Cu(II)-Loaded Polydopamine-Coated Urchin-like Titanate Microspheres as a High-Performance IMAC Adsorbent for Hemoglobin Separation.

Immobilized metal ion affinity chromatography (IMAC) adsorbents generally have excellent affinity for histidine-rich proteins. However, the leaching of metal ions from the adsorbent usually affects its adsorption performance, which greatly affects the reusable performance of the adsorbent, resulting in many limitations in practical applications. Herein, a novel IMAC adsorbent, i.e., Cu(II)-loaded polydopamine-coated urchin-like titanate microspheres (Cu-PDA-UTMS), was prepared via metal coordination to make Cu ions uniformly decorate polydopamine-coated titanate microspheres. The as-synthesized microspheres exhibit an urchin-like structure, providing more binding sites for hemoglobin. Cu-PDA-UTMS exhibit favorable selectivity for hemoglobin adsorption and have a desirable adsorption capacity towards hemoglobin up to 2704.6 mg g-1. Using 0.1% CTAB as eluent, the adsorbed hemoglobin was easily eluted with a recovery rate of 86.8%. In addition, Cu-PDA-UTMS shows good reusability up to six cycles. In the end, the adsorption properties by Cu-PDA-UTMS towards hemoglobin from human blood samples were analyzed by SDS-PAGE. The results showed that Cu-PDA-UTMS are a high-performance IMAC adsorbent for hemoglobin separation, which provides a new method for the effective separation and purification of hemoglobin from complex biological samples.

Metabolism-triggered sensor array aided by machine learning for rapid identification of pathogens.

Chemical-nose strategy has achieved certain success in the discrimination and identification of pathogens. However, this strategy usually relies on non-specific interactions, which are prone to be significantly disturbed by the change of environment thus limiting its practical usefulness. Herein, we present a novel chemical-nose sensing approach leveraging the difference in the dynamic metabolic variation during peptidoglycan metabolism among different species for rapid pathogen discrimination. Pathogens were first tethered with clickable handles through metabolic labeling at two different acidities (pH = 5 and 7) for 20 and 60 min, respectively, followed by click reaction with fluorescence up-conversion nanoparticles to generate a four-dimensional signal output. This discriminative multi-dimensional signal allowed eight types of model bacteria to be successfully classified within the training set into strains, genera, and Gram phenotypes. As the difference in signals of the four sensing channels reflects the difference in the amount/activity of enzymes involved in metabolic labeling, this strategy has good anti-interference capability, which enables precise pathogen identification within 2 h with 100% accuracy in spiked urinary samples and allows classification of unknown species out of the training set into the right phenotype. The robustness of this approach holds significant promise for its widespread application in pathogen identification and surveillance.

Machine Learning-Assistant Colorimetric Sensor Arrays for Intelligent and Rapid Diagnosis of Urinary Tract Infection.

Urinary tract infections (UTIs), which can lead to pyelonephritis, urosepsis, and even death, are among the most prevalent infectious diseases worldwide, with a notable increase in treatment costs due to the emergence of drug-resistant pathogens. Current diagnostic strategies for UTIs, such as urine culture and flow cytometry, require time-consuming protocols and expensive equipment. We present here a machine learning-assisted colorimetric sensor array based on recognition of ligand-functionalized Fe single-atom nanozymes (SANs) for the identification of microorganisms at the order, genus, and species levels. Colorimetric sensor arrays are built from the SAN Fe1-NC functionalized with four types of recognition ligands, generating unique microbial identification fingerprints. By integrating the colorimetric sensor arrays with a trained computational classification model, the platform can identify more than 10 microorganisms in UTI urine samples within 1 h. Diagnostic accuracy of up to 97% was achieved in 60 UTI clinical samples, holding great potential for translation into clinical practice applications.

Collective Cell Radial Ordered Migration in Spatial Confinement.

Collective cells, a typical active matter system, exhibit complex coordinated behaviors fundamental for various developmental and physiological processes. The present work discovers a collective radial ordered migration behavior of NIH3T3 fibroblasts that depends on persistent top-down regulation with 2D spatial confinement. Remarkably, individual cells move in a weak-oriented, diffusive-like rather than strong-oriented ballistic manner. Despite this, the collective movement is spatiotemporal heterogeneous and radial ordering at supracellular scale, manifesting as a radial ordered wavefront originated from the boundary and propagated toward the center of pattern. Combining bottom-up cell-to-extracellular matrix (ECM) interaction strategy, numerical simulations based on a developed mechanical model well reproduce and explain above observations. The model further predicts the independence of geometric features on this ordering behavior, which is validated by experiments. These results together indicate such radial ordered collective migration is ascribed to the couple of top-down regulation with spatial restriction and bottom-up cellular endogenous nature.

A 10-m national-scale map of ground-mounted photovoltaic power stations in China of 2020.

We provide a remote sensing derived dataset for large-scale ground-mounted photovoltaic (PV) power stations in China of 2020, which has high spatial resolution of 10 meters. The dataset is based on the Google Earth Engine (GEE) cloud computing platform via random forest classifier and active learning strategy. Specifically, ground samples are carefully collected across China via both field survey and visual interpretation. Afterwards, spectral and texture features are calculated from publicly available Sentinel-2 imagery. Meanwhile, topographic features consisting of slope and aspect that are sensitive to PV locations are also included, aiming to construct a multi-dimensional and discriminative feature space. Finally, the trained random forest model is adopted to predict PV power stations of China parallelly on GEE. Technical validation has been carefully performed across China which achieved a satisfactory accuracy over 89%. Above all, as the first publicly released 10-m national-scale distribution dataset of China's ground-mounted PV power stations, it can provide data references for relevant researchers in fields such as energy, land, remote sensing and environmental sciences.

Advances in Machine Learning Processing of Big Data from Disease Diagnosis Sensors.

Exploring accurate, noninvasive, and inexpensive disease diagnostic sensors is a critical task in the fields of chemistry, biology, and medicine. The complexity of biological systems and the explosive growth of biomarker data have driven machine learning to become a powerful tool for mining and processing big data from disease diagnosis sensors. With the development of bioinformatics and artificial intelligence (AI), machine learning models formed by data mining have been able to guide more sensitive and accurate molecular computing. This review presents an overview of big data collection approaches and fundamental machine learning algorithms and discusses recent advances in machine learning and molecular computational disease diagnostic sensors. More specifically, we highlight existing modular workflows and key opportunities and challenges for machine learning to achieve disease diagnosis through big data mining.

Terminal Trajectory Planning for Synthetic Aperture Radar Imaging Guidance Based on Chronological Iterative Search Framework.

Synthetic aperture radar (SAR) is capable of obtaining the high-resolution 2-D image of the interested target scene, which enables advanced remote sensing and military applications, such as missile terminal guidance. In this article, the terminal trajectory planning for SAR imaging guidance is first investigated. It is found that the guidance performance of an attack platform is determined by the adopted terminal trajectory. Therefore, the aim of the terminal trajectory planning is to generate a set of feasible flight paths to guide the attack platform toward the target and meanwhile obtain the optimized SAR imaging performance for enhanced guidance precision. The trajectory planning is then modeled as a constrained multiobjective optimization problem given a high-dimensional search space, where the trajectory control and SAR imaging performance are comprehensively considered. By utilizing the temporal-order-dependent property of the trajectory planning problem, a chronological iterative search framework (CISF) is proposed. The problem is decomposed into a series of subproblems, where the search space, objective functions, and constraints are reformulated in chronological order. The difficulty of solving the trajectory planning problem is thus significantly alleviated. Then, the search strategy of CISF is devised to solve the subproblems successively. The optimization results of the preceding subproblem can be utilized as the initial input of the subsequent subproblems to enhance the convergence and search performance. Finally, a trajectory planning method is put forward based on CISF. Experimental studies demonstrate the effectiveness and superiority of the proposed CISF compared with the state-of-the-art multiobjective evolutionary methods. The proposed trajectory planning method can generate a set of feasible terminal trajectories with optimized mission performance.

Chemical Nose Strategy with Metabolic Labeling and "Antibiotic-Responsive Spectrum" Enables Accurate and Rapid Pathogen Identification.

The worldwide antimicrobial resistance (AMR) dilemma urgently requires rapid and accurate pathogen phenotype discrimination and antibiotic resistance identification. The conventional protocols are either time-consuming or depend on expensive instrumentations. Herein, we demonstrate a metabolic-labeling-assisted chemical nose strategy for phenotyping classification and antibiotic resistance identification of pathogens based on the "antibiotic-responsive spectrum" of different pathogens. d-Amino acids with click handles were metabolically incorporated into the cell wall of pathogens for further clicking with dibenzocyclooctyne-functionalized upconversion nanoparticles (DBCO-UCNPs) in the presence/absence of six types of antibiotics, which generates seven-channel sensing responses. With the assistance of machine learning algorithms, eight types of pathogens, including three types of antibiotic-resistant bacteria, can be well classified and discriminated in terms of microbial taxonomies, Gram phenotypes, and antibiotic resistance. The present metabolic-labeling-assisted strategy exhibits good anti-interference capability and improved discrimination ability rooted in the unique sensing mechanism. Sensitive identification of pathogens with 100% accuracy from artificial urinary tract infection samples at a concentration as low as 105 CFU/mL was achieved. Pathogens outside of the training set can also be discriminated well. This clearly demonstrated the potential of the present strategy in the identification of unknown pathogens in clinical samples.

Quantitatively mapping local quality of super-resolution microscopy by rolling Fourier ring correlation.

In fluorescence microscopy, computational algorithms have been developed to suppress noise, enhance contrast, and even enable super-resolution (SR). However, the local quality of the images may vary on multiple scales, and these differences can lead to misconceptions. Current mapping methods fail to finely estimate the local quality, challenging to associate the SR scale content. Here, we develop a rolling Fourier ring correlation (rFRC) method to evaluate the reconstruction uncertainties down to SR scale. To visually pinpoint regions with low reliability, a filtered rFRC is combined with a modified resolution-scaled error map (RSM), offering a comprehensive and concise map for further examination. We demonstrate their performances on various SR imaging modalities, and the resulting quantitative maps enable better SR images integrated from different reconstructions. Overall, we expect that our framework can become a routinely used tool for biologists in assessing their image datasets in general and inspire further advances in the rapidly developing field of computational imaging.

Systematic Dissection of Sequence Features Affecting the Binding Specificity of a Pioneer Factor Reveals Binding Synergy Between FOXA1 and AP-1.

Despite the unique ability of pioneer transcription factors (PFs) to target nucleosomal sites in closed chromatin, they only bind a small fraction of their genomic motifs. The underlying mechanism of this selectivity is not well understood. Here, we design a high-throughput assay called ChIP-ISO to systematically dissect sequence features affecting the binding specificity of a classic PF, FOXA1. Combining ChIP-ISO with in vitro and neural network analyses, we find that 1) FOXA1 binding is strongly affected by co-binding TFs AP-1 and CEBPB, 2) FOXA1 and AP-1 show binding cooperativity in vitro, 3) FOXA1's binding is determined more by local sequences than chromatin context, including eu-/heterochromatin, and 4) AP-1 is partially responsible for differential binding of FOXA1 in different cell types. Our study presents a framework for elucidating genetic rules underlying PF binding specificity and reveals a mechanism for context-specific regulation of its binding.

SEM: sized-based expectation maximization for characterizing nucleosome positions and subtypes.

Genome-wide nucleosome profiles are predominantly characterized using MNase-seq, which involves extensive MNase digestion and size selection to enrich for mono-nucleosome-sized fragments. Most available MNase-seq analysis packages assume that nucleosomes uniformly protect 147bp DNA fragments. However, some nucleosomes with atypical histone or chemical compositions protect shorter lengths of DNA. The rigid assumptions imposed by current nucleosome analysis packages ignore variation in nucleosome lengths, potentially blinding investigators to regulatory roles played by atypical nucleosomes. To enable the characterization of different nucleosome types from MNase-seq data, we introduce the Size-based Expectation Maximization (SEM) nucleosome calling package. SEM employs a hierarchical Gaussian mixture model to estimate the positions and subtype identity of nucleosomes from MNase-seq fragments. Nucleosome subtypes are automatically identified based on the distribution of protected DNA fragment lengths at nucleosome positions. Benchmark analysis indicates that SEM is on par with existing packages in terms of standard nucleosome-calling accuracy metrics, while uniquely providing the ability to characterize nucleosome subtype identities. Using SEM on a low-dose MNase H2B MNase-ChIP-seq dataset from mouse embryonic stem cells, we identified three nucleosome types: short-fragment nucleosomes, canonical nucleosomes, and di-nucleosomes. The short-fragment nucleosomes can be divided further into two subtypes based on their chromatin accessibility. Interestingly, the subset of short-fragment nucleosomes in accessible regions exhibit high MNase sensitivity and display distribution patterns around transcription start sites (TSSs) and CTCF peaks, similar to the previously reported "fragile nucleosomes". These SEM-defined accessible short-fragment nucleosomes are found not just in promoters, but also in enhancers and other regulatory regions. Additional investigations reveal their co-localization with the chromatin remodelers Chd6, Chd8, and Ep400. In summary, SEM provides an effective platform for distinguishing various nucleosome subtypes, paving the way for future exploration of non-standard nucleosomes.

Joint sequence & chromatin neural networks characterize the differential abilities of Forkhead transcription factors to engage inaccessible chromatin.

The DNA-binding activities of transcription factors (TFs) are influenced by both intrinsic sequence preferences and extrinsic interactions with cell-specific chromatin landscapes and other regulatory proteins. Disentangling the roles of these binding determinants remains challenging. For example, the FoxA subfamily of Forkhead domain (Fox) TFs are known pioneer factors that can bind to relatively inaccessible sites during development. Yet FoxA TF binding also varies across cell types, pointing to a combination of intrinsic and extrinsic forces guiding their binding. While other Forkhead domain TFs are often assumed to have pioneering abilities, how sequence and chromatin features influence the binding of related Fox TFs has not been systematically characterized. Here, we present a principled approach to compare the relative contributions of intrinsic DNA sequence preference and cell-specific chromatin environments to a TF's DNA-binding activities. We apply our approach to investigate how a selection of Fox TFs (FoxA1, FoxC1, FoxG1, FoxL2, and FoxP3) vary in their binding specificity. We over-express the selected Fox TFs in mouse embryonic stem cells, which offer a platform to contrast each TF's binding activity within the same preexisting chromatin background. By applying a convolutional neural network to interpret the Fox TF binding patterns, we evaluate how sequence and preexisting chromatin features jointly contribute to induced TF binding. We demonstrate that Fox TFs bind different DNA targets, and drive differential gene expression patterns, even when induced in identical chromatin settings. Despite the association between Forkhead domains and pioneering activities, the selected Fox TFs display a wide range of affinities for preexiting chromatin states. Using sequence and chromatin feature attribution techniques to interpret the neural network predictions, we show that differential sequence preferences combined with differential abilities to engage relatively inaccessible chromatin together explain Fox TF binding patterns at individual sites and genome-wide.

The role and mechanism of TGF-ß1 in the antidepressant-like effects of tetrahydrocurcumin.

Astrocytes and the activation of inflammatory factors are associated with depression. Tetrahydrocurcumin (THC), the principal metabolite of natural curcumin, is renowned for its anti-inflammatory properties. In this research, we explored the impact of THC on the expression of inflammatory factors, neurotrophins, and transforming growth factor ß1 (TGF-ß1) in the prefrontal cortex after chronic restraint stress (CRS) in mice and in lipopolysaccharide (LPS)-induced TNC1 astrocytes. Our findings indicated that THC mitigated the anxiety and depression-like behaviours observed in CRS mice. It also influenced the expression of TGF-ß1, p-SMAD3/SMAD3, sirtuin 1 (SIRT1), brain-derived neurotrophic factor (BDNF), glial cell line-derived neurotrophic factor (GDNF), inducible nitric oxide synthase (iNOS), and tumour necrosis factor α (TNF-α). Specifically, THC augmented the expressions of TGF-ß1, p-SMAD3/SMAD3, SIRT1, BDNF, and GDNF, whilst diminishing the expressions of iNOS and TNF-α in LPS-induced astrocytes. However, when pre-treated with SB431542, a TGF-ß1 receptor inhibitor, it nullified the aforementioned effects of THC on astrocytes. Our results propose that THC delivers its anti-depressive effects through the activation of TGF-ß1, enhancement of p-SMAD3/SMAD3 and SIRT1 expression, upregulation of BDNF and GDNF, and downregulation of iNOS and TNF-α. This research furnishes new perspectives on the anti-inflammatory mechanism that underpins the antidepressant-like impact of THC.

Causal inference from cross-sectional earth system data with geographical convergent cross mapping.

Causal inference in complex systems has been largely promoted by the proposal of some advanced temporal causation models. However, temporal models have serious limitations when time series data are not available or present insignificant variations, which causes a common challenge for earth system science. Meanwhile, there are few spatial causation models for fully exploring the rich spatial cross-sectional data in Earth systems. The generalized embedding theorem proves that observations can be combined together to construct the state space of the dynamic system, and if two variables are from the same dynamic system, they are causally linked. Inspired by this, here we show a Geographical Convergent Cross Mapping (GCCM) model for spatial causal inference with spatial cross-sectional data-based cross-mapping prediction in reconstructed state space. Three typical cases, where clearly existing causations cannot be measured through temporal models, demonstrate that GCCM could detect weak-moderate causations when the correlation is not significant. When the coupling between two variables is significant and strong, GCCM is advantageous in identifying the primary causation direction and better revealing the bidirectional asymmetric causation, overcoming the mirroring effect.

Beyond Pattern Variance: Unsupervised 3-D Action Representation Learning With Point Cloud Sequence.

This work pays the first research effort to address unsupervised 3-D action representation learning with point cloud sequence, which is different from existing unsupervised methods that rely on 3-D skeleton information. Our proposition is built on the state-of-the-art 3-D action descriptor 3-D dynamic voxel (3DV) with contrastive learning (CL). The 3DV can compress the point cloud sequence into a compact point cloud of 3-D motion information. Spatiotemporal data augmentations are conducted on it to drive CL. However, we find that existing CL methods (e.g., SimCLR or MoCo v2) often suffer from high pattern variance toward the augmented 3DV samples from the same action instance, that is, the augmented 3DV samples are still of high feature complementarity after CL, while the complementary discriminative clues within them have not been well exploited yet. To address this, a feature augmentation adapted CL (FACL) approach is proposed, which facilitates 3-D action representation via concerning the features from all augmented 3DV samples jointly, in spirit of feature augmentation. FACL runs in a global-local way: one branch learns global feature that involves the discriminative clues from the raw and augmented 3DV samples, and the other focuses on enhancing the discriminative power of local feature learned from each augmented 3DV sample. The global and local features are fused to characterize 3-D action jointly via concatenation. To fit FACL, a series of spatiotemporal data augmentation approaches is also studied on 3DV. Wide-range experiments verify the superiority of our unsupervised learning method for 3-D action feature learning. It outperforms the state-of-the-art skeleton-based counterparts by 6.4% and 3.6% with the cross-setup and cross-subject test settings on NTU RGB + D 120, respectively. The source code is available at https://github.com/tangent-T/FACL.

Theoretical Analysis and Experimental Verification of the Influence of Polarization on Counter-Propagating Optical Tweezers.

Counter-propagating optical tweezers are experimental platforms for the frontier exploration of science and precision measurement. The polarization of the trapping beams significantly affects the trapping status. Using the T-matrix method, we numerically analyzed the optical force distribution and the resonant frequency of counter-propagating optical tweezers in different polarizations. We also verified the theoretical result by comparing it with the experimentally observed resonant frequency. Our analysis shows that polarization has little influence on the radial axis motion, while the axial axis force distribution and the resonant frequency are sensitive to polarization change. Our work can be used in designing harmonic oscillators which can change their stiffness conveniently, and monitoring polarization in counter-propagating optical tweezers.

Mesenchymal Migration on Adhesive-Nonadhesive Alternate Surfaces in Macrophages.

Mesenchymal migration usually happens on adhesive substrates, while cells adopt amoeboid migration on low/nonadhesive surfaces. Protein-repelling reagents, e.g., poly(ethylene) glycol (PEG), are routinely employed to resist cell adhering and migrating. Contrary to these perceptions, this work discovers a unique locomotion of macrophages on adhesive-nonadhesive alternate substrates in vitro that they can overcome nonadhesive PEG gaps to reach adhesive regions in the mesenchymal mode. Adhering to extracellular matrix regions is a prerequisite for macrophages to perform further locomotion on the PEG regions. Podosomes are found highly enriched on the PEG region in macrophages and support their migration across the nonadhesive regions. Increasing podosome density through myosin IIA inhibition facilitates cell motility on adhesive-nonadhesive alternate substrates. Moreover, a developed cellular Potts model reproduces this mesenchymal migration. These findings together uncover a new migratory behavior on adhesive-nonadhesive alternate substrates in macrophages.

Analysis of cuproptosis-related lncRNA signature for predicting prognosis and tumor immune microenvironment in pancreatic cancer.

Pancreatic cancer (PC) is a highly malignant digestive tract tumor, with a dismal 5-year survival rate. Recently, cuproptosis was found to be copper-dependent cell death. This work aims to establish a cuproptosis-related lncRNA signature which could predict the prognosis of PC patients and help clinical decision-making. Firstly, cuproptosis-related lncRNAs were identified in the TCGA-PAAD database. Next, a cuproptosis-related lncRNA signature based on five lncRNAs was established. Besides, the ICGC cohort and our samples from 30 PC patients served as external validation groups to verify the predictive power of the risk signature. Then, the expression of CASC8 was verified in PC samples, scRNA-seq dataset CRA001160, and PC cell lines. The correlation between CASC8 and cuproptosis-related genes was validated by Real-Time PCR. Additionally, the roles of CASC8 in PC progression and immune microenvironment characterization were explored by loss-of-function assay. As showed in the results, the prognosis of patients with higher risk scores was prominently worse than that with lower risk scores. Real-Time PCR and single cell analysis suggested that CASC8 was highly expressed in pancreatic cancer and related to cuproptosis. Additionally, gene inhibition of CASC8 impacted the proliferation, apoptosis and migration of PC cells. Furthermore, CASC8 was demonstrated to impact the expression of CD274 and several chemokines, and serve as a key indicator in tumor immune microenvironment characterization. In conclusion, the cuproptosis-related lncRNA signature could provide valuable indications for the prognosis of PC patients, and CASC8 was a candidate biomarker for not only predicting the progression of PC patients but also their antitumor immune responses.