and migration of T cells within tumours, remain unknown. The enormous T cell receptor (TCR) repertoire, which is required for the recognition of foreign and self-antigens2, could serve as lineage tags to track these T cells in tumours3. Here we obtained transcriptomes of 11,138 single T cells from 12 patients with colorectal cancer, and developed single T cell analysis by RNA sequencing and TCR tracking (STARTRAC) indices to quantitatively analyse the dynamic relationships among 20 identified T cell subsets with distinct functions and clonalities. Although both CD8+ effector and 'exhausted' T cells exhibited high clonal expansion, they were independently connected with tumour-resident CD8+ effector memory cells, implicating a TCR-based fate decision. Of the CD4+ T cells, most tumour-infiltrating T regulatory (Treg) cells showed clonal exclusivity, whereas certain Treg cell clones were developmentally linked to several T helper (TH) cell clones. Notably, we identified two IFNG+ TH1-like cell clusters in tumours that were associated with distinct IFNγ-regulating transcription factors -the GZMK+ effector memory T cells, which were associated with EOMES and RUNX3, and CXCL13+BHLHE40+ TH1-like cell clusters, which were associated with BHLHE40. Only CXCL13+BHLHE40+ TH1-like cells were preferentially enriched in patients with microsatellite-instable tumours, and this might explain their favourable responses to immune-checkpoint blockade. Furthermore, IGFLR1 was highly expressed in both CXCL13+BHLHE40+ TH1-like cells and CD8+ exhausted T cells and possessed co-stimulatory functions. Our integrated STARTRAC analyses provide a powerful approach to dissect the T cell properties in colorectal cancer comprehensively, and could provide insights into the dynamic relationships of T cells in other cancers.

Artificial Intelligence (AI)-driven dental education: Exploring the role of chatbots in a clinical learning environment.

STATEMENT OF PROBLEM: Despite their widespread use in various educational contexts, the integration of chatbots into dental clinical education has not been thoroughly investigated. The noted discrepancy signifies a lack of understanding of how chatbots could enhance the personalized and interactive learning experiences of predoctoral dental students. PURPOSE: The purpose of this study was to evaluate the awareness and perceptions of artificial intelligence (AI) technology, interaction experiences, and concerns about a custom-developed chatbot (CB) intervention in the clinical education of predoctoral dental students at the University of Illinois Chicago, College of Dentistry (UIC-COD) compared with the traditional Blackboard (BB) online platform. MATERIAL AND METHODS: Eligible participants (n=86) providing verbal consent were allocated via the random block method into BB (n=43) and CB (n=43) groups and asked to engage with their designated platforms for 10 to 15 minutes by focusing on clinical inquiries in a predoctoral implant clinic and supported by a list of 35 typical questions. After the interaction, participants responded on a 5-point Likert scale to a 19-item survey probing AI awareness, platform engagement, and technological concerns. Survey data were anonymized and analyzed using descriptive, inferential statistics and nonparametric Mann-Whitney U tests to compare interventions. The Bonferroni correction for multiple comparisons was performed (α=.0045). RESULTS: Neither the BB or CB group showed any difference in their awareness and perception of AI technology. The CB group demonstrated improved timeliness (P<.001), more interaction (P<.001), reduced faculty workload (P=.001), enhanced receptiveness (P=.002), and less anxiety (P<.001) and was more satisfied (P<.001) when compared with the BB group. However, concerns regarding the potential for incorrect information (P=.003) were more pronounced in the CB group. CONCLUSIONS: The integration of chatbot technology into dental clinical education significantly enhanced learning and student engagement, highlighting the potential for future technological enrichment of the educational landscape.

Uncovering Potentially Therapeutic Phytochemicals, In silico Analysis, and Biological Assessment of South-Chinese Red Dragon Fruit (Hylocereus polyrhizus).

Red dragon fruit is gaining popularity globally due to its nutritional value and bioactive components. The study aimed to assess the phytochemical, nutritional composition, antioxidant, antibacterial, and cytotoxic properties of extracts from the South Chinese red dragon fruit peel, flesh, and seeds. Extract fractions with increasing polarity (ethyl acetate

The synergetic effect of an aqua ligand and metal site on the performance of single-atom catalysts in H2O2 synthesis: a density functional theory study.

Studying the effect of the coordination field on the catalytic property is critical for the rational design of outstanding electrocatalysts for H2O2 synthesis. Herein, via density functional theory (DFT) calculations and ab initio molecular dynamic (AIMD) simulations, we built an effective computational framework to identify the synergetic effect of an aqua ligand and metal ion on the 2e- ORR catalytic performance under gas condition and aqua solvent. Specifically, the screening results of 29 single-atom catalysts (SACs), TM@C6N6 (TM = transition metal), indicated that Cu@C6N6 features excellent catalytic property with thermal stability, lowest 2e- ORR overpotential (0.02 V) and high selectivity of 99.99%. Once an aqua ligand binds with the Cu site, the activity is reduced to the overpotential of 0.42 V and the selectivity decreased slightly (99.98%) due to the reduction of the adsorption strength for the reaction intermediates. A combination of geometric structures and electronic properties revealed that such changes are correlated with the charge of the Cu site. Furthermore, based on molecular orbital theory, the essence of the high catalytic property deeply lies in the effect of the moderate electron back donation bond (dyz & dxz→) between Cu and O2. This work will provide a route to better design high-performance SACs for H2O2 synthesis effectively.

Clinical application of percutaneous left atrial appendage occlusion guided only by transesophageal echocardiography without fluoroscopy and angiography in the patients with nonvalvular atrial fibrillation.

BACKGROUND AND AIM: The objective of this study was to understand the clinical efficacy and application of the percutaneous left atrial appendage occlusion (PLAAO) guided only by the transesophageal echocardiography (TEE) in patients with nonvalvular atrial fibrillation (NVAF), without using the fluoroscopy and angiography. METHODS: During the time period of this study from June 2020 to June 2021, 32 patients underwent PLAAO and all underwent a TEE guided approach. The anatomical features of the left atrial appendage (LAA) were evaluated and observed by TEE before and during the procedure. LAA occluder device was selected for the appropriate size. Intraoperative TEE guided and monitored the process of PLAAO in real-time, and also evaluated the stability and tightness of the occluder device, following monitored postoperative complications. RESULTS: The PLAAO procedure was successful in all the patients. No serious complications like dislocation of the occluder and embolism were seen. Postoperative TEE demonstrated that the PLAAO occluder devices were in a good position without residual shunting. CONCLUSIONS: PLAAO only guided by TEE may become a safe and reliable surgical procedure, which can protect surgeons and patients from radiation, and can gradually become a novel surgical method of PLAAO with the practical application value.

Summary of the Experiences and Results of Transesophageal Ultrasound-Guided Ventricular Septal Defect and Atrial Septal Defect Closure Operation.

BACKGROUND: Ventricular septal defect (VSD) and atrial septal defect (ASD) are congenital heart diseases. The techniques of transthoracic closure (TC) and percutaneous closure (PC) for the treatment of VSD and ASD have continuously improved and matured. This study aimed to retrospectively analyze the therapeutic effects of TC and PC on VSD and ASD patients. METHODS: We retrospectively reviewed 928 patients (552 VSD and 376 ASD) who had undergone TC or PC guided by transesophageal ultrasound at the Department of Cardiac Macrovascular Surgery of the First Affiliated Hospital of Nanchang University between August 2010 and August 2020. We collected and evaluated the clinical data of the patients, including age, gender, weight, inlet and outlet diameters of defect, and the operation results of TC and PC. Descriptive statistics were used to analyze means and standard deviations (SD), and the Chi-square test was used to evaluate the difference between groups. RESULTS: Among the 928 patients who were treated with the closure operation, there were no casualties, with 907 patients (97.7%) showing successful closure. Among the 552 VSD patients who were treated with TC, 540 showed successful close, while 12 cases required extracorporeal circulation after the failure of TC. Among the 376 patients with ASD, 256 patients were treated with TC, of which 251 were successful, and five were failures, including three shedding cases. In addition, among the 120 patients who were treated with PC, 116 were successful, and four were failures, including two shedding cases. Postoperative follow up for patients with successful closure operations demonstrated that the complications of aortic and tricuspid regurgitation, hydro-pericardium, III° atrioventricular block, shedding of closure umbrella, hemolysis, and thrombosis had not occurred. CONCLUSION: Closure operation of VSD and ASD by esophageal ultrasound has the advantages of lower trauma and blood loss, shorter hospital stay, simple operation, fewer postoperative complications, and significant therapeutic efficacy.

Apralogs: Apramycin 5-O-Glycosides and Ethers with Improved Antibacterial Activity and Ribosomal Selectivity and Reduced Susceptibility to the Aminoacyltranserferase (3)-IV Resistance Determinant.

Apramycin is a structurally unique member of the 2-deoxystreptamine class of aminoglycoside antibiotics characterized by a monosubstituted 2-deoxystreptamine ring that carries an unusual bicyclic eight-carbon dialdose moiety. Because of its unusual structure, apramycin is not susceptible to the most prevalent mechanisms of aminoglycoside resistance including the aminoglycoside-modifying enzymes and the ribosomal methyltransferases whose widespread presence severely compromises all aminoglycosides in current clinical practice. These attributes coupled with minimal ototoxocity in animal models combine to make apramycin an excellent starting point for the development of next-generation aminoglycoside antibiotics for the treatment of multidrug-resistant bacterial infections, particularly the ESKAPE pathogens. With this in mind, we describe the design, synthesis, and evaluation of three series of apramycin derivatives, all functionalized at the 5-position, with the goals of increasing the antibacterial potency without sacrificing selectivity between bacterial and eukaryotic ribosomes and of overcoming the rare aminoglycoside acetyltransferase (3)-IV class of aminoglycoside-modifying enzymes that constitutes the only documented mechanism of antimicrobial resistance to apramycin. We show that several apramycin-5-O-ß-d-ribofuranosides, 5-O-ß-d-eryrthofuranosides, and even simple 5-O-aminoalkyl ethers are effective in this respect through the use of cell-free translation assays with wild-type bacterial and humanized bacterial ribosomes and of extensive antibacterial assays with wild-type and resistant Gram negative bacteria carrying either single or multiple resistance determinants. Ex vivo studies with mouse cochlear explants confirm the low levels of ototoxicity predicted on the basis of selectivity at the target level, while the mouse thigh infection model was used to demonstrate the superiority of an apramycin-5-O-glycoside in reducing the bacterial burden in vivo.

Self-assemblies of TTF derivatives programmed by alkyl chains and functional groups.

Tetrathiafulvalenes (TTFs) are a class of important functional materials whose intermolecular interaction, which will contribute to constructing a supramolecular structure, still needs further understanding. In this study, the self-assembly behavior and structure of a series of TTFs bearing different alkyl chains and substituents were investigated by scanning tunneling microscopy (STM) in combination with density functional theory (DFT) calculations. Contrary to previous reports, herein, a series of benzoic acid-functionalized TTFs (CnTTFCOOH) and pyridine-functionalized TTFs (CnTTFN) with different lengths of alkyl chains have been substituted on the sulfur atom, where n is equal to 8, 10, 14, or 16. Due to the weak intra- and intermolecular interactions, CnTTFN (n = 8 and 10) molecules cannot be observed during STM scanning. For other cases, various self-assembled monolayers with different nanostructures were observed depending on different substituents. The results reveal that the alkyl chains and functional groups on the TTF skeleton synergistically affect the molecular self-assembly process, which results from the synergism of van der Waals, hydrogen bonding, and SS interactions. These results not only help to explain the relationship between structures and properties, but also help to design better molecular structures for various fields.

[Event-related potentials of working memory impairment in children with primary nocturnal enuresis].

OBJECTIVE: To study the cognitive neural mechanism of working memory impairment in children with primary nocturnal enuresis using event-related potential (ERP). METHODS: A total of 14 children with primary nocturnal enuresis were enrolled as enuresis group, and 14 normal children were enrolled as control group. The learning-recognition task test was applied, and the ERP components (P2, N2, and P3) at Fz lead while identifying old pictures (learned) and new ones (unlearned) were measured and compared between the two groups. RESULTS: While identifying the old pictures, the enuresis group had a lower amplitude of P2 and N2 than the control group (P<0.05). There were no significant differences between the two groups in the latency of P2, N2, and P3 and the amplitude of P3. While identifying the new pictures, the enuresis group had a longer latency of P2 and a significantly lower amplitude of N2 than the control group (P<0.05). There were no significant differences between the two groups in the amplitude of P2 and P3 and the latency of N2 and P3. CONCLUSIONS: Compared with normal children, the children with primary nocturnal enuresis have reduced abilities of classified information extraction, a prolonged reaction time, and reductions in memory capacity, memory consolidation, and conflict monitoring, which causes working memory impairment.

Polymer-KLAK Peptide Conjugates Induce Cancer Cell Death through Synergistic Effects of Mitochondria Damage and Autophagy Blockage.

Nanoscaled polymer-peptide conjugates (PPCs) containing both functional peptides and synthetic polymer comprise a new family of biomaterials that can circumvent the limitation of peptides alone. Our previous work showed that PPCs with the therapeutic peptide KLAK, especially PPCs with shorter PEG spacers and a higher degree of polymerization, exhibit enhanced antitumor effects through disrupting mitochondrial membranes. However, as PPCs have a spherical nanostructure (45-60 nm), this may have other effects besides the conjugated therapeutic peptide KLAK itself when they enter cancer cells. In this research, we compared the proteome differences of U87 cells treated with KLAK, polymer, and their conjugates (P-KLAK) through quantitative proteomics technology. The result reveals that proteins involved in oxidative stress response and the Nrf2/ARE pathway were significantly up-regulated after P-KLAK treatment. Moreover, the overexpression of sequestosome 1, a protein substrate that is selectively incorporated into the formation of autophagosome and degraded by autophagy, is found in our study and has not been reported previously in the study of KLAK toxicity. Additional experiments suggest that upon endocytosis, P-KLAK causes lysosome impairment and results in autophagosomes accumulation. Hence, P-KLAK might induce U87 cell death by autophagy blockage due to lysosome impairment as well as mitochondria damage synergistically.

[Event-related potential and behavioral characteristics in children with attention deficit hyperactivity disorder of different school entrance ages: a comparative study].

OBJECTIVE: To evaluate the effects of school entrance age on cognition and behaviors in children with attention deficit hyperactivity disorder (ADHD) using mathematical event-related potential (ERP), behavioral test, and Conners Parent Symptom Questionnaire (PSQ). METHODS: Fifty-eight ADHD children aged 7-12 years were enrolled and classified into older age and younger age groups according to the school entrance age (n=29 each). The children in the older age group were admitted at an age of 6 years and 6 months to 6 years and 11 months, and those in the younger age group were admitted at an age of 6 years to 6 years and 5 months. The ERP with a mathematical task was used to detect the difference in brain electrical activity between the two groups, and the behavioral test results were compared. The children's parents were asked to complete the PSQ, and the scores on each subscale were compared. RESULTS: The ERP detection showed that the older age group had a significantly higher P2 amplitude for wrong answers than the younger age group (10.9±5.0 µv vs 8.5±3.6 µv; P<0.05). The younger age group had a significantly shorter time of response to wrong answers than the older age group (619±340 ms vs 870±418 ms; P<0.05). The scores on the subscales of learning problems and impulse-hyperactivity of PSQ were significantly higher in the younger age group than in the older age group (P<0.05). CONCLUSIONS: School entrance age can affect cognition and behaviors in children with ADHD, and the ADHD children with a younger school entrance age have an obvious defect in executive function, especially the function of error detection, which leads to the prominent problems in impulse-hyperactivity and learning.

[Correlation between event-related potential and behavioral problems in early school-age children with attention deficit hyperactivity disorder].

OBJECTIVE: To investigate the cognitive characteristics in early school-age children with attention deficit hyperactivity disorder (ADHD) using event-related potential (ERP) and Achenbach Child Behavior Checklist (CBCL), as well as the correlation between ERP and behavioral problems. METHODS: A total of 22 children aged 6-7 years with ADHD and 19 healthy children matched by age were enrolled. Continue Performance Test-AX (CPT-AX) was performed for ERP test. The amplitude and latency of N2 and P3 of Go and Nogo were compared. The CBCL was completed by the parents, and the correlation between behavioral factors and ERP was analyzed. RESULTS: The ADHD group had a significantly higher number of ERP omissions than the normal control group (10±8 vs 5±4; P<0.05), while the reaction time and number of commission errors showed no significant differences between the two groups (P>0.05). The ADHD group showed a significantly lower Go-N2 amplitude than the normal control group (-8±5 µV vs -10±4 µV; P<0.05). In the ADHD group, the detection rates of hyperactivity, attack, and discipline violation were 27%, 27% and 9% respectively. The scores on attack and discipline violation subscales were negatively correlated with the Go-N2 amplitude of ERP (r=-0.43 and -0.48 respectively; P<0.05), while the score on hyperactivity subscale was positively correlated with the latency of Go-P3 (r=0.50, P<0.05). CONCLUSIONS: The early school-age children with ADHD show the tendency to the impairment of attention/executive function, but the inhibition function defect has not been noted. In early school-age children with ADHD, the behavioral problems such as hyperactivity, attack, and discipline violation are associated with ERP.

Effect of Clinical Experience on Accuracy of Implant Placement Using Dynamic Navigation and Static Guidance: an in vitro Study.

This study aimed to investigate the accuracy of implants placed by clinicians with varying dental implant experience using dynamic navigation (DN) and static guidance (SG). Sixty identical custom-made drillable maxillary models were fabricated, missing the right central incisor (#8) and left first molar (#14) with simulated gingival tissue. Models planned with a dynamic navigation system and guided surgery software were randomly allocated to an experienced clinician, an inexperienced clinician, and a nonexperienced clinician. The accuracy of implant placement was evaluated by overlaying the preoperative virtual surgical plan with the postoperative Cone Beam Computed Tomography (CBCT) scan. Deviations between the placed and planned implants were quantified using a mathematical algorithm. Independent-sample t-tests revealed significant differences (p < 0.001) in angular deviation but not in coronal and apical deviations when comparing dynamic navigation with static guidance for all three clinicians. One-way ANOVA and Tukey post-hoc test found no significant differences between clinicians of varying dental implant experience in dynamic navigation and static guidance groups. The study concluded that the level of dental implant experience and surgical site do not significantly impact the accuracy of implant placement when either dynamic navigation or static guidance is used. Dynamic navigation produced less angular deviation in comparison with static guidance. This finding suggests dynamic navigation could benefit clinical settings, particularly for less experienced clinicians.

Nutrition, phytochemical profiling, in vitro biological activities, and in silico studies of South Chinese white pitaya (Hylocereus undatus).

Background: White pitaya, a popular tropical fruit, is known for its high nutritional value. It is commercially cultivated worldwide for its potential use in the food and pharmaceutical industries. This study aims to assess the nutritional and phytochemical contents and biological potential of the South Chinese White Pitaya (SCWP) peel, flesh, and seed extracts. Methods: Extract fractions with increasing polarity (ethyl acetate < acetone < ethanol < methanol < aqueous) were prepared. Antibacterial potential was tested against multidrug-resistant (MDR) bacteria, and antioxidant activity was determined using, 2-diphenyl-1-picrylhydrazyl (DPPH) and 2,2'-Azino-bis(3-ethylbenzothiazoline-6-sulphonic acid) (ABTS) radical scavenging assays, and cytotoxic activity against human keratinocyte cells using 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl-2H-tetrazolium bromide (MTT) assay. Pharmacological screening and molecular docking simulations were conducted to identify potential antibacterial compounds with druggable characteristics. Molecular dynamics simulation (MDS) was employed to validate the binding stability of the promising ligand-protein complexes. Results: All parts of the fruit exhibited a substantial amount of crucial nutrients (minerals, sugars, proteins, vitamins, and fatty acids). The ethanol (ET) and acetone (AC) fractions of all samples demonstrated notable inhibitory effects against tested MDR bacteria, with MIC50 ranges of 74-925 µg/mL. Both ET and AC fractions also displayed remarkable antioxidant activity, with MIC50 ranges of 3-39 µg/mL. Cytotoxicity assays on HaCaT cells revealed no adverse effects from the crude extract fractions. LC-MS/MS analyses identified a diverse array of compounds, known and unknown, with antibacterial and antioxidant activities. Molecular docking simulations and pharmacological property screening highlighted two active compounds, baicalein (BCN) and lenticin (LTN), showing strong binding affinity with selected target proteins and adhering to pharmacological parameters. MDS indicated a stable interaction between the ligands (BCN and LTN) and the receptor proteins over a 100-ns simulation period. Conclusion: Our study provides essential information on the nutritional profile and pharmacological potential of the peel, flesh, and seeds of SCWP. Furthermore, our findings contribute to the identification of novel antioxidants and antibacterial agents that could be capable of overcoming the resistance barrier posed by MDR bacteria.

scBlood: A comprehensive single-cell accessible chromatin database of blood cells.

The advent of single cell transposase-accessible chromatin sequencing (scATAC-seq) technology enables us to explore the genomic characteristics and chromatin accessibility of blood cells at the single-cell level. To fully make sense of the roles and regulatory complexities of blood cells, it is critical to collect and analyze these rapidly accumulating scATAC-seq datasets at a system level. Here, we present scBlood (https://bio.liclab.net/scBlood/), a comprehensive single-cell accessible chromatin database of blood cells. The current version of scBlood catalogs 770,907 blood cells and 452,247 non-blood cells from ∼400 high-quality scATAC-seq samples covering 30 tissues and 21 disease types. All data hosted on scBlood have undergone preprocessing from raw fastq files and multiple standards of quality control. Furthermore, we conducted comprehensive downstream analyses, including multi-sample integration analysis, cell clustering and annotation, differential chromatin accessibility analysis, functional enrichment analysis, co-accessibility analysis, gene activity score calculation, and transcription factor (TF) enrichment analysis. In summary, scBlood provides a user-friendly interface for searching, browsing, analyzing, visualizing, and downloading scATAC-seq data of interest. This platform facilitates insights into the functions and regulatory mechanisms of blood cells, as well as their involvement in blood-related diseases.

Computational and artificial intelligence-based methods for antibody development.

Due to their high target specificity and binding affinity, therapeutic antibodies are currently the largest class of biotherapeutics. The traditional largely empirical antibody development process is, while mature and robust, cumbersome and has significant limitations. Substantial recent advances in computational and artificial intelligence (AI) technologies are now starting to overcome many of these limitations and are increasingly integrated into development pipelines. Here, we provide an overview of AI methods relevant for antibody development, including databases, computational predictors of antibody properties and structure, and computational antibody design methods with an emphasis on machine learning (ML) models, and the design of complementarity-determining region (CDR) loops, antibody structural components critical for binding.

Formation process of extension knee joint contracture following external immobilization in rats.

BACKGROUND: Current research lacks a model of knee extension contracture in rats. AIM: To elucidate the formation process of knee extension contracture. METHODS: We developed a rat model using an aluminum external fixator. Sixty male Sprague-Dawley rats with mature bones were divided into the control group (n = 6) and groups that had the left knee immobilized with an aluminum external fixator for 1, 2, and 3 d, and 1, 2, 3, 4, 6, and 8 wk (n = 6 in each group). The passive extension range of motion, histology, and expression of fibrosis-related proteins were compared between the control group and the immobilization groups. RESULTS: Myogenic contracture progressed very quickly during the initial 2 wk of immobilization. After 2 wk, the contracture gradually changed from myogenic to arthrogenic. The arthrogenic contracture progressed slowly during the 1st week, rapidly progressed until the 3rd week, and then showed a steady progression until the 4rd week. Histological analyses confirmed that the anterior joint capsule of the extended fixed knee became increasingly thicker over time. Correspondingly, the level of transforming growth factor beta 1 (TGF-ß1) and phosphorylated mothers against decapentaplegic homolog 2 (p-Smad2) in the anterior joint capsule also increased with the immobilization time. Over time, the cross-sectional area of muscle fibers gradually decreased, while the amount of intermuscular collagen and TGF-ß1, p-Smad2, and p-Smad3 was increased. Unexpectedly, the amount of intermuscular collagen and TGF-ß1, p-Smad2, and p-Smad3 was decreased during the late stage of immobilization (6-8 wk). The myogenic contracture was stabilized after 2 wk of immobilization, whereas the arthrogenic contracture was stabilized after 3 wk of immobilization and completely stable in 4 wk. CONCLUSION: This rat model may be a useful tool to study the etiology of joint contracture and establish therapeutic approaches.