Consensus-based clustering of single cells by reconstructing cell-to-cell dissimilarity.

The development of single-cell ribonucleic acid (RNA) sequencing (scRNA-seq) technology has led to great opportunities for the identification of heterogeneous cell types in complex tissues. Clustering algorithms are of great importance to effectively identify different cell types. In addition, the definition of the distance between each two cells is a critical step for most clustering algorithms. In this study, we found that different distance measures have considerably different effects on clustering algorithms. Moreover, there is no specific distance measure that is applicable to all datasets. In this study, we introduce a new single-cell clustering method called SD-h, which generates an applicable distance measure for different kinds of datasets by optimally synthesizing commonly used distance measures. Then, hierarchical clustering is performed based on the new distance measure for more accurate cell-type clustering. SD-h was tested on nine frequently used scRNA-seq datasets and it showed great superiority over almost all the compared leading single-cell clustering algorithms.

Investigation into fabrication and optical characteristics of tunable optofluidic microlenses using two-photon polymerization.

Optofluidic systems, integrating microfluidic and micro-optical technologies, have emerged as transformative tools for various applications, from molecular detection to flow cytometry. However, existing optofluidic microlenses often rely on external forces for tunability, hindering seamless integration into systems. This work presents an approach using two-photon polymerization (TPP) to fabricate inherently tunable microlens arrays, eliminating the need for supplementary equipment. The optofluidic design incorporates a three-layered structure enabling dynamic manipulation of refractive indices within microchannels, leading to tunable focusing characteristics. It is shown that the TPP fabricated optofluidic microlenses exhibit inherent tunable focal lengths, numerical apertures, and spot sizes without reliance on external forces. This work signifies some advancements in optofluidic technology, offering precise and tunable microlenses with potential applications in adaptive imaging and variable focal length microscopy.

Development and validation of an ultrasound-based deep learning radiomics nomogram for predicting the malignant risk of ovarian tumours.

BACKGROUND: The timely identification and management of ovarian cancer are critical determinants of patient prognosis. In this study, we developed and validated a deep learning radiomics nomogram (DLR_Nomogram) based on ultrasound (US) imaging to accurately predict the malignant risk of ovarian tumours and compared the diagnostic performance of the DLR_Nomogram to that of the ovarian-adnexal reporting and data system (O-RADS). METHODS: This study encompasses two research tasks. Patients were randomly divided into training and testing sets in an 8:2 ratio for both tasks. In task 1, we assessed the malignancy risk of 849 patients with ovarian tumours. In task 2, we evaluated the malignancy risk of 391 patients with O-RADS 4 and O-RADS 5 ovarian neoplasms. Three models were developed and validated to predict the risk of malignancy in ovarian tumours. The predicted outcomes of the models for each sample were merged to form a new feature set that was utilised as an input for the logistic regression (LR) model for constructing a combined model, visualised as the DLR_Nomogram. Then, the diagnostic performance of these models was evaluated by the receiver operating characteristic curve (ROC). RESULTS: The DLR_Nomogram demonstrated superior predictive performance in predicting the malignant risk of ovarian tumours, as evidenced by area under the ROC curve (AUC) values of 0.985 and 0.928 for the training and testing sets of task 1, respectively. The AUC value of its testing set was lower than that of the O-RADS; however, the difference was not statistically significant. The DLR_Nomogram exhibited the highest AUC values of 0.955 and 0.869 in the training and testing sets of task 2, respectively. The DLR_Nomogram showed satisfactory fitting performance for both tasks in Hosmer-Lemeshow testing. Decision curve analysis demonstrated that the DLR_Nomogram yielded greater net clinical benefits for predicting malignant ovarian tumours within a specific range of threshold values. CONCLUSIONS: The US-based DLR_Nomogram has shown the capability to accurately predict the malignant risk of ovarian tumours, exhibiting a predictive efficacy comparable to that of O-RADS.

TransRef enables accurate transcriptome assembly by redefining accurate neo-splicing graphs.

RNA-seq technology is widely employed in various research areas related to transcriptome analyses, and the identification of all the expressed transcripts from short sequencing reads presents a considerable computational challenge. In this study, we introduce TransRef, a new computational algorithm for accurate transcriptome assembly by redefining a novel graph model, the neo-splicing graph, and then iteratively applying a constrained dynamic programming to reconstruct all the expressed transcripts for each graph. When TransRef is utilized to analyze both real and simulated datasets, its performance is notably better than those of several state-of-the-art assemblers, including StringTie2, Cufflinks and Scallop. In particular, the performance of TransRef is notably strong in identifying novel transcripts and transcripts with low-expression levels, while the other assemblers are less effective.

Femtosecond laser multibeam parallel processing for variable focal-length optofluidic chips.

Optofluidic chips are frequently utilized in applications such as biological observation, chemical detection, dynamic displays, imaging, holography, and sensing. Yet, developing continuously zoomable technology has been challenging in the production of optical devices. Using a spatial light modulator to shape a femtosecond laser to achieve multibeam parallel pulse punching, we propose an easy-to-fabricate, stable, and reliable tuning technique in this Letter. We then propose the addition of a liquid medium with a continuously variable refractive index to achieve controllable zooming without changing the position and morphology of the microlens. By pumping various concentrations of the liquid medium into the optofluidic chip, continuous tunability of the device was experimentally verified.

Exosomes in the hypoxic TME: from release, uptake and biofunctions to clinical applications.

Hypoxia is a remarkable trait of the tumor microenvironment (TME). When facing selective pressure, tumor cells show various adaptive characteristics, such as changes in the expression of cancer hallmarks (increased proliferation, suppressed apoptosis, immune evasion, and so on) and more frequent cell communication. Because of the adaptation of cancer cells to hypoxia, exploring the association between cell communication mediators and hypoxia has become increasingly important. Exosomes are important information carriers in cell-to-cell communication. Abundant evidence has proven that hypoxia effects in the TME are mediated by exosomes, with the occasional formation of feedback loops. In this review, we equally focus on the biogenesis and heterogeneity of cancer-derived exosomes and their functions under hypoxia and describe the known and potential mechanism ascribed to exosomes and hypoxia. Notably, we call attention to the size change of hypoxic cancer cell-derived exosomes, a characteristic long neglected, and propose some possible effects of this size change. Finally, jointly considering recent developments in the understanding of exosomes and tumors, we describe noteworthy problems in this field that urgently need to be solved for better research and clinical application.

Sequence-specific minimizers via polar sets.

MOTIVATION: Minimizers are efficient methods to sample k-mers from genomic sequences that unconditionally preserve sufficiently long matches between sequences. Well-established methods to construct efficient minimizers focus on sampling fewer k-mers on a random sequence and use universal hitting sets (sets of k-mers that appear frequently enough) to upper bound the sketch size. In contrast, the problem of sequence-specific minimizers, which is to construct efficient minimizers to sample fewer k-mers on a specific sequence such as the reference genome, is less studied. Currently, the theoretical understanding of this problem is lacking, and existing methods do not specialize well to sketch specific sequences. RESULTS: We propose the concept of polar sets, complementary to the existing idea of universal hitting sets. Polar sets are k-mer sets that are spread out enough on the reference, and provably specialize well to specific sequences. Link energy measures how well spread out a polar set is, and with it, the sketch size can be bounded from above and below in a theoretically sound way. This allows for direct optimization of sketch size. We propose efficient heuristics to construct polar sets, and via experiments on the human reference genome, show their practical superiority in designing efficient sequence-specific minimizers. AVAILABILITY AND IMPLEMENTATION: A reference implementation and code for analyses under an open-source license are at https://github.com/kingsford-group/polarset. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Spatially modulated femtosecond laser direct ablation-based preparation of ultra-flexible multifunctional copper mesh electrodes and its application.

Multifunctional electrodes possess superior properties such as high photoelectric properties and high stability. Laser manufacturing process is one of the widely used method for electrode fabrication. However, the current multifunctional electrode laser manufacturing process suffers from low fabrication speed. Here, we report a high-efficiency laser digital patterning process to fabricate copper-based flexible transparent conducting electrodes. By using a spatially modulated, one single laser spot is modulated into an array of spots with equal intensity, and the fabrication speed can be improved by more than 20 times over the traditional single pulse processing. In addition, copper mesh electrodes with a high photoelectric property have been fabricated. A transparent touch screen panel and multifunctional windows are fabricated with transparent electrodes to demonstrate their use in vehicle defogging, portable heating, and wearable devices.

Femtosecond laser nanoprinting of anisotropic plasmonic surfaces: coloration and anticounterfeiting.

An anisotropic plasmonic surface of nanoellipsoid arrays is successfully fabricated on an Au film using slit-shaping-based femtosecond laser nanoprinting. The size and orientation of the nanoellipsoid can be exquisitely and flexibly controlled by adjusting the width and direction of the slit and the laser pulse energy. By dark-field optical micro-spectroscopy, anisotropic plasmonic color rendering as well as resonant light scattering from the lateral and vertical modes are experimentally and theoretically investigated in the visible spectral range. In addition, prospective use in the fields of steganographic encryption and multidimensional optical multiplexing is also proposed.

Extracellular vesicle PD-L1 in reshaping tumor immune microenvironment: biological function and potential therapy strategies.

Programmed cell death 1 ligand 1 (PD-L1) is the ligand for programmed death protein-1 (PD-1), is associated with immunosuppression. Signaling via PD-1/PD-L1 will transmits negative regulatory signals to T cells, inducing T-cell inhibition, reducing CD8+ T-cell proliferation, or promoting T-cell apoptosis, which effectively reduces the immune response and leads to large-scale tumor growth. Accordingly, many antibody preparations targeting PD-1 or PD-L1 have been designed to block the binding of these two proteins and restore T-cell proliferation and cytotoxicity of T cells. However, these drugs are ineffective in clinical practice. Recently, numerous of studies have shown that, in addition to the surface of tumor cells, PD-L1 is also found on the surface of extracellular vesicles secreted by these cells. Extracellular vesicle PD-L1 can also interact with PD-1 on the surface of T cells, leading to immunosuppression, and has been proposed as a potential mechanism underlying PD-1/PD-L1-targeted drug resistance. Therefore, it is important to explore the production, regulation and tumor immunosuppression of PD-L1 on the surface of tumor cells and extracellular vesicles, as well as the potential clinical application of extracellular vesicle PD-L1 as tumor biomarkers and therapeutic targets. Video Abstract.

FEGS: a novel feature extraction model for protein sequences and its applications.

BACKGROUND: Feature extraction of protein sequences is widely used in various research areas related to protein analysis, such as protein similarity analysis and prediction of protein functions or interactions. RESULTS: In this study, we introduce FEGS (Feature Extraction based on Graphical and Statistical features), a novel feature extraction model of protein sequences, by developing a new technique for graphical representation of protein sequences based on the physicochemical properties of amino acids and effectively employing the statistical features of protein sequences. By fusing the graphical and statistical features, FEGS transforms a protein sequence into a 578-dimensional numerical vector. When FEGS is applied to phylogenetic analysis on five protein sequence data sets, its performance is notably better than all of the other compared methods. CONCLUSION: The FEGS method is carefully designed, which is practically powerful for extracting features of protein sequences. The current version of FEGS is developed to be user-friendly and is expected to play a crucial role in the related studies of protein sequence analyses.

Improved design and analysis of practical minimizers.

MOTIVATION: Minimizers are methods to sample k-mers from a string, with the guarantee that similar set of k-mers will be chosen on similar strings. It is parameterized by the k-mer length k, a window length w and an order on the k-mers. Minimizers are used in a large number of softwares and pipelines to improve computation efficiency and decrease memory usage. Despite the method's popularity, many theoretical questions regarding its performance remain open. The core metric for measuring performance of a minimizer is the density, which measures the sparsity of sampled k-mers. The theoretical optimal density for a minimizer is 1/w, provably not achievable in general. For given k and w, little is known about asymptotically optimal minimizers, that is minimizers with density O(1/w). RESULTS: We derive a necessary and sufficient condition for existence of asymptotically optimal minimizers. We also provide a randomized algorithm, called the Miniception, to design minimizers with the best theoretical guarantee to date on density in practical scenarios. Constructing and using the Miniception is as easy as constructing and using a random minimizer, which allows the design of efficient minimizers that scale to the values of k and w used in current bioinformatics software programs. AVAILABILITY AND IMPLEMENTATION: Reference implementation of the Miniception and the codes for analysis can be found at https://github.com/kingsford-group/miniception. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Effects of different thermal insulation methods on the nasopharyngeal temperature in patients undergoing laparoscopic hysterectomy: a prospective randomized controlled trial.

BACKGROUND: This study explored the comparison of the thermal insulation effect of incubator to infusion thermometer in laparoscopic hysterectomy. METHODS: We assigned 75 patients enrolled in the study randomly to three groups: Group A: Used warming blanket; group B: Used warming blanket and infusion thermometer; group C: Used warming blanket and incubator. The nasopharyngeal temperature at different time points during the operation served as the primary outcome. RESULTS: The nasopharyngeal temperature of the infusion heating group was significantly higher than that of the incubator group 60 min from the beginning of surgery (T3): 36.10 ± 0.20 vs 35.81 ± 0.20 (P<0.001)90 min from the beginning of surgery (T4): 36.35 ± 0.20 vs 35.85 ± 0.17 (P<0.001). Besides, the nasopharyngeal temperature of the incubator group was significantly higher compared to that of the control group 60 min from the beginning of surgery (T3): 35.81 ± 0.20 vs 35.62 ± 0.18 (P<0.001); 90 min from the beginning of surgery (T4): 35.85 ± 0.17 vs 35.60 ± 0.17 (P<0.001). Regarding the wake-up time, that of the control group was significantly higher compared to the infusion heating group: 24 ± 4 vs 21 ± 4 (P = 0.004) and the incubator group: 24 ± 4 vs 22 ± 4 (P = 0.035). CONCLUSION: Warming blanket (38 °C) combined infusion thermometer (37 °C) provides better perioperative thermal insulation. Hospitals without an infusion thermometer can opt for an incubator as a substitute. TRIAL REGISTRATION: This trial was registered with ChiCTR2000039162 , 20 October 2020.

[Comparative study on anti-depressant effect of Zhizichi Decoction and its solid fermentation product on CUMS rats].

Chronic unpredicted mild stress(CUMS) combined with isolated feeding was used to induce depressed rat model. The anti-depressant effects of Zhizichi Decoction(ZZCD) and its solid fermented product(ZZC) were analyzed by behavioral test and comparison of pathological tissues of hippocampus and liver, metabolic characteristics of intestinal flora, and relative abundance of species. The results showed that ZZC could increase sucrose preference, shorten the immobility time in the forced swim test and tail suspension test(P<0.05), and repair damaged hippocampus and liver tissues, and the effect was superior to that of ZZCD. The results of Biolog ECO plates showed that the average well color development(AWCD) of intestinal flora in the model group significantly decreased and the metabolic levels of sugar and amino acids were reduced, while the AWCD of the treatment groups increased. The metabolic levels of the two carbon sources were improved in the ZZC group, while only sugar metabolic level was elevated in the ZZCD group. Metagenomic analysis of intestinal flora showed that the ratio of Firmicutes/Bacteroidetes was 3.87 in the control group, 21.77 in the model group, 5.91 in the ZZC group, and 18.48 in the ZZCD group. Lactobacillus increased by 3.28 times, and Prevotella and Bacteroidetes decreased by 75.59% and 76.39%, respectively in the model group as compared with that in the control group. Lactobacillus decreased by 31.13%, and Prevotella and Bacteroidetes increased by more than three times in the ZZC group as compared with that in the model group, while the corresponding changes in the ZZCD group were not significant. ZZC could improve depression-like beha-viors by regulating the structure of intestinal flora and metabolic functions and repairing damaged hippocampus and liver tissues in depressed rats, showing an anti-depressant effect superior to that of ZZCD. This study is expected to provide a basis for the development of new anti-depressant food products.

Downregulation of MicroRNA-551b Correlates With Dissemination of Human Oral Squamous Cell Carcinoma.

PURPOSE: Altered expression of microRNAs contributes to invasion and metastasis of many human cancers; however, the importance of microRNAs in head and neck cancers remains to be elucidated. In this study, we examined whether altered microRNA (miR)-551b expression correlated with invasive phenotypes of human oral squamous cell carcinoma (OSCC) in vivo and in vitro. MATERIALS AND METHODS: Real-time polymerase chain reaction was used to detect the expression level of miR-551b in 71 OSCC tissues with lymph node metastasis and 50 nonmetastatic OSCC tissues. We also constructed miR-551b mimic-transfected cell lines HN4 and HN12. The effects of overexpressing miR-551b on the proliferation, migration, and invasion of OSCC cells were examined using Cell Counting Kit 8 (Dojindo, Kumamoto, Japan), plate clone formation, wound healing, and Transwell invasion experiments (Corning, Corning, NY). The association between clinical pathologic parameters and the expression level of miR-551b was analyzed using Kaplan-Meier survival analysis. RESULTS: The expression of miR-551b measured 0.33 ± 0.11 in the 71 OSCC tissues with lymph node metastasis versus 0.54 ± 0.06 in the 50 tissues with non-lymph node metastasis (P = .021). Regarding OSCC patients, the expression of miR-551b negatively correlated with patients' overall survival (P = .035). The ectopic expression of miR-551b inhibited the invasion and migration of OSCC cells. CONCLUSIONS: This is the first report showing that reduced miR-551b expression may be an event leading to OSCC invasion and metastasis.

Gender and Age Differences of Temporomandibular Joint Disc Perforation: A Cross-Sectional Study in a Population of Patients With Temporomandibular Disorders.

The presence or absence of disc perforation (DP) has great value for the treatment planning of temporomandibular disorders (TMDs). Epidemiologic features of DP are limited in the literature. The present study investigated the epidemiologic features of DP by retrospectively reviewing 13,556 temporomandibular joint arthrographic examinations. Pearson Chi-squared test demonstrated that the rate of male patients who received the examinations more than once was significantly lower than that of female patients and the rate of DP in males was significantly lower than that in females. The age of all patients showed a bimodal distribution, with a 1st peak around 21 years of age, and a 2nd peak around 53 years of age. Linear regression analysis showed that the rate of DP was positively correlated with ages. The DP rate was increased by 0.3% for every 1 year of age. This retrospective cross-sectional study validated some findings about the gender and age differences of temporomandibular joint DP in the literature, and more importantly uncovered the exact relationship between the DP rate and the age in a large TMD patient population.

[Chemical constituents from lipophilic parts of stems of Celastrus monospermus].

The chemical constituents from lipophilic parts of the stems of Celastrus monospermus were studied in this paper. The compounds were separated and purified by repeated column chromatographic methods including silica gel, ODS and Sephadex LH-20, and the structures of compounds were determined by spectral data analyses. Twenty six compounds were obtained and identified as 3-oxofriedelane(1), 3-oxofriedelan-28-al(2), 3,12-dioxofriedelane(3), 3ß-hydroxyolean-12-en(4), 3-oxo-28-hydroxyfriedelane(5), 3-oxo-29-hydroxyfriedelane(6), 3-oxo-11ß-hydroxyfriedel-ane(7), 3-oxo-16α-hydroxyfriedelane(8), 3,12-dioxo-28-hydroxyfriedelane(9), 1,3-dioxo-15α-hydroxyfriedelane(10), 3ß,6α-dihydroxyolean-12-en(11), 3-oxo-7α,26-dihydroxyfriedel-ane(12), oleanolic acid(13), 3,15-dioxofriedelane(14), 3α-friedelinol(15), 3,12-dioxofriedelan-28-al(16), 3-oxo-12α-hydroxyfriedelane(17), 3,15-dioxo-12α-hydroxyfriedelane(18), 3ß,11ß-dihydroxyolean-12-en(19), 1ß,3ß-dihydroxylupan-20(29)-en(20), 3-oxo-12α,28-dihydroxyfriedelane(21), 3ß,23-epoxyfriedelan-28-oic acid(22), salaquinone A(23), 2α,3ß-dihydroxyfriedelan-28-oic acid(24), 23-nor-6-oxodemethylpristimerol(25) and 3-oxo-friedelan-27,28-dioic acid(26). Among them, compounds 8, 10-15, 18-20, 22-26 were obtained from this plant for the first time, and compounds 8, 10, 12, 14-15, 18, 22-24, 26 were separated from the genus Celastrus for the first time.

Copy number variation of a gene cluster encoding endopolygalacturonase mediates flesh texture and stone adhesion in peach.

Texture is an important attribute affecting consumer perception of fruit quality. Peach melting flesh and flesh adhesion to stone (endocarp) are simply inherited and controlled by the F-M locus on linkage group (LG) 4. Here, we report that two genes encoding endopolygalacturonase (endoPG) in the F-M locus, designated PpendoPGF and PpendoPGM, are associated with the melting flesh and stone adhesion traits. PpendoPGM controls melting flesh while PpendoPGF has pleiotropic effects on both melting flesh and stone adhesion. The F-M locus has three allelic copy number variants of endoPG, H1 (PpendoPGF and PpendoPGM), H2 (PpendoPGM), and H3 (null). The H2 haplotype represents the ancestral one while the H1 and H3 haplotypes are two variants due to duplication and deletion of PpendoPGM, respectively. Accessions with H1H1, H1H2, or H1H3 genotypes show the freestone or semi-freestone and melting flesh phenotype, while both H2H2 and H2H3 accessions have the clingstone and melting flesh phenotype. The H3H3 accessions have the clingstone and non-melting flesh phenotype. Our study not only demonstrates a driving role of gene copy number variations in flesh texture diversification in fruit trees, but also provides a useful diagnostic tool for early seedling selection in peach breeding programmes.

Correlation Between Nuclear Factor E2-Related Factor 2 Expression and Gastric Cancer Progression.

BACKGROUND: Nuclear factor E2-related factor 2 (Nrf2) plays an anti-oxidative and phase II detoxification function via its up-regulation on various antioxidant response elements (ARE) genes. Nrf2 can protect both normal and cancer cells from damages of cell stress, thereby exerting a critical role in the development of cancer. The expression and significance of Nrf2 in gastric cancer, however, has not been reported. This study thus aimed to investigate the expression of Nrf2 in gastric cancer tissues via immunohistochemical (IHC) staining. MATERIAL AND METHODS: Gastric carcinoma tissues from a total of 175 patients during surgical resection were examined for Nfr2 expression profiles using IHC staining on paraffin-embedded slides. Between-group-comparisons were performed by chi-square, Fisher's exact, or Mann-Whitney U test. The correlation between Nfr2 expression and clinical indexes was further analyzed by Kaplan-Meier test, univariate/multivariate analysis, and log-rank test. RESULTS: Nrf2 is mainly expressed in nuclei of gastric carcinoma tissues, with significant correlation with clinical indexes, including tumor size, invasive depth, lymph node metastasis, and invasion. Patients with Nrf2-positive expression had significantly lower survival rates compared to those in the negative group (p<0.01), with chemo-resistance against 5-fluorouracil (5-FU) (p<0.05). CONCLUSIONS: Nrf2 expression is positively correlated with invasive gastric cancer, suggesting its utility as a predictive index for unfavorable prognosis.

Optical absorption enhancement in a Si nanohole structure with hexagonal unit cell for solar cell application.

Periodic hexagonal unit cell silicon nanohole (SiNH) structures with different structural dimensions have been fabricated using polystyrene spheres and investigated in terms of their microstructures and optical reflectance. Compared with a planar Si wafer, such structures exhibit much lower reflectance due to the enhanced scattering introduced by the SiNHs. Optical simulation using the finite element method has also been carried out in order to optimize the structural periodicity and hole diameter for maximum light absorption. The optimum structure is found to have a periodicity of 693 nm and hole diameter of 560 nm, and it yields the highest ultimate efficiency of 28.8%.