ConvNeXt-MHC: improving MHC-peptide affinity prediction by structure-derived degenerate coding and the ConvNeXt model.

Peptide binding to major histocompatibility complex (MHC) proteins plays a critical role in T-cell recognition and the specificity of the immune response. Experimental validation such peptides is extremely resource-intensive. As a result, accurate computational prediction of binding peptides is highly important, particularly in the context of cancer immunotherapy applications, such as the identification of neoantigens. In recent years, there is a significant need to continually improve the existing prediction methods to meet the demands of this field. We developed ConvNeXt-MHC, a method for predicting MHC-I-peptide binding affinity. It introduces a degenerate encoding approach to enhance well-established panspecific methods and integrates transfer learning and semi-supervised learning methods into the cutting-edge deep learning framework ConvNeXt. Comprehensive benchmark results demonstrate that ConvNeXt-MHC outperforms state-of-the-art methods in terms of accuracy. We expect that ConvNeXt-MHC will help us foster new discoveries in the field of immunoinformatics in the distant future. We constructed a user-friendly website at http://www.combio-lezhang.online/predict/, where users can access our data and application.

PREDAC-CNN: predicting antigenic clusters of seasonal influenza A viruses with convolutional neural network.

Vaccination stands as the most effective and economical strategy for prevention and control of influenza. The primary target of neutralizing antibodies is the surface antigen hemagglutinin (HA). However, ongoing mutations in the HA sequence result in antigenic drift. The success of a vaccine is contingent on its antigenic congruence with circulating strains. Thus, predicting antigenic variants and deducing antigenic clusters of influenza viruses are pivotal for recommendation of vaccine strains. The antigenicity of influenza A viruses is determined by the interplay of amino acids in the HA1 sequence. In this study, we exploit the ability of convolutional neural networks (CNNs) to extract spatial feature representations in the convolutional layers, which can discern interactions between amino acid sites. We introduce PREDAC-CNN, a model designed to track antigenic evolution of seasonal influenza A viruses. Accessible at http://predac-cnn.cloudna.cn, PREDAC-CNN formulates a spatially oriented representation of the HA1 sequence, optimized for the convolutional framework. It effectively probes interactions among amino acid sites in the HA1 sequence. Also, PREDAC-CNN focuses exclusively on physicochemical attributes crucial for the antigenicity of influenza viruses, thereby eliminating unnecessary amino acid embeddings. Together, PREDAC-CNN is adept at capturing interactions of amino acid sites within the HA1 sequence and examining the collective impact of point mutations on antigenic variation. Through 5-fold cross-validation and retrospective testing, PREDAC-CNN has shown superior performance in predicting antigenic variants compared to its counterparts. Additionally, PREDAC-CNN has been instrumental in identifying predominant antigenic clusters for A/H3N2 (1968-2023) and A/H1N1 (1977-2023) viruses, significantly aiding in vaccine strain recommendation.

M-N3 Configuration on Boron Nitride Boosts Singlet Oxygen Generation via Peroxymonosulfate Activation for Selective Oxidation.

Singlet oxygen (1O2) is an essential reactive species responsible for selective oxidation of organic matter, especially in Fenton-like processes. However, due to the great limitations in synthesizing catalysts with well-defined active sites, the controllable production and practical application of 1O2 remain challenging. Herein, guided by theoretical simulations, a series of boron nitride-based single-atom catalysts (BvBN/M, M=Co, Fe, Cu, Ni and Mn) were synthesized to regulate 1O2 generation by activating peroxymonosulfate (PMS). All the fabricated BvBN/M catalysts with explicit M-N3 sites promoted the self-decomposition of the two PMS molecules to generate 1O2 with high selectivity, where BvBN/Co possessed moderate adsorption energy and d-band center exhibited superior catalytic activity. As an outcome, the BvBN/Co-PMS system coupled with membrane filtration technology could continuously transform aromatic alcohols to aldehydes with nearly 100 % selectivity and conversion rate under mild conditions, suggesting the potential of this novel catalytic system for green organic synthesis.

[Three-dimensional virtual dolphin treatment system for children with autism spectrum disorder].

In order to address the problem of traditional dolphin adjuvant therapy such as high cost and its limitation in time and place, this paper introduces a three-dimensional virtual dolphin adjuvant therapy system based on virtual reality technology. By adopting Oculus wearable three-dimensional display, the system combined natural human-computer interaction based on Leap Motion with high-precision gesture recognition and cognitive training, and achieved immersive three-dimensional interactive game for child rehabilitation training purposes. The experimental data showed that the system can effectively improve the cognitive and social abilities of those children with autism spectrum disorder, providing a useful exploration for the rehabilitation of those children.

LiveRetro: Visual Analytics for Strategic Retrospect in Livestream E-Commerce.

Livestream e-commerce integrates live streaming and online shopping, allowing viewers to make purchases while watching. However, effective marketing strategies remain a challenge due to limited empirical research and subjective biases from the absence of quantitative data. Current tools fail to capture the interdependence between live performances and feedback. This study identified computational features, formulated design requirements, and developed LiveRetro, an interactive visual analytics system. It enables comprehensive retrospective analysis of livestream e-commerce for streamers, viewers, and merchandise. LiveRetro employs enhanced visualization and time-series forecasting models to align performance features and feedback, identifying influences at channel, merchandise, feature, and segment levels. Through case studies and expert interviews, the system provides deep insights into the relationship between live performance and streaming statistics, enabling efficient strategic analysis from multiple perspectives.

Selective removal of organic contaminants and ascorbic acid enhancement effect based on the magnetic Fe0/FeS2-doped carbon nanolayer.

Developing highly effective iron-based catalyst to selectively remove organic contaminants has garnered considerable attention. Herein, a magnetic Fe0/FeS2-doped carbon nanolayer (S-Fe@NC) was synthesized through a straightforward one-step pyrolysis method, pyrolyzing a mixture composed of 4,6-dihydroxypyrimidine, trithiocyanuric acid, and FeCl3·6H2O. With the presence of PMS, S-Fe@NC demonstrated the ability to remove almost 100% bisphenol-A (50 µM) within 3 min, attributed to its excellent graphitization degree and high FeS2/Fe0 content. Furthermore, the S-Fe@NC catalyst demonstrated an impressive kobs value of 1.476 min-1, which surpassed the traditional Fenton system by 77 times and even exceeded the commercial Fe0 catalyst by 127 times. More importantly, the S-Fe@NC/PMS system succeeded in selectively removing organic contaminants based on the hydrophobic interaction between catalyst and contaminants. Besides, the result of electron paramagnetic resonance and the radical quenching experiments indicated that ·OH, SO4·-, 1O2, and O2·- were involved in the organic contaminants removal. Interestingly, after adding ascorbic acid (AA) to the S-Fe@NC/PMS system, more ROS could be generated to result in the kobs augmenting by 4.16 times (6.133 min-1), completely different from the common sense that AA was usually used as a radical quencher. Additionally, the magnetically separable catalyst also exhibited excellent reusability and broad pH adaptability (2.0-12.0). This study provided a valuable insight for developing highly selective and effective Fe-based catalyst for practical wastewater treatment.

Separation and reutilization of heavy metal ions in wastewater assisted by p-BN adsorbent.

Extracting heavy metal ions from wastewater has significant implications for both environmental remediation and resource preservation. However, the conventional adsorbents still suffer from incomplete ion removal and low utilization efficiency of the recovered metals. Herein, we present an extraction and reutilization method assisted by porous boron nitride (p-BN) containing high-density N atoms for metal recovery with simultaneous catalyst formation. The p-BN exhibits stable and efficient metal adsorption performance, particularly for ultra-trace-level water purification. The distribution coefficients towards Pb2+, Cd2+, Co2+ and Fe3+ can exceed 106 mL g-1 and the residual concentrations that reduced from 1 mg L-1 to 0.8-1.3 µg L-1 are much lower than the acceptable limits in drinking water standards of World Health Organization. Meanwhile, the used p-BN after Co ion adsorption can be directly adopted as a high-efficiency catalyst for activating peroxymonosulfate (PMS) in organic pollutant degradation without additional post-treatment, avoiding the secondary metal pollution and the problems of neglected manpower and energy consumption. Moreover, a flow-through multistage utilization system assisted by p-BN/polyvinylidene fluoride (PVDF) membrane is constructed for achieving both metal ion separation and reutilization in the removal of organic pollutants, providing a new avenue for sustainable wastewater remediation.

Discovering hematoma-stimulated circuits for secondary brain injury after intraventricular hemorrhage by spatial transcriptome analysis.

Introduction: Central nervous system (CNS) diseases, such as neurodegenerative disorders and brain diseases caused by acute injuries, are important, yet challenging to study due to disease lesion locations and other complexities. Methods: Utilizing the powerful method of spatial transcriptome analysis together with novel algorithms we developed for the study, we report here for the first time a 3D trajectory map of gene expression changes in the brain following acute neural injury using a mouse model of intraventricular hemorrhage (IVH). IVH is a common and representative complication after various acute brain injuries with severe mortality and mobility implications. Results: Our data identified three main 3D global pseudospace-time trajectory bundles that represent the main neural circuits from the lateral ventricle to the hippocampus and primary cortex affected by experimental IVH stimulation. Further analysis indicated a rapid response in the primary cortex, as well as a direct and integrated effect on the hippocampus after IVH stimulation. Discussion: These results are informative for understanding the pathophysiological changes, including the spatial and temporal patterns of gene expression changes, in IVH patients after acute brain injury, strategizing more effective clinical management regimens, and developing novel bioinformatics strategies for the study of other CNS diseases. The algorithm strategies used in this study are searchable via a web service (www.combio-lezhang.online/3dstivh/home).

A polymer tethering strategy to achieve high metal loading on catalysts for Fenton reactions.

The development of heterogenous catalysts based on the synthesis of 2D carbon-supported metal nanocatalysts with high metal loading and dispersion is important. However, such practices remain challenging to develop. Here, we report a self-polymerization confinement strategy to fabricate a series of ultrafine metal embedded N-doped carbon nanosheets (M@N-C) with loadings of up to 30 wt%. Systematic investigation confirms that abundant catechol groups for anchoring metal ions and entangled polymer networks with the stable coordinate environment are essential for realizing high-loading M@N-C catalysts. As a demonstration, Fe@N-C exhibits the dual high-efficiency performance in Fenton reaction with both impressive catalytic activity (0.818 min-1) and H2O2 utilization efficiency (84.1%) using sulfamethoxazole as the probe, which has not yet been achieved simultaneously. Theoretical calculations reveal that the abundant Fe nanocrystals increase the electron density of the N-doped carbon frameworks, thereby facilitating the continuous generation of long-lasting surface-bound •OH through lowering the energy barrier for H2O2 activation. This facile and universal strategy paves the way for the fabrication of diverse high-loading heterogeneous catalysts for broad applications.

Intracranial electrophysiological and structural basis of BOLD functional connectivity in human brain white matter.

While functional MRI (fMRI) studies have mainly focused on gray matter, recent studies have consistently found that blood-oxygenation-level-dependent (BOLD) signals can be reliably detected in white matter, and functional connectivity (FC) has been organized into distributed networks in white matter. Nevertheless, it remains unclear whether this white matter FC reflects underlying electrophysiological synchronization. To address this question, we employ intracranial stereotactic-electroencephalography (SEEG) and resting-state fMRI data from a group of 16 patients with drug-resistant epilepsy. We find that BOLD FC is correlated with SEEG FC in white matter, and this result is consistent across a wide range of frequency bands for each participant. By including diffusion spectrum imaging data, we also find that white matter FC from both SEEG and fMRI are correlated with white matter structural connectivity, suggesting that anatomical fiber tracts underlie the functional synchronization in white matter. These results provide evidence for the electrophysiological and structural basis of white matter BOLD FC, which could be a potential biomarker for psychiatric and neurological disorders.

Nitrogen-doped carbon nanosheets with Fe-based nanoparticles for highly efficient degradation of antibiotics and sulfate ion enhancement effect.

Developing Fe-based catalysts with high-effective and environmentally friendly features in Fenton-like system for treating wastewater is still a challenge. Novel nitrogen-doped carbon nanosheets with Fe0/Fe3C nano-particles (Fe@NCS-900) were prepared through a simple solvent-free strategy by pyrolyzing the mixture of 2,6-diaminopyridine and ferric chloride hexahydrate under 900 °C. The Fe@NCS-900 possessed almost 100% removal efficiency and 66.5% mineralization rate for the degradation of CBZ in 10 min. Moreover, the Fe@NCS-900 exhibited an apparent first-order constant as high as 0.8809 min-1, which is 22 and 29 times higher than that of the commercial Fe0 and traditional Fenton system, respectively, which could be attribute to the high graphitization degree and rich nitrogen content. Besides, the results of the radical quenching experiments, electron paramagnetic resonance (EPR) and the probe experiments demonstrated that a large number of high valent iron species (Fe (IV)) besides singlet oxygen (1O2) and superoxide radicals (O2•-) existed and contributed to the CBZ degradation. More interestingly, the addition of coexisting anion SO42- in the reaction system could significantly boost the concentration of •OH and SO4•- by 28.3 times and 9.7 times, respectively, resulting in the increase of the apparent first-order constant by 5.9 times (5.1733 min-1), which was entirely different from previous reports that SO42- had no effect on the catalytic activity or even displayed slightly inhibitory effect. In addition, the catalyst exhibited broad pH adaptability in the pH range of 2-9. The intermediate products of CBZ degradation were investigated by liquid chromatography mass spectrometry (LC-MS) and the degradation pathway was proposed. This paper provides new insights for developing a promising Fe-based nitrogen-doped catalyst for practical wastewater treatment.

Long-term Care Facility and its Elderly Chronic Diseases in Jishou: Insights into Underdeveloped Area of China.

Insight into the current status of long-term care facilities (LTCFs) and chronic diseases in underdeveloped areas in China is scant. Using a census method to survey older adults ≥60 years old (154 older adult residents) in all LTCFs in Jishou area. The International Resident Assessment Instrument for Long-Term Care Facilities (interRAI-LTCF) was used to collect information and analyze the current status of chronic diseases among older adult residents. There were 62 187 residents ≥60 years old in Jishou area. According to the survey, there were only 154 older adult residents living in the LTCFs of Jishou, with a ratio was 0.3% of all older adult residents, which was much lower than China's 3.0%. Of respondents (109 older adult residents), the prevalence of chronic diseases was 70.6%. The prevalence increases with age, as well as in the female is higher than in the male. The top 3 chronic diseases were hypertension (41.3%), bone and joint disease (12.8%) and cerebrovascular disease (12.8%). It was found that different age groups and genders lead to differences in the prevalence and the order of chronic diseases. The prevalence of older adults with impaired balance ability, sleep disturbance and swallowing disturbance was higher than that of normal older adults. The results of the one-way analysis of variance showed that the age and balance ability of the older adults with chronic diseases were statistically significant (P < .05). In addition, the prevalence of chronic diseases in the LTCFs older adult was higher than the home care (HC) older adults in Jishou. The age and the prevalence of chronic diseases of LTCFs in older adults with professional nursing staff were higher than in those without. This study provides a theoretical basis for the healthcare distribution, prevention and treatment of chronic diseases in underdeveloped areas. The undeveloped area has lower LTCFs staying rate and chronic disease prevalence of older adults than relatively developed areas. More public health attention and capital investment are needed to increase the LTCFs number and strengthen disease testing and screening. As well as, the proportion of professional nursing staff and specialist doctors in LTCFs and improve the quality of care and medical treatment for older adults.

[Effects on biomechanical properties of hip articular cartilage degeneration following the femoral neck fracture in rabbits].

Osteotomies were performed through post-lateral approach under the base of femoral neck on 60 New Zealand white rabbits. The changes of the thickness and biomechanical properties of acetabular cartilage following the cartilage degeneration and the relationship to the postoperative time 2, 4, 6, 8, 12, 16 weeks later were measured respectively. The cartilage specimens were harvested and measured by the automated creep indentation apparatus to obtain the thickness and biomechanical properties. The cartilage became thicker within 6 weeks after operation, cartilage degeneration developed critically from the surface with the lost of the biomechanical properties. The degeneration progressed till the eartilage became thinner and thinner and the to be torn out into pieces at last. The matrix of articular cartilage degraded markedly for the absence of normal stress load following the femoral neck fracture, led to the decline of the biomechanical properties and kept the degeneration progress to osteoarthritis.

CT value analysis and clinical significance before and after percutaneous lumbar discectomy.

OBJECTIVE: To provide theoretical basis for effect and mechanism of percutaneous lumbar discectomy in clinic. METHODS: A total of 180 patients with lumbar intervertebral disc herniation were evaluated by CT on the fifth day before and after operation. Meanwhile, CT value was measured in the determined level and region. RESULTS: After operation, CT value of the central and posterior determined point of herniated intervertebral disc was lower significantly than that before operation (P<0.01), but CT value of the anterior determined point was different insignificantly. The excellent and good results of the patients together were 83% postoperatively. CONCLUSIONS: The curative effect of percutaneous lumbar discectomy is achieved through reduction of lumbar intradiscal pressure.

[Surgical reconstruction of the stability of lower cervical spine in children].

OBJECTIVE: To investigate surgical reconstruction of stability of lower cervical spine in children suffering trauma, tuberculosis and tumor. METHODS: From January 1998 to September 2001, 8 cases of unstable lower cervical spine were treated by operations, of anterior decompression, massive iliac bone grafting, posterior fixation with spinous process tension band wiring, and fusion with heterogeneous iliac bone grafting. RESULTS: With an average following up of 1 year and 9 months (6 months to 4 years and 3 months), 3 cases recovered excellently, 4 cases recovered well and 1 case died of pulmonary infection. CONCLUSION: The above results indicate that anterior decompression, massive iliac bone grafting, posterior fixation with spinous process tension band wiring and fusion with heterogeneous iliac bone grafting can be used as one of the methods to reconstruct the stability of lower cervical spine in children.