Ror2 signaling regulates Golgi structure and transport through IFT20 for tumor invasiveness

Advancements in hydrogel design for articular cartilage regeneration: A comprehensive review

This review paper explores the cutting-edge advancements in hydrogel design for articular cartilage regeneration (CR). Articular cartilage (AC) defects are a common occurrence worldwide that can lead to joint breakdown at a later stage of the disease, necessitating immediate intervention to prevent progressive degeneration of cartilage. Decades of research into the biomedical applications of hydrogels have revealed their tremendous potential, particularly in soft tissue engineering, including CR. Hydrogels are highly tunable and can be designed to meet the key criteria needed for a template in CR. This paper aims to identify those criteria, including the hydrogel components, mechanical properties, biodegradability, structural design, and integration capability with the adjacent native tissue and delves into the benefits that CR can obtain through appropriate design. Stratified-structural hydrogels that emulate the native cartilage structure, as well as the impact of environmental stimuli on the regeneration outcome, have also been discussed. By examining recent advances and emerging techniques, this paper offers valuable insights into developing effective hydrogel-based therapies for AC repair.

True-T - Improving T-cell response quantification with holistic artificial intelligence based prediction in immunohistochemistry images

The immune response associated with oncogenesis and potential oncological ther- apeutic interventions has dominated the field of cancer research over the last decade. T-cell lymphocytes in the tumor microenvironment are a crucial aspect of cancer's adaptive immunity, and the quantification of T-cells in specific can- cer types has been suggested as a potential diagnostic aid. However, this is cur- rently not part of routine diagnostics. To address this challenge, we present a new method called True-T, which employs artificial intelligence-based techniques to quantify T-cells in colorectal cancer (CRC) using immunohistochemistry (IHC) images. True-T analyses the chromogenic tissue hybridization signal of three widely recognized T-cell markers (CD3, CD4, and CD8). Our method employs a pipeline consisting of three stages: T-cell segmentation, density estimation from the segmented mask, and prediction of individual five-year survival rates. In the first stage, we utilize the U-Net method, where a pre-trained ResNet-34 is em- ployed as an encoder to extract clinically relevant T-cell features. The segmenta- tion model is trained and evaluated individually, demonstrating its generalization in detecting the CD3, CD4, and CD8 biomarkers in IHC images. In the second stage, the density of T-cells is estimated using the predicted mask, which serves as a crucial indicator for patient survival statistics in the third stage. This ap- proach was developed and tested in 1041 patients from four reference diagnostic institutions, ensuring broad applicability. The clinical effectiveness of True-T is demonstrated in stages II-IV CRC by offering valuable prognostic information that surpasses previous quantitative gold standards, opening possibilities for po- tential clinical applications. Finally, to evaluate the robustness and broader ap- plicability of our approach without additional training, we assessed the universal accuracy of the CD3 component of the True-T algorithm across 13 distinct solid tumors.

From molecular mechanisms of prostate cancer to translational applications: based on multi-omics fusion analysis and intelligent medicine

Prostate cancer is the most common cancer in men worldwide and has a high mortality rate. The complex and heterogeneous development of prostate cancer has become a core obstacle in the treatment of prostate cancer. Simultaneously, the issues of overtreatment in early-stage diagnosis, oligometastasis and dormant tumor recognition, as well as personalized drug utilization, are also specific concerns that require attention in the clinical management of prostate cancer. Some typical genetic mutations have been proved to be associated with prostate cancer's initiation and progression. However, single-omic studies usually are not able to explain the causal relationship between molecular alterations and clinical phenotypes. Exploration from a systems genetics perspective is also lacking in this field, that is, the impact of gene network, the environmental factors, and even lifestyle behaviors on disease progression. At the meantime, current trend emphasizes the utilization of artificial intelligence (AI) and machine learning techniques to process extensive multidimensional data, including multi-omics. These technologies unveil the potential patterns, correlations, and insights related to diseases, thereby aiding the interpretable clinical decision making and applications, namely intelligent medicine. Therefore, there is a pressing need to integrate multidimensional data for identification of molecular subtypes, prediction of cancer progression and aggressiveness, along with perosonalized treatment performing. In this review, we systematically elaborated the landscape from molecular mechanism discovery of prostate cancer to clinical translational applications. We discussed the molecular profiles and clinical manifestations of prostate cancer heterogeneity, the identification of different states of prostate cancer, as well as corresponding precision medicine practices. Taking multi-omics fusion, systems genetics, and intelligence medicine as the main perspectives, the current research results and knowledge-driven research path of prostate cancer were summarized.

A novel cell source for therapy of knee osteoarthritis using atelocollagen microsphere-adhered adipose-derived stem cells: Impact of synovial fluid exposure on cell activity

Introduction

Administration of adipose-derived stem cells (ADSCs) into the joint cavity has been shown to alleviate the symptoms of knee osteoarthritis (OA) by releasing exosomes and anti-inflammatory cytokines. However, the therapeutic effect of these cells is limited by their rapid disappearance after administration. Thus, it is necessary to prolong cell survival in the joint cavity. This study aimed to investigate the potential application of ADSCs adhered to atelocollagen microspheres (AMSs) for cell therapy of knee OA.

Methods

ADSCs were cultured for 2, 4, and 7 days in AMS suspension or adherent culture dishes. The supernatants were analyzed for IL-10 and exosome secretion via enzyme-linked immunosorbent assay and Nanosight. The effect of AMS was compared with that of adherent-cultured ADSCs (2D-cultured ADSCs) using transcriptome analysis. Moreover, the solubility of AMS and viability of ADSCs were evaluated using synovial fluid (SF) from patients with knee OA.

Results

Compared with 2D-cultured ADSCs, AMS-cultured ADSCs exhibited a significant increase in secretion of exosomes and IL-10, and the expression of several genes involved in extracellular matrix and immune regulation were altered. Furthermore, when AMS-cultured ADSCs were cultured in SF from knee OA patients to mimic the intra-articular environment, the SF dissolved the AMSs and released viable ADSCs. In addition, AMS-cultured ADSCs showed significantly higher long-term cell viability than 2D-cultured ADSCs.

Conclusion

Increased survival of AMS-adhered ADSCs was observed in the intra-articular environment, and AMSs were found to gradually dissipate. These results suggest that AMS-adhered ADSCs are promising source for cell therapy of knee OA.

Computational pathology: A survey review and the way forward

Computational Pathology (CPath) is an interdisciplinary science that augments developments of computational approaches to analyze and model medical histopathology images. The main objective for CPath is to develop infrastructure and workflows of digital diagnostics as an assistive CAD system for clinical pathology, facilitating transformational changes in the diagnosis and treatment of cancer that are mainly address by CPath tools. With evergrowing developments in deep learning and computer vision algorithms, and the ease of the data flow from digital pathology, currently CPath is witnessing a paradigm shift. Despite the sheer volume of engineering and scientific works being introduced for cancer image analysis, there is still a considerable gap of adopting and integrating these algorithms in clinical practice. This raises a significant question regarding the direction and trends that are undertaken in CPath. In this article we provide a comprehensive review of more than 800 papers to address the challenges faced in problem design all-the-way to the application and implementation viewpoints. We have catalogued each paper into a model-card by examining the key works and challenges faced to layout the current landscape in CPath. We hope this helps the community to locate relevant works and facilitate understanding of the field's future directions. In a nutshell, we oversee the CPath developments in cycle of stages which are required to be cohesively linked together to address the challenges associated with such multidisciplinary science. We overview this cycle from different perspectives of data-centric, model-centric, and application-centric problems. We finally sketch remaining challenges and provide directions for future technical developments and clinical integration of CPath. For updated information on this survey review paper and accessing to the original model cards repository, please refer to GitHub. Updated version of this draft can also be found from arXiv.

Temporal dynamics in gastrointestinal helminth infections of sympatric mouse lemur species (Microcebus murinus and Microcebus ravelobensis) in Northwestern Madagascar

Madagascar's lemur populations are declining in dwindling habitats due to anthropogenic expansion and changing climatic conditions. Gastrointestinal parasites can be important indicators to assess the health status of threatened species. However, parasites, hosts and the environment are connected in complex interactions. The present study aimed to disentangle the impact of seasonal and several host-specific factors (sex, species, age, reproductive status, and body mass) on endoparasitism in two small-bodied, co-occurring lemur species (Microcebus murinus and Microcebus ravelobensis) in the Ankarafantsika National Park. Helminth prevalence and egg shedding intensity was investigated via copromicroscopic examination of 810 fecal samples that were obtained from 178 individuals across an 11-month period with a longitudinal approach via repeated captures in a 30.6 ha forest area. Both mouse lemur hosts shed seven morphologically distinct egg types (assigned to Subulura baeri, unidentified Enterobiinae, Spirura sp., Lemuricola sp., two Hymenolepididae spp., one unidentified ascarid). Postmortem examination of two deceased individuals enabled assignment of adult worms to egg morphotypes of S. baeri, Spirura sp. and one Hymenolepididae sp., supported by molecular analysis. A significant seasonal variation was observed in the occurrence of the three most common helminth species S. baeri (total prevalence 71%), unidentified Enterobiinae (46%) and Spirura sp. (38%), with a higher likelihood of infection with advancing dry season. Neither host species, sex nor reproductive status had a significant effect on gastrointestinal helminth infections. Host body mass showed pronounced seasonal changes but did not differ significantly between infected and non-infected individuals. The pathogenic effects of gastrointestinal helminths therefore likely remained within compensable limits in the studied mouse lemur populations. Our findings highlight the prominent influence of seasonal changes on helminth communities. The results of combined morphologic and genetic approaches can furthermore help to overcome limitations of parasite identification via copromicroscopy by linking egg morphology to DNA sequences.

Electronic structure of the strongly correlated electron system plutonium hexaboride: A study from single-particle approximations and many-body calculations

The electronic structure of the strongly correlated electron system plutonium hexaboride is studied by using single-particle approximations and a many-body approach. Imaginary components of impurity Green's functions show that 5fj=5/2 and 5fj=7/2 manifolds are in conducting and insulating regimes, respectively. Quasi-particle weights and their ratio suggest that the intermediate coupling mechanism is applicable for Pu 5f electrons, and PuB6 might be in the orbital-selective localized state. The weighted summation of occupation probabilities yields the interconfiguration fluctuation and average occupation number of 5f electrons n5f ~ 5.101. The interplay of 5f-5f correlation, spin-orbit coupling, Hund's exchange interaction, many-body transition of 5f configurations, and final state effects might be responsible for the quasiparticle multiplets in electronic spectrum functions. Prominent characters in the density of state, such as the coexistence of atomic multiplet peaks in the vicinity of the Fermi level and broad Hubbard bands in the high-lying regime, suggest that PuB6 could be identified as a Racah material. Finally, the quasiparticle band structure is also presented.

Evodiamine and its nano-based approaches for enhanced cancer therapy: recent advances and challenges

Evodiamine is a bioactive alkaloid extracted from the Evodia rutaecarpa plant. It has various pharmacological effects including anti-cancer, anti-bacterial, anti-obesity, anti-neurodegenerative, anti-depressant, and cardiac protective properties. Evodiamine demonstrates potent anti-cancer activity by inhibiting the proliferation of cancer cells in vitro and in vivo. Despite the health-promoting properties of evodiamine, its clinical use is hindered by low water solubility, poor bioavailability, and toxicity. Thus, there is a need to develop alternative drug delivery systems for evodiamine to enhance its solubility, permeability, and stability, as well as to facilitate targeted, prolonged, and controlled drug release. Nanocarriers can increase the therapeutic potential of evodiamine in cancer therapy while reducing adverse side effects. To date, numerous attempts have been made through the development of smart nanocarriers to overcome the drawbacks of evodiamine. This review focuses on the pharmacological applications, anti-cancer mechanisms, and limitations of evodiamine. Various nanocarriers, including lipid-based nanoparticles, polymeric nanoparticles, cyclodextrins, and so forth, have been discussed extensively for evodiamine delivery. Nano-drug delivery systems could increase the solubility, bioavailability, stability, and therapeutic efficacy of evodiamine. This review aims to present a comprehensive and critical evaluation of several nano-formulations of evodiamine for cancer therapy. © 2024 Society of Chemical Industry.

Can gait patterns be explained by joint structure in people with and without radiographic knee osteoarthritis? Data from the IMI-APPROACH cohort

OBJECTIVE

To determine the association between joint structure and gait in patients with knee osteoarthritis (OA).

METHODS

IMI-APPROACH recruited 297 clinical knee OA patients. Gait data was collected (GaitSmart®) and OA-related joint measures determined from knee radiographs (KIDA) and MRIs (qMRI/MOAKS). Patients were divided into those with/without radiographic OA (ROA). Principal component analyses (PCA) were performed on gait parameters; linear regression models were used to evaluate whether image-based structural and demographic parameters were associated with gait principal components.

RESULTS

Two hundred seventy-one patients (age median 68.0, BMI 27.0, 77% female) could be analyzed; 149 (55%) had ROA. PCA identified two components: upper leg (primarily walking speed, stride duration, hip range of motion [ROM], thigh ROM) and lower leg (calf ROM, knee ROM in swing and stance phases). Increased age, BMI, and radiographic subchondral bone density (sclerosis), decreased radiographic varus angle deviation, and female sex were statistically significantly associated with worse lower leg gait (i.e. reduced ROM) in patients without ROA (R2 = 0.24); in ROA patients, increased BMI, radiographic osteophytes, MRI meniscal extrusion and female sex showed significantly worse lower leg gait (R2 = 0.18). Higher BMI was significantly associated with reduced upper leg function for non-ROA patients (R2 = 0.05); ROA patients with male sex, higher BMI and less MRI synovitis showed significantly worse upper leg gait (R2 = 0.12).

CONCLUSION

Structural OA pathology was significantly associated with gait in patients with clinical knee OA, though BMI may be more important. While associations were not strong, these results provide a significant association between OA symptoms (gait) and joint structure.

Single-center experience of thoracoscopic sympathectomy for palmar hyperhidrosis with long-term postoperative questionnaire survey

OBJECTIVES

Thoracoscopic sympathectomy is an effective treatment for palmar hyperhidrosis. However, compensatory hyperhidrosis occurs frequently as a postoperative complication of the procedure. The goal of this study was to elucidate the clinical significance of thoracoscopic sympathectomy using our surgical procedure.

METHODS

Consecutive 151 patients who underwent thoracoscopic sympathectomy for palmar hyperhidrosis were studied. In addition, to investigate patients' satisfaction and long-term quality of life, 111 patients were asked to complete a mailing questionnaire survey, and 84 responded (response rate of 75.7%).

RESULTS

All of the 151 patients reported a reduction in palmar sweating during the immediate postoperative period. None of the patients had pneumothorax, hemothorax, Horner's syndrome, or worsening of bradycardia. Based on the questionnaire, the surgical success rate was 98.8%. None of the patients had a recurrence of palmar hyperhidrosis during the long-term postoperative period. However, compensatory hyperhidrosis was reported in 82 patients (97.6%). In total, 94.0% of patients had high levels of postoperative satisfaction.

CONCLUSIONS

Thoracoscopic sympathectomy is an effective surgical treatment for palmar hyperhidrosis. By contrast, the careful preoperative explanation of compensatory hyperhidrosis is considered to be very important.

Oral delivery of electrohydrodynamically encapsulated Lactiplantibacillus plantarum CRD7 modulates gut health, antioxidant activity, and cytokines-related inflammation and immunity in mice

The current study aimed to evaluate the effects of L. plantarum CRD7 on performance and gut health biomarkers in a Swiss albino mouse model. The results showed that supplementation with non-encapsulated (NLP) and electrohydrodyanamically encapsulated L. plantarum CRD7 (ELP) for four weeks significantly increased (P < 0.05) body weight and weekly feed intake of mice. Specifically, these interventions strengthened the gut barrier functions, as evidenced by the increased expression of tight junction proteins (claudin-1, ZO-1, and occludin), inhibiting pro-inflammatory factors (TNF-α, MCP-1, and IL-6), and promoting short-chain fatty acid production. Histopathological examination revealed no probiotic-related adverse effects in liver and intestinal tissues. Furthermore, ELP and NLP possess the ability to regulate immunity and antioxidant capacity in mice. Notably, the supplementation of ELP modified the gut microbiota by promoting beneficial bacteria (Lactobacillus and Bifibacterium) and suppressing pathogenic bacteria (E. coli and C. perfringens), thereby restoring a balanced gut microbiota. Taken together, oral delivery of encapsulated L. plantarum CRD7 can modify the composition of the gut microbiota, fortify the intestinal barrier functions, maintain the gastrointestinal equilibrium, and augment the immune and antioxidant capacity. This comprehensive study provides valuable insights for the potential application of encapsulated probiotic products in food and feed formulations aimed at alleviating gut diseases.

Integrated analysis of gene expressions and targeted mirnas for explaining crosstalk between oral and esophageal squamous cell carcinomas through an interpretable machine learning approach

This study explores the bidirectional relation of esophageal squamous cell carcinoma (ESCC) and oral squamous cell carcinoma (OSCC), examining shared risk factors and underlying molecular mechanisms. By employing random forest (RF) classifier, enhanced with interpretable machine learning (IML) through SHapley Additive exPlanations (SHAP), we analyzed gene expression from two GEO datasets (GSE30784 and GSE44021). The GSE30784 dataset comprises 167 OSCC samples and 45 control group, whereas the GSE44021 dataset encompasses 113 ESCC samples and 113 control group. Our analysis led to identification of 20 key genes, such as XBP1, VGLL1, and RAD1, which are significantly associated with development of ESCC and OSCC. Further investigations were conducted using tools like NetworkAnalyst 3.0, Single Cell Portal, and miRNET 2.0, which highlighted complex interactions between these genes and specific miRNA targets including hsa-mir-124-3p and hsa-mir-1-3p. Our model achieved high precision in identifying genes linked to crucial processes like programmed cell death and cancer pathways, suggesting new avenues for diagnosis and treatment. This study confirms the bidirectional relationship between OSCC and ESCC, laying groundwork for targeted therapeutic approaches. This study helps to identify shared biological pathways and genetic factors of these conditions for designing personalized medicine strategies and to improve disease management.

Dietary Chlorella vulgaris supplementation modulates health, microbiota and the response to oxidative stress of Atlantic salmon

Microalgae are emerging as functional feed ingredients in aquaculture due to their immune-stimulating and stress-modulating properties. We investigated the potential of the microalgae Chlorella vulgaris as a feed supplement to improve the health and modulate microbiota and stress responses of Atlantic salmon. Triplicate groups of Atlantic salmon (~ 126 g) were reared in a recirculating aquaculture system (RAS) at 15 °C and received diets supplemented with 2% (CV2) or 14% (CV14) spray-dried C. vulgaris daily, 14% once weekly (CV14w), or a control diet (CD) for 8 weeks. Subsequently, all groups were exposed to an acute one-hour peracetic acid (CH3CO3H; PAA) treatment, a commonly used disinfectant in RAS. While CV14 increased feed conversion (FCR) significantly, feeding the diets CV2 and CV14w improved protein retention efficiency. CV14 significantly modulated beta-diversity in the intestinal digesta and mucosa, but this effect was already visible in fish fed CV2. Feeding CV14 and, to a lesser degree, CV2 increased the relative abundances of Paenarthrobacter and Trichococcus in the digesta and mucosa, which are able to metabolize complex carbohydrates. However, the same diets reduced the abundance of the lactic acid bacteria Lactobacillus and Weissella in the digesta and Floricoccus in the mucosa. Peracetic acid exposure induced systemic stress (increase in plasma glucose and cortisol) and a local immune response in the gill, with the most prominent upregulation of several immune- and stress-regulated genes (clra, cebpb, marco, tnfrsf14, ikba, c1ql2, drtp1) 18 h after exposure in fish fed the control diet. Fish receiving CV14 once a week showed a reduced transcriptional response to PAA exposure. Catalase protein abundance in the liver increased following exposure to PAA, while superoxide dismutase abundance in the gill and liver was increased in response to C. vulgaris inclusion before stress. Overall, the results highlight that a high (14%) inclusion rate of C. vulgaris in feed for Atlantic salmon impairs feed conversion and shifts the intestinal microbiota composition in digesta and mucosa. Weekly feeding of C. vulgaris proves a viable approach in improving protein retention and improving transcriptional resilience towards oxidative stress in increasingly intensive production systems. Thereby this study may motivate future studies on optimizing temporal feeding schedules for health-promoting aquafeeds.

Maturation of pluripotent stem cell-derived cardiomyocytes: limitations and challenges from metabolic aspects

Acute coronary syndromes, such as myocardial infarction (MI), lack effective therapies beyond heart transplantation, which is often hindered by donor scarcity and postoperative complications. Human induced pluripotent stem cells (hiPSCs) offer the possibility of myocardial regeneration by differentiating into cardiomyocytes. However, hiPSC-derived cardiomyocytes (hiPSC-cardiomyocytes) exhibit fetal-like calcium flux and energy metabolism, which inhibits their engraftment. Several strategies have been explored to improve the therapeutic efficacy of hiPSC-cardiomyocytes, such as selectively enhancing energy substrate utilization and improving the transplantation environment. In this review, we have discussed the impact of altered mitochondrial biogenesis and metabolic switching on the maturation of hiPSC-cardiomyocytes. Additionally, we have discussed the limitations inherent in current methodologies for assessing metabolism in hiPSC-cardiomyocytes, and the challenges in achieving sufficient metabolic flexibility akin to that in the healthy adult heart.

Rebamipide nanocrystal with improved physicomechanical properties and its assessment through bio-mimicking 3D intestinal permeability model

This study investigated the formulation and characterization of rebamipide nanocrystals (REB-NCs) to enhance the solubility and permeability of rebamipide, an anti-ulcer medication known for its low aqueous solubility and permeability, classified as BCS class IV. Employing high-pressure homogenization and wet milling techniques, we successfully achieved nanonization of rebamipide, resulting in stable nanosuspensions that were subsequently freeze-dried to produce REB-NCs with an average particle size of 223 nm. Comprehensive characterization techniques, including Fourier transform infrared spectroscopy (FTIR), scanning electron microscopy (SEM), X-ray diffraction (XRD), and differential scanning calorimetry (DSC) confirmed the crystalline nature of the nanocrystals and their compatibility with the selected excipients. The saturation solubility study revealed a remarkable three-fold enhancement in PBS pH 7.4 compared to rebamipide API, indicating the effectiveness of the nanocrystal formulation in improving drug solubility. Furthermore, 3D in-vitro permeability assessments conducted on Caco-2 cell monolayers demonstrated an noticeable increase in the permeability of REB-NCs relative to the pure active pharmaceutical ingredient (API), highlighting the promise of this formulation to enhance drug absorption. The dissolution profile of the nanocrystal tablets exhibited immediate release characteristics, significantly outperforming conventional formulations in terms of the dissolution rate. This research underscores the potential of nanomilling as a scalable, environment-friendly, and less toxic approach to significantly enhance the bioavailability of rebamipide. By addressing the challenges associated with the solubility and permeability of poorly water-soluble drugs, our outcome offers insightful information into developing efficient nanomedicine strategies for enhancing therapeutic outcomes.

The mitochondrial genome of Lavandula angustifolia Mill. (Lamiaceae) sheds light on its genome structure and gene transfer between organelles

BACKGROUND

Lavandula angustifolia holds importance as an aromatic plant with extensive applications spanning the fragrance, perfume, cosmetics, aromatherapy, and spa sectors. Beyond its aesthetic and sensory applications, this plant offers medicinal benefits as a natural herbal remedy and finds use in household cleaning products. While extensive genomic data, inclusive of plastid and nuclear genomes, are available for this species, researchers have yet to characterize its mitochondrial genome. This gap in knowledge hampers deeper understanding of the genome organization and its evolutionary significance.

RESULTS

Through the course of this study, we successfully assembled and annotated the mitochondrial genome of L. angustifolia, marking a first in this domain. This assembled genome encompasses 61 genes, which comprise 34 protein-coding genes, 24 transfer RNA genes, and three ribosomal RNA genes. We identified a chloroplast sequence insertion into the mitogenome, which spans a length of 10,645 bp, accounting for 2.94% of the mitogenome size. Within these inserted sequences, there are seven intact tRNA genes (trnH-GUG, trnW-CCA, trnD-GUC, trnS-GGA, trnN-GUU, trnT-GGU, trnP-UGG) and four complete protein-coding genes (psbA, rps15, petL, petG) of chloroplast derivation. Additional discoveries include 88 microsatellites, 15 tandem repeats, 74 palindromic repeats, and 87 forward long repeats. An RNA editing analysis highlighted an elevated count of editing sites in the cytochrome c oxidase genes, notably ccmB with 34 editing sites, ccmFN with 32, and ccmC with 29. All protein-coding genes showed evidence of cytidine-to-uracil conversion. A phylogenetic analysis, utilizing common protein-coding genes from 23 Lamiales species, yielded a tree with consistent topology, supported by high confidence values.

CONCLUSIONS

Analysis of the current mitogenome resource revealed its typical circular genome structure. Notably, sequences originally from the chloroplast genome were found within the mitogenome, pointing to the occurrence of horizontal gene transfer between organelles. This assembled mitogenome stands as a valuable resource for subsequent studies on mitogenome structures, their evolution, and molecular biology.

CuCo2S4 nanoparticles synthesized via a thermal decomposition approach: evaluation of their potential as peroxidase mimics

The current study demonstrates the synthesis of CuCo2S4 nanoparticles using a novel thermal decomposition approach. The CuCo2S4 nanoparticles were synthesized under various conditions by changing the source of sulfur and the solvent. The CuCo2S4 nanoparticles were characterized using an array of analytical techniques. Powder XRD results indicate the successful formation of CuCo2S4 nanoparticles. TEM results show agglomerated nanoparticles with close to spherical morphology and XPS measurements indicate the presence of Cu2+, Cu+, Co3+, Co2+, and S2- in the samples. The CuCo2S4 nanoparticles exhibit weak ferromagnetic and paramagnetic behaviour at 5 K and 300 K, respectively. The CuCo2S4 nanoparticles were explored for their enzyme mimetic activity using 3,3',5,5' tetramethylbenzidine (TMB) as a substrate. They exhibit better catalytic activity compared to that of a natural enzyme (horseradish peroxidase) and other metal sulfide nanoparticles reported in the literature.

Docetaxel-tethered di-Carboxylic Acid Derivatised Fullerenes: A Promising Drug Delivery Approach for Breast Cancer

Docetaxel (DTX) has become widely accepted as a first-line treatment for metastatic breast cancer; however, the frequent development of resistance provides challenges in treating the disease.C60 fullerene introduces a unique molecular form of carbon, exhibiting attractive chemical and physical properties. Our study aimed to develop dicarboxylic acid-derivatized C60 fullerenes as a novel DTX delivery carrier. This study investigated the potential of water-soluble fullerenes to deliver the anti-cancer drug DTX through a hydrophilic linker. The synthesis was carried out using the Prato reaction. The spectroscopic analysis confirmed the successful conjugation of DTX molecules over fullerenes. The particle size of nanoconjugate was reported to be 122.13 ± 1.63 nm with a conjugation efficiency of 76.7 ± 0.14%. The designed conjugate offers pH-dependent release with significantly less plasma pH, ensuring maximum release at the target site. In-vitro cell viability studies demonstrated the enhanced cytotoxic nature of the developed nanoconjugate compared to DTX. These synthesized nanoscaffolds were highly compatible with erythrocytes, indicating the safer intravenous route administration. Pharmacokinetic studies confirmed the higher bioavailability (~ 6 times) and decreased drug clearance from the system vis-à-vis plain drug. The histological studies reveal that nanoconjugate-treated tumour cells exhibit similar morphology to normal cells. Therefore, it was concluded that this developed formulation would be a valuable option for clinical use.

Nanoporous Metatitanic acid on γ-Al2O3 aerogel for higher CO2 adsorption capacity and lower energy consumption

Carbon dioxide capture has become an important issue in reducing atmospheric heat these days. In this study, adsorption of carbon dioxide by aerogel Gamma Alumina-Metatitanic Acid has been investigated and optimized. Morphological and structural analyses such as BET, FESEM, FT-IR, and XRD have also been conducted. In addition, Response surface methodology has been applied in order to achieve the optimal conditions, using a five-level Central composite design. The highest amount of adsorption, 12.874 (mmol/g), was recorded at a temperature of 20 (°C), pressure of 7 (bar), and 25 (%wt) of Metatitanic Acid. This was approximately 11.46% and 4.84% higher than those of mesoporous MgO and 4Azeolite, respectively. Regeneration of the adsorbent was also studied at different temperatures and process durations. Metatitanic acid, as a catalyst, reduces the temperature and regeneration time of the adsorbent by creating active sites and surface hydroxyl groups. It also lowers the required activation energy and enhances the thermal conductivity of the composite material. The optimal result was achieved at a temperature of 100 (°C) and a duration of 30 (min). Finally, isothermal and thermodynamic experiments were conducted to establish the most accurate predictive model and conditions, including Enthalpy, Entropy, and Gibbs free energy. The results indicate that the Freundlich model aligned well with the laboratory findings. Additionally, the negative values of Enthalpy, Entropy, and Gibbs free energy suggested that the adsorption process was physical, exothermic, and spontaneous.

A network comprising ELONGATED HYPOCOTYL 5, microRNA397b, and auxin-associated factors regulates root hair growth in Arabidopsis

ELONGATED HYPOCOTYL 5 (HY5) is a major light-associated transcription factor involved in plant growth and development. In Arabidopsis (Arabidopsis thaliana), the role of HY5 is very well defined in regulating primary root growth and lateral root formation; however, information regarding its role in root hair development is still lacking, and little is known about the genetic pathways regulating this process. In this study, we investigated the role of HY5 and its associated components in root hair development. Detailed analysis of root hair phenotype in wild-type and light signaling mutants under light and dark conditions revealed the importance of light-dependent HY5-mediated root hair initiation. Altered auxin levels in the root apex of the hy5 mutant and interaction of HY5 with promoters of root hair developmental genes were responsible for differential expression of root hair developmental genes and phenotype in the hy5 mutant. The partial complementation of root hair in the hy5 mutant after external supplementation of auxin and regaining of root hair in PIN-FORMED 2 and PIN-FORMED 2 mutants after grafting suggested that the auxin-mediated root hair development pathway requires HY5. Furthermore, miR397b overexpression (miR397bOX) and CRISPR/Cas9-based mutants (miR397bCR) indicated miR397b targets genes encoding reduced residual arabinose (RRA1/RRA2), which in turn regulate root hair growth. The regulation of the miR397b-(RRA1/RRA2) module by HY5 demonstrated its indirect role by targeting root hair cell wall genes. Together, this study demonstrated that HY5 controls root hair development by integrating auxin signaling and other miRNA-mediated pathways.

Design, synthesis and in vitro anti-proliferative evaluation of new pyridine-2,3-dihydrothiazole/thiazolidin-4-one hybrids as dual CDK2/GSK3β kinase inhibitors

Herein, the molecular hybridization drug discovery approach was used in the design and synthesis of twelve novel pyridine-2,3-dihydrothiazole hybrids (2a,b-5a,b and 13a,b-14a,b) and fourteen pyridine-thiazolidin-4-one hybrids (6a,b-12a,b) as anti-proliferative analogues targeting CDK2 and GSK3β kinase inhibition. Almost all of the newly synthesized hybrids, including their precursors (1a,b), were evaluated for their anti-proliferative activity against three human cancer cell lines-MCF-7, HepG2 and HEp-2-as well as normal Vero cell lines. Both compounds 1a (pyridine-thiourea precursor) and 8a (pyridine-5-acetyl-thiazolidin-4-one hybrid) exhibited excellent anti-proliferative activity against HEp-2 (IC50 = 7.5 μg mL-1, 5.9 μg mL-1, respectively). Additionally, 13a (pyridine-5-(p-tolyldiazenyl-2,3-dihydrothiazole)) hybrid demonstrated excellent anti-proliferative activity against HepG2 (IC50 = 9.5 μg mL-1), with an acceptable safety profile against Vero (<45% inhibition at 100 μg mL-1) in the cases of 8a and 13a alone. The three promising anti-proliferative hybrids (1a, 8a, 13a) were selected for the assessment of their in vitro inhibitory kinase activity against CDK2/GSK3β using roscovitine (IC50 = 0.88 μg mL-1) and CHIR-99021 (IC50 = 0.07 μg mL-1) as references, respectively. Compound 13a was the most potent dual CDK2/GSK3β inhibitor (IC50 = 0.396 μg mL-1, 0.118 μg mL-1, respectively) followed by 8a (IC50 = 0.675 μg mL-1, 0.134 μg mL-1, respectively), and the weakest was 1a. To elucidate the mechanism of the most potent anti-proliferative 13a hybrid, further cell cycle analysis was performed revealing that it caused G1 cell cycle arrest and induced apoptosis. Moreover, it resulted in an increase in Bax and caspase-3 with a decrease in Bcl-2 levels in HepG2 cells compared with untreated cells. Finally, in silico drug likeness/ADME prediction for the three potent compounds as well as a molecular docking simulation study were conducted in order to explore the binding affinity and interactions in the binding site of each enzyme, which inspired their usage as anti-proliferative leads for further modification.

Fighting the flu: a brief review on anti-influenza agents

The influenza virus causes one of the most prevalent and lethal infectious viral diseases of the respiratory system; the disease progression varies from acute self-limiting mild fever to disease chronicity and death. Although both the preventive and treatment measures have been vital in protecting humans against seasonal epidemics or sporadic pandemics, there are several challenges to curb the influenza virus such as limited or poor cross-protection against circulating virus strains, moderate protection in immune-compromised patients, and rapid emergence of resistance. Currently, there are four US-FDA-approved anti-influenza drugs to treat flu infection, viz. Rapivab, Relenza, Tamiflu, and Xofluza. These drugs are classified based on their mode of action against the viral replication cycle with the first three being Neuraminidase inhibitors, and the fourth one targeting the viral polymerase. The emergence of the drug-resistant strains of influenza, however, underscores the need for continuous innovation towards development and discovery of new anti-influenza agents with enhanced antiviral effects, greater safety, and improved tolerability. Here in this review, we highlighted commercially available antiviral agents besides those that are at different stages of development including under clinical trials, with a brief account of their antiviral mechanisms.

Post-COVID fatigue: Reduced quality-of-life associated with clinically relevant fatigue in mild disease courses

Fatigue is a pervasive symptom experienced by many individuals after COVID-19. Despite its widespread occurrence, fatigue remains a poorly understood and complex phenomenon. Our aim is to evaluate the subjective experience of mental fatigue after COVID-19 and to assess its significance for daily life functioning. In this online questionnaire study (N = 220), the Fatigue Severity Scale (FSS), World Health Organization Quality-of-Life assessment (WHOQoL) and a subjective severity rating of the COVID-19 disease progression were used. For our statistical analyses we utilized independent samples t-tests, one-way ANOVA with post-hoc analyses, and a multiple regression. As expected our findings revealed the COVID group reported significantly higher levels of subjective fatigue compared to the control group. Moreover, there was a significant difference between experienced fatigue across the four severity groups. Participants who had a milder course of disease also experienced severe subjective fatigue. Subjective fatigue explained 40% variance in quality-of-life. In conclusion, severe subjective fatigue appears to be associated with increased self-reported COVID-19 symptom severity and lower quality-of-life but is already observable in milder cases. This underscores, firstly, the importance of considering also less severe cases and, secondly, the need to develop rehabilitation and psychological interventions for fatigue.

The influence of digestive tract protein on cytotoxicity of polyvinyl chloride microplastics

Microplastics in food and drinking water can enter the human body through oral exposure, posing potential health risks to the human health. Most studies on the toxic effects of microplastics have focused on aquatic organisms, but the effects of the human digestive environment on the physicochemical properties of microplastics and their potential toxicity during gastrointestinal digestion are often limited. In this study, we first studied the influence of interactions between digestive tract protein (α-amylase, pepsin, and trypsin) and microplastics on the activity and conformation of digestive enzymes, and the physicochemical properties of polyvinyl chloride microplastics (PVC-MPs). Subsequently, a simulated digestion assay was performed to determine the biotransformation of PVC-MPs in the digestive tract and the intestinal toxicity of PVC-MPs. The in vitro experiments showed that the protein structure and activity of digestive enzymes were changed after adsorption by microplastics. After digestion, the static contact angle of PVC-MPs was decreased, indicating that the hydrophilicity of the PVC-MPs increased, which will increase its mobility in organisms. Cell experiment showed that the altered physicochemical property of PVC-MPs after digestion process also affect its cytotoxicity, including cellular uptake, cell viability, cell membrane integrity, reactive oxygen species levels, and mitochondrial membrane potential. Transcriptome analyses further confirmed the enhanced biotoxic effect of PVC-MPs after digestion treatment. Therefore, the ecological risk of microplastics may be underestimated owing to the interactions of microplastics and digestive tract protein during biological ingestion.

A role of epigenetic mechanisms in regulating female reproductive responses to temperature in a pest beetle

Many species are threatened by climate change and must rapidly respond to survive in changing environments. Epigenetic modifications, such as DNA methylation, can facilitate plastic responses by regulating gene expression in response to environmental cues. Understanding epigenetic responses is therefore essential for predicting species' ability to rapidly adapt in the context of global environmental change. Here, we investigated the functional significance of different methylation-associated cellular processes on temperature-dependent life history in seed beetles, Callosobruchus maculatus Fabricius 1775 (Coleoptera: Bruchidae). We assessed changes under thermal stress in (1) DNA methyltransferase (Dnmt1 and Dnmt2) expression levels, (2) genome-wide methylation and (3) reproductive performance, with (2) and (3) following treatment with 3-aminobenzamide (3AB) and zebularine (Zeb) over two generations. These drugs are well-documented to alter DNA methylation across the tree of life. We found that Dnmt1 and Dnmt2 were expressed throughout the body in males and females, but were highly expressed in females compared with males and exhibited temperature dependence. However, whole-genome methylation did not significantly vary with temperature, and only marginally or inconclusively with drug treatment. Both 3AB and Zeb led to profound temperature-dependent shifts in female reproductive life history trade-off allocation, often increasing fitness compared with control beetles. Mismatch between magnitude of treatment effects on DNA methylation versus life history effects suggest potential of 3AB and Zeb to alter reproductive trade-offs via changes in DNA repair and recycling processes, rather than or in addition to (subtle) changes in DNA methylation. Together, our results suggest that epigenetic mechanisms relating to Dnmt expression, DNA repair and recycling pathways, and possibly DNA methylation, are strongly implicated in modulating insect life history trade-offs in response to temperature change.

The Effect of Spin Relaxation on Magnetic Compass Sensitivity in ErCry4a

This study explores the impact of thermal motion on the magnetic compass mechanism in migratory birds, focusing on the radical pair mechanism within cryptochrome photoreceptors. The coherence of radical pairs, crucial for magnetic field inference, is curbed by spin relaxation induced by intra-protein motion. Molecular dynamics simulations, density-functional-theory-based calculations, and spin dynamics calculations were employed, utilizing Bloch-Redfield-Wangsness (BRW) relaxation theory, to investigate compass sensitivity. Previous research hypothesized that European robin's cryptochrome 4a (ErCry4a) optimized intra-protein motion to minimize spin relaxation, enhancing magnetic sensing compared to the plant Arabidopsis thaliana's cryptochrome 1 (AtCry1). Different correlation times of the nuclear hyperfine coupling constants in AtCry1 and ErCry4a were indeed found, leading to distinct radical pair recombination yields in the two species, with ErCry4a showing optimized sensitivity. However, this optimization is likely negligible in realistic spin systems with numerous nuclear spins. Beyond insights in magnetic sensing, the study presents a detailed method employing molecular dynamics simulations to assess for spin relaxation effects on chemical reactions with realistically modelled protein motion, relevant for studying radical pair reactions at finite temperature.

The structural insights of L-asparaginase from Pseudomonas aeruginosa CSPS4 at elevated temperatures highlight its thermophilic nature

In the present investigation, a novel thermophilic L-asparaginase (Asn_PA) from Pseudomonas aeruginosa CSPS4 was investigated to explore its structural insights at elevated temperatures. Sequence analysis of Asn_PA depicted three conserved motifs (VVILATGGTIAG, DGIVITHGTDTLEETAYFL, and, LRKQGVQIIRSSHVNAGGF), of them, two motifs exhibit catalytically-important residues i.e., T45 and T125. A homology modelling-based structure model for Asn_PA was generated with 4PGA as the top-matched template. The predicted structure was validated and energy was minimized. Molecular docking was carried out cantered at the active site for asparagine and glutamine as its substrate ligands. The enzyme-substrate interaction analysis showed binding affinities of  - 4.8 and  - 4.1 kcal/mol for asparagine and glutamine respectively. Molecular dynamics (MD) simulation studies showed a better stability of Asn_PA at temperatures of 60 °C, over 40, 50 and, 80 °C, making this enzyme a novel L-asparaginase from other mesophilic P. aeruginosa strain. The trajectory analysis showed that RMSD, Rg, and, SASA values correlate well with each other in the different tested temperatures during the MD analysis. Thus, the present findings encourage extensive characterization of the Asn_PA using laboratory experiments to understand the structural behavior of the active site loop in an open or closed state with and without the substrate molecules.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-024-04072-w.

PbS-based SWIR micro-spectrometer with on-chip Fabry-Perot filter array

Miniaturized and portable on-chip spectrometers have been widely explored to facilitate many applications including chemical analysis, environmental monitoring, medical diagnostics, and astronomical observations. However, the optical spectra of micro-spectrometers are mostly within the visible range. Here, we develop high-performance short-wave infrared (SWIR) micro-spectrometers through the integration of wafer-scale uniform lead sulfide (PbS) thin films with an on-chip Fabry-Perot filter array. The optoelectronic performance of PbS-based detectors could be markedly improved through the optimization of chemical bath deposition (CBD) conditions. The high-sensitivity PbS detectors based on the Fabry-Perot filter array demonstrate chemical analysis application.

Elucidating the Mechanisms of Cell-to-Cell Crosstalk in Probiotics Co-culture: A Proteomics Study of Limosilactobacillus reuteri ZJ625 and Ligilactobacillus salivarius ZJ614

Limosilactobacillus reuteri ZJ625 and Ligilactobacillus salivarius ZJ614 are potential probiotic bacteria with improved benefits when administered to the host as a multi-strain preparation. To elucidate the mechanisms of cell-to-cell crosstalk between these two strains, we studied their intracellular and extracellular proteomes in co-culture by liquid-chromatography mass-spectrometry (LC-MS) using Dionex Nano-RSLC and fusion mass spectrometer. The experiment consisted of five biological replicates, and samples were collected during the mid-exponential growth phase. The quantitative proteomic profiles revealed several differentially expressed proteins (DEPs), which are down- or up-regulated between and within groups for both the intracellular and extracellular proteomes. These DEPs include proteins synthesising autoinducer-2, a sensor compound for cell-to-cell bacterial crosstalk during quorum sensing in mixed culture. Other important DEPs identified include enolase, phosphoglycerate kinase, and l-lactate dehydrogenase, which play roles in carbohydrate metabolism. Proteins associated with transcription, ATP production and transport across the membrane, DNA repair, and those with the potential to bind to the host epithelium were also identified. The post-translational modifications associated with the proteins include oxidation, deamidation, and ammonia loss. Importantly, this study revealed a significant expression of S-ribosylhomocysteine lyase (luxS) involved in synthesising autoinducer-2 that plays important roles in quorum sensing, aiding bacterial cell-to-cell crosstalk in co-cultures. The proteome of L. salivarius ZJ614 was most affected when co-cultured with L. reuteri ZJ625. In contrast, omitting some medium components from the defined medium exerted more effects on L. reuteri ZJ625 than L. salivarius ZJ614.

Structural and transcriptional signatures of arithmetic abilities in children

Arithmetic ability is critical for daily life, academic achievement, career development, and future economic success. Individual differences in arithmetic skills among children and adolescents are related to variations in brain structures. Most existing studies have used hypothesis-driven region of interest analysis. To identify distributed brain regions related to arithmetic ability, we used data-driven cross-validated predictive models to analyze cross-sectional behavioral and structural MRI data in children and adolescents. The gray matter volume (GMV) of widespread brain regions reliably predicted arithmetic abilities measured by the Comprehensive Mathematical Abilities Test. Furthermore, we applied neuroimaging-transcriptome association analysis to explore transcriptional signatures associated with structural patterns of arithmetic ability. Structural patterns of arithmetic ability primarily correlated with transcriptional profiles enriched for genes involved in transmembrane transport and synaptic signaling. Our findings enhance our understanding of the neural and genetic mechanisms underlying children's arithmetic ability and offer a practical predictor for arithmetic skills during development.

Computational imaging for rapid detection of grade-I cerebral small vessel disease (cSVD)

An early identification and subsequent management of cerebral small vessel disease (cSVD) grade 1 can delay progression into grades II and III. Machine learning algorithms have shown considerable promise in medical image interpretation automation. An experimental cross-sectional study aimed to develop an automated computer-aided diagnostic system based on AI (artificial intelligence) tools to detect grade 1-cSVD with improved accuracy. Patients with Fazekas grade 1 cSVD on Non-Contrast Magnetic Resonance Imaging (MRI) Brain of age >40 years of both genders were included. The dataset was pre-processed to be fed into a 3D convolutional neural network (CNN) model. A 3D stack with the shape (120, 128, 128, 1) containing axial slices from the brain magnetic resonance image was created. The model was created from scratch and contained four convolutional and three fully connected (FC) layers. The dataset was preprocessed by making a 3D stack, and normalizing, resizing, and completing the stack was performed. A 3D-CNN model architecture was designed to train and test preprocessed images. We achieved an accuracy of 93.12 % when 2D axial slices were used. When the 2D slices of a patient were stacked to form a 3D image, an accuracy of 85.71 % was achieved on the test set. Overall, the 3D-CNN model performed very well on the test set. The earliest and the most accurate diagnosis from computational imaging methods can help reduce the huge burden of cSVD and its associated morbidity in the form of vascular dementia.

Anti-inflammatory Prowess of endothelial progenitor cells in the realm of biology and medicine

Endothelial inflammation plays a crucial role in vascular-related diseases, a leading cause of global mortality. Among various cellular players, endothelial progenitor cells (EPCs) emerge as non-differentiated endothelial cells circulating in the bloodstream. Recent evidence highlights the transformative role of EPCs in shifting from an inflammatory/immunosuppressive crisis to an anti-inflammatory/immunomodulatory response. Despite the importance of these functions, the regulatory mechanisms governing EPC activities and their physiological significance in vascular regenerative medicine remain elusive. Surprisingly, the current literature lacks a comprehensive review of EPCs' effects on inflammatory processes. This narrative review aims to fill this gap by exploring the cutting-edge role of EPCs against inflammation, from molecular intricacies to broader medical perspectives. By examining how EPCs modulate inflammatory responses, we aim to unravel their anti-inflammatory significance in vascular regenerative medicine, deepening insights into EPCs' molecular mechanisms and guiding future therapeutic strategies targeting vascular-related diseases.

Chlorin e6-Loaded Nanostructured Lipid Carriers Targeted by Angiopep-2: Advancing Photodynamic Therapy in Glioblastoma

Glioblastoma (GBM) is a highly aggressive brain tumor known for its resistance to standard treatments. Despite surgery being a primary option, it often leads to incomplete removal and high recurrence rates. Photodynamic therapy (PDT) holds promise as an adjunctive treatment, but safety concerns and the need for high-power lasers have limited its widespread use. This research addresses these challenges by introducing a novel PDT approach, using chlorin e6 (Ce6) enclosed in nanostructured lipid carriers (Ang-Ce6-NLCs) and targeted to GBM with the angiopep-2 peptide. Remarkably, a single 5-min irradiation session with LEDs at 660 nm and low power density (10 mW cm- 2) proves effective against GBM, while reducing safety risks associated with high-power lasers. Encapsulation improves Ce6 stability and performance in physiological environments, while angiopep-2 targeting enhances delivery to GBM cells, maximizing treatment efficacy and minimizing off-target effects. The findings demonstrate that Ang-Ce6-NLCs-mediated PDT brings about a significant reduction in GBM cell viability, increases oxidative stress, reduces tumor migration, and enhances apoptosis. Overall, such treatment holds potential as a safe and efficient intraoperative removal of GBM infiltrating cells that cannot be reached by surgery, using low-power LED light to minimize harm to surrounding healthy tissue while maximizing tumor treatment.

Aphthous stomatitis - computational biology suggests external biotic stimulus and immunogenic cell death involved

BACKGROUND

The exact cause of recurrent aphthous stomatitis is still unknown, making it a challenge to develop effective treatments. This study employs computational biology to investigate the molecular basis of recurrent aphthous stomatitis, aiming to identify the nature of the stimuli triggering these ulcers and the type of cell death involved.

METHODS

To understand the molecular underpinnings of recurrent aphthous stomatitis, we used the Génie tool for gene identification, targeting those associated with cell death in recurrent aphthous stomatitis. The ToppGene Suite was employed for functional enrichment analysis. We also used Reactome and InteractiVenn for protein integration and prioritization against a PANoptosis gene list, enabling the construction of a protein-protein interaction network to pinpoint key proteins in recurrent aphthous stomatitis pathogenesis.

RESULTS

The study's computational approach identified 1,375 protein-coding genes linked to recurrent aphthous stomatitis. Critical among these were proteins responsive to bacterial stimuli, especially high mobility group protein B1 (HMGB1), toll-like receptor 2 (TLR2), and toll-like receptor 4 (TLR4). The enrichment analysis suggested an external biotic factor, likely bacterial, as a triggering agent in recurrent aphthous stomatitis. The protein interaction network highlighted the roles of tumor necrosis factor (TNF), NF-kappa-B essential modulator (IKBKG), and tumor necrosis factor receptor superfamily member 1A (TNFRSF1A), indicating an immunogenic cell death mechanism, potentially PANoptosis, in recurrent aphthous stomatitis.

CONCLUSION

The findings propose that bacterial stimuli could trigger recurrent aphthous stomatitis through a PANoptosis-related cell death pathway. This new understanding of recurrent aphthous stomatitis pathogenesis underscores the significance of oral microbiota in the condition. Future experimental validation and therapeutic strategy development based on these findings are necessary.

Influence of annealing temperature on persistent luminescence in BaAl2O4:Eu2+/Eu3+ nanocrystals and its application for latent fingerprint detection

The luminescent properties of europium (Eu) doped BaAl2O4 phosphors were strongly influenced by post-annealing temperatures for blue-green persistent luminescence and latent fingerprints (LFPs). The X-ray powder diffraction patterns of the BaAl2O4: 1 mol% Eu nanophosphor, annealed between 1000 and 1300 °C, indicated a hexagonal ferroelectric phase. The X-ray photoelectron spectroscopy (XPS) revealed that the Ba atoms occupied two different sites in the BaAl2O4. The XPS and photoluminescence (PL) results revealed the presence of Eu3+ and Eu2+ states. The Eu-doped BaAl2O4 showed the characteristic red emission of Eu3+ at 251 and 464 nm excitations, while excitations at 340 and 380 nm showed yellowish-green emission. Strong evidence of energy transfer between a charge transfer band and the different energy levels of Eu2+ and Eu3+ ions was obtained. The existence of the Cr ion impurity in the aluminates was confirmed with UV-VIS diffuse reflectance and PL spectroscopy. The present results suggested that and O''i defects have introduced electron and hole traps in the host that acted as luminescent centers for persistent luminescence. LFPs detection using BaAl2O3:Eu2+/Eu3+ phosphor showed an excellent marking agent for applications in forensic science.

Mechanical properties of freestanding few-layer graphene/boron nitride/polymer heterostacks investigated with local and non-local techniques

van der Waals two-dimensional materials and heterostructures combined with polymer films continue to attract research attention to elucidate their functionality and potential applications. This study presents the fabrication and mechanical testing of 2D material heterostacks, consisting of few-layer boron nitride and graphene heterostructures synthesized via chemical vapor deposition, capped with a polymethyl methacrylate layer and suspended across ∼200 μm wide trenches using a combined wet-dry transfer method. The mechanical characterization of the heterostacks was performed using two independent approaches: (a) non-local testing with a custom-built tensile testing platform and (b) local load-displacement testing employing atomic force microscopy probes, complemented by finite element simulations. Both approaches provided new results, which are in good agreement with each other. Overall, our findings offer new insights into a combined load capacity in complex multi-material two-dimensional systems, and can contribute to advancing micro and nano-scale device designs and implementations.

Atomically dispersed Co-based species containing electron withdrawing groups for electrocatalytic oxygen reduction reactions

Single-atom-based catalysts are a promising catalytic system with advantages of molecular catalysts and conductive supports. In this work, a new hybrid material (CoF/NG) is produced using a low-temperature reaction between an organometallic complex (Co(C5HF6O2)2) (CoF) and N-doped reduced graphene oxide (NG). CoF contains electron-withdrawing CF3 groups in the ligand around a Co atom. Microscopic and chemical characterization studies reveal that Co-based species are coordinated to N sites of NG and molecularly dispersed on the surface of NG. The CoF/NG hybrid shows improved electrocatalytic properties, such as onset (0.91 V) and half-wave (0.80 V) potentials, for the electrochemical oxygen reduction reaction (ORR) relative to the NG material. Control experiments reveal that Co-(N)graphene acts as a major active species for ORR. CoF/NG shows moderate cycling durability and microscopy measurements of CoF/NG-after-cycle indicate the formation of nanoparticles after electrocatalytic measurements. All experimental data support that the incorporation of Co-based organometallic species containing electron-withdrawing groups around the metal center onto the graphene-based networks improves the electrocatalytic ORR performance but diminishes the electrocatalytic stability of the active species.

Thin-film implants for bioelectronic medicine

This article is based on the MRS Mid-Career Researcher Award "for outstanding contributions to the fundamentals and development of organic electronic materials and their application in biology and medicine" presentation given by George G. Malliaras, University of Cambridge, at the 2023 MRS Spring Meeting in San Francisco, Calif.Bioelectronic medicine offers a revolutionary approach to treating disease by stimulating the body with electricity. While current devices show safety and efficacy, limitations, including bulkiness, invasiveness, and scalability, hinder their wider application. Thin-film implants promise to overcome these limitations. Made using microfabrication technologies, these implants conform better to neural tissues, reduce tissue damage and foreign body response, and provide high-density, multimodal interfaces with the body. This article explores how thin-film implants using organic materials and novel designs may contribute to disease management, intraoperative monitoring, and brain mapping applications. Additionally, the technical challenges to be addressed for this technology to succeed are discussed.

Graphical abstract

GraphBNC: Machine Learning-Aided Prediction of Interactions Between Metal Nanoclusters and Blood Proteins

Hybrid nanostructures between biomolecules and inorganic nanomaterials constitute a largely unexplored field of research, with the potential for novel applications in bioimaging, biosensing, and nanomedicine. Developing such applications relies critically on understanding the dynamical properties of the nano-bio interface. This work introduces and validates a strategy to predict atom-scale interactions between water-soluble gold nanoclusters (AuNCs) and a set of blood proteins (albumin, apolipoprotein, immunoglobulin, and fibrinogen). Graph theory and neural networks are utilized to predict the strengths of interactions in AuNC-protein complexes on a coarse-grained level, which are then optimized in Monte Carlo-based structure search and refined to atomic-scale structures. The training data is based on extensive molecular dynamics (MD) simulations of AuNC-protein complexes, and the validating MD simulations show the robustness of the predictions. This strategy can be generalized to any complexes of inorganic nanostructures and biomolecules provided that one generates enough data about the interactions, and the bioactive parts of the nanostructure can be coarse-grained rationally.

α-Graphyne with ultra-low diffusion barriers as a promising sodium-ion battery anode and a computational scheme for accurate estimation of theoretical specific capacity

Sodium-ion batteries are considered as potential alternatives to conventional lithium-ion batteries. To realize their large-scale practical applications, it is essential to identify suitable anode candidates exhibiting promising electrochemical properties such as high specific capacity, low diffusion energy barrier, and excellent cyclic stability. In this work, using density functional theory (DFT) calculations and ab initio molecular dynamics simulations, we examine α-graphyne - a carbon-based 2D material - as a potential anode candidate. Our results show that AGY exhibits an ultra-low diffusion barrier of 0.23 eV along both the horizontal and vertical directions and a low average anodic voltage of 0.36 V. Our AIMD studies at 300 K show excellent thermodynamical stability with the loading of four sodium atoms, resulting in a theoretical specific capacity (TSC) of 279 mA h g-1. Doping studies show that varying the nature of acetylenic links of AGY with electron-rich (nitrogen) or electron-deficient (boron) elements, the adsorption strength and diffusion barriers for Na atoms on AGY can be tuned. Furthermore, treating AGY as a case study, we find that conventional DFT studies are expected to overestimate the TSC by a huge margin. Specific to AGY, this overestimation can be up to ∼300%. We identify that ignoring the probable formation of temperature-driven metal clusters is the main reason behind such overestimations. Furthermore, we develop a scheme to calculate TSC with higher accuracy. The scheme, which can be easily generalized to the universal class of electrodes, is evolved by concurrently employing AIMD simulations, DFT calculations and cluster analysis.

Endothelial extracellular vesicles enhance vascular self-assembly in engineered human cardiac tissues

The fabrication of complex and stable vasculature in engineered cardiac tissues represents a significant hurdle towards building physiologically relevant models of the heart. Here, we implemented a 3D model of cardiac vasculogenesis, incorporating endothelial cells (EC), stromal cells, and human induced pluripotent stem cell (iPSC)-derived cardiomyocytes (CM) in a fibrin hydrogel. The presence of CMs disrupted vessel formation in 3D tissues, resulting in the upregulation of endothelial activation markers and altered extracellular vesicle (EV) signaling in engineered tissues as determined by the proteomic analysis of culture supernatant. miRNA sequencing of CM- and EC-secreted EVs highlighted key EV-miRNAs that were postulated to play differing roles in cardiac vasculogenesis, including the let-7 family and miR-126-3p in EC-EVs. In the absence of CMs, the supplementation of CM-EVs to EC monolayers attenuated EC migration and proliferation and resulted in shorter and more discontinuous self-assembling vessels when applied to 3D vascular tissues. In contrast, supplementation of EC-EVs to the tissue culture media of 3D vascularized cardiac tissues mitigated some of the deleterious effects of CMs on vascular self-assembly, enhancing the average length and continuity of vessel tubes that formed in the presence of CMs. Direct transfection validated the effects of the key EC-EV miRNAs let-7b-5p and miR-126-3p in improving the maintenance of continuous vascular networks. EC-EV supplementation to biofabricated cardiac tissues and microfluidic devices resulted in tissue vascularization, illustrating the use of this approach in the engineering of enhanced, perfusable, microfluidic models of the myocardium.

Exosomal fragment enclosed polyamine-salt nano-complex for co-delivery of docetaxel and mir-34a exhibits higher cytotoxicity and apoptosis in breast cancer cells

A novel core-shell nanocarrier system has been designed for co-delivery of a small anticancer drug, docetaxel (DTX) and tumor suppressor (TS) miR-34a named as Exo(PAN34a+DTX). The core is formed by pH dependent polyamine salt aggregates (PSA) containing both the payloads and the shell is formed by RAW 264.7 cell derived exosomal fragments. Herein, phosphate driven polyallylamine hydrochloride (PAH, MW:17,500 Da) PSA was formed in presence of miR-34a and DTX to form PAN34a+DTX. The formulation exhibited pH dependent DTX release with only 33.55 ± 2.12% DTX release at pH 7.2 and 75.21 ± 1.8% DTX release till 144 h at pH 5.5. At 1.21 molar ratio of phosphate to the amine (known as R value), efficient complexation of miR-34a (3.6 μM) in the PAN particles was obtained. PAN34a+DTX demonstrated particle size (163.86 ± 12.89 nm) and zeta-potential value of 17.53 ± 5.10 mV which upon exosomal fragment layering changed to - 7.23 ± 2.75 mV which is similar to the zeta-potential of the exosomal fragments, i.e., - 8.40 ± 1.79 mV. The final formulation Exo(PAN34a+DTX), loaded with 40 ng/mL DTX and 50 nM miR-34a exhibited 48.20 ± 4.59% cytotoxicity in triple negative breast cancer (TNBC) cells, 4T1. Co-localization of CM-DiI (red fluorescence) stained exosomal fragments and FAM-siRNA (green fluorescence) in the cytoplasm of 4T1 cells after 6 h of Exo(PANFAM) treatment confirmed the efficiency of the designed system to co-deliver two actives. Exo(PAN34a+DTX) also reduced BCL-2 expression (target gene for miR-34a) by 8.98 folds in comparison to free DTX confirming promising co-delivery and apoptosis inducing effect of Exo(PAN34a+DTX) in 4T1.

Nature Products Chlorophyll Derivatives for NIR-II Fluorescence Bioimaging and Plant-Imaging

The second near-infrared window (NIR-II, 1000-1700 nm) fluorescence imaging has attracted significant attention in research fields because of its unique advantages compared with conventional optical windows (400-900 nm). A variety of NIR-II fluorophores have been actively studied because they serve as a key component of fluorescence imaging. Among them, organic small molecule NIR-II fluorophores display outstanding imaging performance and many advantages, but types of small molecule NIR-II fluorophores with high biocompatibility are still quite limited. Novel molecular scaffolds based NIR-II dyes are highly desired. Herein, we hypothesized that chlorophyll is a new promising molecular platform for discovery NIR-II fluorophores. Thus, seven derivatives of derivatives were selected to characterize their optical properties. Interestingly, six chlorophyll derivatives displayed NIR-II fluorescence imaging capability. This characteristic allowed the successful NIR-II imaging of green leaves of various plants. Furthermore, most of these fluorophores showed capacity to monitor viscosity change because of their sensitive for viscosity. For demonstration of its biomedical applications, these probes were successfully used for NIR-II fluorescence-guided surgical resection of lymph nodes. In summary, chlorophylls are novel valuable tool molecules for NIR-II fluorescence imaging and have potential to expand their applications in biomedical field and plant science.

Inhibition of SARS-CoV-2 3CLpro by chemically modified tyrosinase from Agaricus bisporus

Antiviral compounds are crucial to controlling the SARS-CoV-2 pandemic. Approved drugs have been tested for their efficacy against COVID-19, and new pharmaceuticals are being developed as a complementary tool to vaccines. In this work, a cheap and fast purification method for natural tyrosinase from Agaricus bisporus (AbTyr) fresh mushrooms was developed to evaluate the potential of this enzyme as a therapeutic protein via the inhibition of SARS-CoV-2 3CLpro protease activity in vitro. AbTyr showed a mild inhibition of 3CLpro. Thus, different variants of this protein were synthesized through chemical modifications, covalently binding different tailor-made glycans and peptides to the amino terminal groups of the protein. These new tyrosinase conjugates were purified and characterized through circular dichroism and fluorescence spectroscopy analyses, and their stability was evaluated under different conditions. Subsequently, all these tyrosinase conjugates were tested for 3CLpro protease inhibition. From them, the conjugate between tyrosinase and a dextran-aspartic acid (6 kDa) polymer showed the highest inhibition, with an IC50 of 2.5 μg ml-1 and IC90 of 5 μg ml-1, with no cytotoxicity activity by polymer insertion. Finally, SARS-CoV-2 virus infection was studied. It was found that this new AbTyr-Dext6000 protein showed an 80% decrease in viral load. These results show the capacity of these tyrosinase bioconjugates as potential therapeutic proteins, opening the possibility of extension and applicability against other different viruses.

Effect of digested chia seed protein on the gut microbiota and colon morphology of mice fed a high-saturated-fat diet

The present study aimed to investigate the effect of digested total protein (DTP) from chia seed on the gut microbiota and morphology of mice fed with a high-fat diet. Forty-four male C57BL/6 mice were divided into 4 groups: AIN (standard diet), HF (high-fat diet), AIN + DTP (standard diet supplemented with 400 mg of digested chia seed protein), and HF + DTP (high-fat diet supplemented with 400 mg of digested chia seed protein) during 8 weeks. Colon morphology, tight junction's gene expression, and gut microbiota composition were evaluated. The consumption of digested chia seed protein (DTP) increased the crypts width, longitudinal and circular muscular layer. Furthermore, the AIN + DTP group enhanced the expression of tight junction proteins, including occludin and claudin, while the AIN + DTP and HF + DTP groups increase the zonula occludens expression. The α-diversity analysis showed a reduction in bacterial dominance in the HF + DTP group. All the experimental groups were grouped in different cluster, showing differences in the microbiota community in the β-diversity analyzes. The Firmicutes/Bacteroidetes ratio did not differ among the groups. The genera Olsenella and Dubosiella were increased in the AIN + DTP group, but the Oscillospiraceae_unclassified was increased in the HF + DTP group. The Alistipes was increased, while the Roseburia and Akkermansia were decreased in the AIN + DTP and HF + DTP groups. Then, the consumption of DTP from chia seed improved the gut microbiota composition and mucosal integrity, counteracting the adverse effects of high-fat diet.

Machine learning-based evaluation of prognostic factors for mortality and relapse in patients with acute lymphoblastic leukemia: a comparative simulation study

BACKGROUND

Predicting mortality and relapse in children with acute lymphoblastic leukemia (ALL) is crucial for effective treatment and follow-up management. ALL is a common and deadly childhood cancer that often relapses after remission. In this study, we aimed to apply and evaluate machine learning-based models for predicting mortality and relapse in pediatric ALL patients.

METHODS

This retrospective cohort study was conducted on 161 children aged less than 16 years with ALL. Survival status (dead/alive) and patient experience of relapse (yes/no) were considered as the outcome variables. Ten machine learning (ML) algorithms were used to predict mortality and relapse. The performance of the algorithms was evaluated by cross-validation and reported as mean sensitivity, specificity, accuracy and area under the curve (AUC). Finally, prognostic factors were identified based on the best algorithms.

RESULTS

The mean accuracy of the ML algorithms for prediction of patient mortality ranged from 64 to 74% and for prediction of relapse, it varied from 64 to 84% on test data sets. The mean AUC of the ML algorithms for mortality and relapse was above 64%. The most important prognostic factors for predicting both mortality and relapse were identified as age at diagnosis, hemoglobin and platelets. In addition, significant prognostic factors for predicting mortality included clinical side effects such as splenomegaly, hepatomegaly and lymphadenopathy.

CONCLUSIONS

Our results showed that artificial neural networks and bagging algorithms outperformed other algorithms in predicting mortality, while boosting and random forest algorithms excelled in predicting relapse in ALL patients across all criteria. These results offer significant clinical insights into the prognostic factors for children with ALL, which can inform treatment decisions and improve patient outcomes.

Exploring hydrophobicity or hydrophilicity of borophene surface via reactive molecular dynamics simulation

Borophene, a novel two-dimensional material unveiled in 1998, has garnered significant interest among researchers due to its distinct mechanical and electrical characteristics. Efforts to experimentally synthesize borophene continue to captivate researchers' interest in recent years. Given the current lack of experimental studies on the interaction between water and the borophene surface, molecular dynamics simulation offers a valuable approach for predicting the substance's reactivity with water. Additionally, such simulations can assess the hydrophilicity and hydrophobicity of borophene, providing valuable insights into its properties. In our current research, we utilized reactive molecular dynamics simulation to investigate the wetting behavior of borophene. Our findings reveal that the borophene surface exhibits hydrophobic characteristics, demonstrating anisotropic wettability. Specifically, the water contact angle was calculated to be 149.11° along the zigzag direction and 148.4° along the armchair direction. The contour map of the interaction energy between a water molecule and the borophene surface revealed a notable energy barrier in the zigzag direction. This barrier contributes to the asymmetric spreading of the water droplet on the surface. Density profiles and radial pair distribution function (RDF) diagrams of the water droplet on the borophene surface further corroborated the hydrophobic nature of borophene by indicating a significant distance between the water droplet and the surface. Moreover, analysis of the number of hydrogen bonds demonstrated that borophene efficiently utilizes nearly all its capacity to form hydrogen bonds. Additionally, we compared the wettability of borophene with that of other two-dimensional materials, such as various graphene allotropes and phosphorene, which have been subjects of recent investigation.

Harnessing the synergistic potential of TiO2-CuSe composites for enhanced photocatalytic and antibacterial activities

With growing environmental concerns, the removal of toxic industrial dyes from wastewater has become a critical global issue. In this study, TiO2-CuSe composites were synthesized using a cost-effective and simple chemical method to determine the optimal concentration of CuSe for the efficient degradation of methylene blue (MB) under visible light. The TiO2 samples exhibited a mix of rutile and anatase phases, while CuSe formed in a hexagonal phase. Both TiO2 and CuSe were observed to have agglomerated particles with indistinct boundaries. The optical bandgap shifted towards the visible region from 3.25 eV (pure TiO2) to 2.91 eV with increasing the amount of CuSe in the composites. The photocatalytic activity of TiO2, CuSe, and TiO2-CuSe composites was evaluated by monitoring MB degradation, with the composites outperforming the individual components under visible light. Notably, the TiO2-20% CuSe composite (AK-4) demonstrated superior efficiency, removing 98% of MB in just 70 minutes. The photocatalysts also exhibited enhanced antibacterial properties, effectively reducing E. coli colonies from 1.71 × 1012 CFU mL-1 (pure TiO2) to 1 × 1010 CFU mL-1 for the AK-4 composite. This study suggests that visible light-activated TiO2-CuSe composites could be effective for both water purification and bacterial infection control.

De novo Cu-MOF@CNS nanocomposite coated on a cotton fibrils framework for sustainable solar-driven desalination

Environmental researchers are extremely concerned about addressing the declining availability of drinking water, which is a critical issue in many nations. Solar-driven desalination is an emerging and pioneering renewable approach to reduce potable water scarcity that is suitable for remote locations, developing countries, and disaster zones as it does not require additional energy supply. However, there are still issues with the scalable preparation of photothermal materials, such as achieving low cost and widening the assortment of useful applications. Conventional carbon- and metal-based absorbers are intricate and fragile, which make them difficult to install and transport in places with minimal infrastructure. Thus, a universal process for creating adaptable solar evaporators is sorely required. Herein, we have come up with a holistic approach using a solar absorber (GJ-01(Cal)) derived from a Cu-MOF (HKUST-1) and carbon nanosheets (CNSs) for generating potable water from saline water using solar radiation. The as-synthesized material provides high-performance photothermal water evaporation when illuminated under solar irradiation at the air-water interface. Moreover, its porous structure, high photothermal conversion efficiency, rapid water flow, and heat insulation make it appropriate for saline water desalination. CNS play a pivotal role in improving the photothermal features of the solar absorber (GJ-01(Cal)) in terms of conjugation to promote Cu(0) species and pyrrolic nitrogen (P-N) amplification and thereby enrich the p-type nature of the absorber's triphasic configuration. With these photothermal factors, the localised surface plasmon resonance (LSPR) of electrons increases and achieves high solar spectrum absorption. The GJ-01(Cal) was further coated on porous cotton fibrils (CF) that regulate photothermal interfacial evaporation (PTIE) by allowing water transportation via capillary action. This assemblage of the nanocomposite on CF efficiently evaporates water at a higher surface temperature of ∼47 °C under one solar illumination, achieving 4.23 kg m-2 h-1 of evaporation flux and 96.5% light-to-heat conversion efficiency. Interestingly, the GJ-01(Cal) coated over CF can be recycled at least 10 times. Additionally, it offers scalable production for higher photothermal efficiency with a flexible substrate as a solar evaporator and is beneficial for society paving new horizons towards a sustainable environment.

Detailed delineation of the fetal brain in diffusion MRI via multi-task learning

Diffusion-weighted MRI is increasingly used to study the normal and abnormal development of fetal brain inutero. Recent studies have shown that dMRI can offer invaluable insights into the neurodevelopmental processes in the fetal stage. However, because of the low data quality and rapid brain development, reliable analysis of fetal dMRI data requires dedicated computational methods that are currently unavailable. The lack of automated methods for fast, accurate, and reproducible data analysis has seriously limited our ability to tap the potential of fetal brain dMRI for medical and scientific applications. In this work, we developed and validated a unified computational framework to (1) segment the brain tissue into white matter, cortical/subcortical gray matter, and cerebrospinal fluid, (2) segment 31 distinct white matter tracts, and (3) parcellate the brain's cortex and delineate the deep gray nuclei and white matter structures into 96 anatomically meaningful regions. We utilized a set of manual, semi-automatic, and automatic approaches to annotate 97 fetal brains. Using these labels, we developed and validated a multi-task deep learning method to perform the three computations. Our evaluations show that the new method can accurately carry out all three tasks, achieving a mean Dice similarity coefficient of 0.865 on tissue segmentation, 0.825 on white matter tract segmentation, and 0.819 on parcellation. The proposed method can greatly advance the field of fetal neuroimaging as it can lead to substantial improvements in fetal brain tractography, tract-specific analysis, and structural connectivity assessment.