This review systematically summarizes recent advancements in the design of antibacterial hydrogels and the surface-related factors influencing microbial adhesion to polymeric materials.Hydrogels,characterized by their...This review systematically summarizes recent advancements in the design of antibacterial hydrogels and the surface-related factors influencing microbial adhesion to polymeric materials.Hydrogels,characterized by their three-dimensional porous architecture and ultra-high water content,serve as ideal platforms for incorporating antibacterial agents(e.g.,metal ions,natural polymers)through physical/chemical interactions,enabling sustained release and enhanced antibacterial efficacy.For traditional polymers,surface properties(e.g.,roughness,charge,superhydrophobicity,free energy,nanoforce gradients)play critical roles in microbial adhesion.Modifying the surface properties of polymers through surface treatment can regulate antibacterial performance.In particular,by referencing the micro/nanostructures found on natural surfaces such as lotus leaves and cicada wings,antibacterial surfaces with multiple superior functions can be fabricated.Collectively,these findings provide a theoretical basis for the rational design of multifunctional antibacterial materials,offering material-based solutions to address complex infection scenarios and advance infection management strategies.展开更多
Artificial skin should embody a softly functional film that is capable of self-powering,healing and sensing with neuromorphic processing.However,the pursuit of a bionic skin that combines high flexibility,self-healabi...Artificial skin should embody a softly functional film that is capable of self-powering,healing and sensing with neuromorphic processing.However,the pursuit of a bionic skin that combines high flexibility,self-healability,and zero-powered photosynaptic functionality remains elusive.In this study,we report a self-powered and self-healable neuromorphic vision skin,featuring silver nanoparticle-doped ionogel heterostructure as photoacceptor.The localized surface plasmon resonance induced by light in the nanoparticles triggers temperature fluctuations within the heterojunction,facilitating ion migration for visual sensing with synaptic behaviors.The abundant reversible hydrogen bonds in the ionogel endow the skin with remarkable mechanical flexibility and self-healing properties.We assembled a neuromorphic visual skin equipped with a 5×5 photosynapse array,capable of sensing and memorizing diverse light patterns.展开更多
目的探讨可视穿刺针式肾镜治疗特殊类型肾结石的临床疗效及安全性。方法 2016年6月-2017年8月,采用F4.8铂立可视穿刺针式肾镜对46例特殊类型肾结石患者进行钬激光碎石术,其中肾盏憩室内结石8例,肾下盏结石[肾盂肾下盏漏斗夹角(IPA)<3...目的探讨可视穿刺针式肾镜治疗特殊类型肾结石的临床疗效及安全性。方法 2016年6月-2017年8月,采用F4.8铂立可视穿刺针式肾镜对46例特殊类型肾结石患者进行钬激光碎石术,其中肾盏憩室内结石8例,肾下盏结石[肾盂肾下盏漏斗夹角(IPA)<30°]7例,输尿管软镜治疗失败4例,集合系统无扩张肾结石17例,儿童肾结石4例,乙状结肠直肠膀胱术(Mainz-Ⅱ)术后并发肾结石6例。结石大小<1.5 cm 28例、大小>1.5 cm 18例,结石平均直径(1.6±0.4)cm。位于肾下盏、中盏、上盏、肾盂合并肾盏结石分别为20、10、5和11例。术中均"一针见石"建立经皮肾手术通道后碎石。结果术中所有患者均采用单通道,35例F4.8可视肾镜钬激光碎石,11例较大铸型结石术中再扩至F20行钬激光或超声碎石清石术,手术时间为25~50 min,平均为(37.4±9.2)min,术后35例完全无管化、11例留置肾造瘘管或双J管,术后所有患者均未出现活动性出血,3例患者出现发热,经常规抗感染治疗后,症状很快消失,术后住院时间为(2.4±0.8)d,术后1个月结石清除率为91.3%(42/46)。4例有残石患者辅助予以体外冲击波碎石、物理振动及药物促进排石治疗,再随访1个月结石均排净。结论 F4.8可视穿刺针式肾镜治疗特殊类型肾结石更加安全有效,成功率高,清石率高,且并发症低,近似无出血手术,患者恢复快,值得临床推广应用。展开更多
The release of AlphaFold2 has sparked a rapid expansion in protein model databases.Efficient protein structure retrieval is crucial for the analysis of structure models,while measuring the similarity between structure...The release of AlphaFold2 has sparked a rapid expansion in protein model databases.Efficient protein structure retrieval is crucial for the analysis of structure models,while measuring the similarity between structures is the key challenge in structural retrieval.Although existing structure alignment algorithms can address this challenge,they are often time-consuming.Currently,the state-of-the-art approach involves converting protein structures into three-dimensional(3D)Zernike descriptors and assessing similarity using Euclidean distance.However,the methods for computing 3D Zernike descriptors mainly rely on structural surfaces and are predominantly web-based,thus limiting their application in studying custom datasets.To overcome this limitation,we developed FP-Zernike,a user-friendly toolkit for computing different types of Zernike descriptors based on feature points.Users simply need to enter a single line of command to calculate the Zernike descriptors of all structures in customized datasets.FP-Zernike outperforms the leading method in terms of retrieval accuracy and binary classification accuracy across diverse benchmark datasets.In addition,we showed the application of FP-Zernike in the construction of the descriptor database and the protocol used for the Protein Data Bank(PDB)dataset to facilitate the local deployment of this tool for interested readers.Our demonstration contained 590,685 structures,and at this scale,our system required only 4-9 s to complete a retrieval.The experiments confirmed that it achieved the state-of-the-art accuracy level.FP-Zernike is an open-source toolkit,with the source code and related data accessible at https://ngdc.cncb.ac.cn/biocode/tools/BT007365/releases/0.1,as well as through a webserver at http://www.structbioinfo.cn/.展开更多
It is our great honor to announce the publication of this special section on AI and big data analytics in biology and medicine in the Journal of Computing Science and Technology(JCST).As more and more modern biologica...It is our great honor to announce the publication of this special section on AI and big data analytics in biology and medicine in the Journal of Computing Science and Technology(JCST).As more and more modern biological and medical data are produced,artificial intelligence(AI)and big data analytics are playing an increasingly important role in helping to draw meaningful and logical conclusions about biology and medicine.展开更多
This article is the 17th in the Fungal Diversity Notes series which allows the researchers to publish fungal collections with updated reports of fungus-host and fungus-geography.Herein we report 97 taxa with four new ...This article is the 17th in the Fungal Diversity Notes series which allows the researchers to publish fungal collections with updated reports of fungus-host and fungus-geography.Herein we report 97 taxa with four new genera distributed in three phyla(Ascomycota,Glomeromycota and Mucoromycota),11 classes,38 orders and 62 families collected from various regions worldwide.This collection is further classified into taxa from 69 genera with four novel genera namely Jinshana,Lithophyllospora,Parapolyplosphaeria and Stegonsporiicola.Furthermore,71 new species,21 new records,one new combination and four novel phylogenetic placements are provided.The new species comprise Acrocalymma estuarinum,Aggregatorygma isidiatum,Alleppeysporonites elsikii,Amphibambusa aquatica,Apiospora hongheensis,Arthrobotrys tachengensis,Calonectria potisiana,Collariella hongheensis,Colletotrichum squamosae,Corynespora chengduensis,Diaporthe beijingensis,Dicellaesporites plicatus,Dicellaesporites verrucatus,Dictyoarthrinium endophyticum,Distoseptispora chiangraiensis,Dothiora eucalypti,Epicoccum indicum,Exesisporites chandrae,Fitzroyomyces pseudopandanicola,Fomitiporia exigua,Fomitiporia rondonii,Fulvifomes subthailandicus,Gigaspora siqueirae,Gymnopus ailaoensis,Hyalorbilia yunnanensis,Hygrocybe minimiholatra,H.mitsinjoensis,H.parviholatra,H.solis,H.vintsy,Helicogermslita kunmingensis,Jinshana tangtangiae,Kirschsteiniothelia dujuanhuensis,Lamproderma subcristatum,Leucoagaricus madagascarensis,Leucocoprinus mantadiaensis,Lithophyllospora australis,Marasmius qujingensis,Melomastia aquilariae,Monoporisporites jansoniusii,M.pattersonii,Monoporisporites valdiyae,Mucispora maesotensis,Mucor soli,Muyocopron yunnanensis,Nigrospora tomentosae,Ocellularia psorirregularis,Ophiocordyceps duyunensis,Oxneriaria nigrodisca,Oxydothis aquatica,O.filiforme,Phacidiella xishuangbannaensis,Phlebiopsis subgriseofuscescens,Pleurothecium takense,Pleurotus tuber-regium,Pseudochaetosphaeronema puerensis,Pseudodactylaria guttulate,Racheliella chinensis,Rhexoacrodictys fangensis,Roussoella neoaquatica,Rubroboletus pruinosus,Sanghuangporus subzonatus,Scytalidium assmuthi,Shrungabeeja kudremukhensis,Spirographa skorinae,Stanjehughesia bambusicola,Stegonsporiicola aurantiaca,Umbelopsis hingganensis,Vararia tenuata,Verruconis pakchongensis,Wongia bandungensis,and Zygosporium cymodoceae.The new combination is Parapolyplosphaeria thailandica(≡Polyplosphaeria thailandica).The 21 new hosts,geographical and habitat records comprise Acrocalymma fici,Apiculospora spartii,Aspergillus subramanianii,Camposporium ramosum,Clonostachys rogersoniana,Colletotrichum brevisporum,C.plurivorum,Collybiopsis gibbosa,Dictyosporium tratense,Distoseptispora adscendens,Exosporium livistonae,Ganoderma gibbosum,Graphis mikuraensis,Gymnosporangium paraphysatum,Lasiodiplodia thailandica,Moesziomyces bullatus,Penicillium cremeogriseum,P.echinulonalgiovense,P.javanicum,P.lanosocoeruleum,P.polonicum,and Pleurotus tuber-regium.Graphis chlorotica,G.panhalensis and G.parilis are given as novel phylogenetic placements.In addition,we provide the morphology of Tarzetta tibetensis which was missing in the previous Fungal Diversity Notes 1611–1716.Identification of characterization of all these taxa are supported by morphological and multigene phylogenetic analyses.展开更多
(S)-Pregabalin(S-PGB)is extensively employed in analgesic therapy.One of the current chemical processes used to produce S-PGB involves the Hofmann rearrangement of(R)-3-isobutyl glutaric acid monoamide(R-IBM).However,...(S)-Pregabalin(S-PGB)is extensively employed in analgesic therapy.One of the current chemical processes used to produce S-PGB involves the Hofmann rearrangement of(R)-3-isobutyl glutaric acid monoamide(R-IBM).However,the chemical resolution of R-IBM is inefficient and environmentally unsustainable.In this study,we established an enzyme-catalyzed route to R-IBM that proceeds with exceptional optical purity and yield.We successfully resculpted the substrate-binding pocket of D-hydantoinase by attenuating the steric hindrance and enhancing hydrophilicity,resulting in accelerated substrate transport and restricted side-chain rotation during the asymmetric hydrolysis process.Notably,both optical purity and yield for the generation of R-IBM from the prochiral substrate 3-isobutyl glutarimide(IBI)were enhanced for the M3(L64A/F66H/C318T)mutant;the enantiomeric excess increased from 65.51%±5.85%to 98.62%±0.28%(ee_(p))and k_(cat)/K_(m) increased from 14.92 to 207.06 s^(-1)·M^(-1).The ancestral sequence reconstruction(ASR)and consensus analyses guided further engineering of the flexible C-terminal region of D-hydantoinase to enhance the thermostability of the enzyme.The final mutant,M6(L64A/F66H/C318T/R99G/A265P/G466N/E470A),demonstrated a remarkable improvement in R-IBM production efficiency;thus,500 mM IBI was completely transformed into R-IBM in 24 h.This study therefore showcases a new enzyme that offers a green,enzymatic route for R-IBM production.展开更多
Advances in cryo-electron tomography(cryo-ET)have enabled the visualization of molecules within their native cellular environments in three-dimensions(3D).These visualizations are essential for studying the functions ...Advances in cryo-electron tomography(cryo-ET)have enabled the visualization of molecules within their native cellular environments in three-dimensions(3D).These visualizations are essential for studying the functions of biological entities in their natural conditions.Recently,deep learning techniques have shown significant success in tackling the challenge of particle detection in cryo-ET data.However,accurately identifying and classifying multi-class molecules remain challenging due to factors like low signal-to-noise ratios and the wide range of particle sizes.In this study,we introduce a novel framework CFNPicker for 3D object detection applied to cryo-ET analysis.A major advantage of our method is the design of central feature network(CFN)to integrate central features across multiple scales,allowing for the accurate detection of both small(⩽200)and large(⩾600)molecules.Additionally,we propose an adaptive weighted sampling training strategy to distinguish the complex noise distribution in the background,reducing false positive particles.We also construct the localization label to explicitly utilize the size and position variations of multi-class protein structures.Compared with existing methods,CFN improves the F1 score for classification by 3.6%,7.3%,6.6%,and 5.1%for the four smallest molecules tested respectively,while preserving similar or higher F1 scores for other molecules analyzed.展开更多
Single particle analysis, which can be regarded as an average of signals from thousands or even millions of particle projections, is an efficient method to study the three-dimensional structures of biological macro- m...Single particle analysis, which can be regarded as an average of signals from thousands or even millions of particle projections, is an efficient method to study the three-dimensional structures of biological macro- molecules. An intrinsic assumption in single particle analysis is that all the analyzed particles must have identical composition and conformation. Thus specimen heterogeneity in either composition or conformation has raised great challenges for high-resolution analysis. For particles with multiple conformations, inaccurate align- ments and orientation parameters will yield an averaged map with diminished resolution and smeared density. Besides extensive classification approaches, here based on the assumption that the macromolecular complex is made up of multiple rigid modules whose relative orien- tations and positions are in slight fluctuation around equilibriums, we propose a new method called as local optimization refinement to address this conformational heterogeneity for an improved resolution. The key idea is to optimize the orientation and shift parameters of each rigid module and then reconstruct their three-dimen- sional structures individually. Using simulated data of 80S/70S ribosomes with relative fluctuations between the large （60S/50S） and the small （40S/30S） subunits, we tested this algorithm and found that the resolutions of both subunits are significantly improved. Our method provides a proof-of-principle solution for high-resolutionsingle particle analysis of macromolecular complexes with dynamic conformations.展开更多
Lead halide perovskites have drawn extensive attention over recent decades owing to their outstanding photo-electric performances.However,their toxicity and instability are big issues that need to be solved for furthe...Lead halide perovskites have drawn extensive attention over recent decades owing to their outstanding photo-electric performances.However,their toxicity and instability are big issues that need to be solved for further commercialization.Herein,we adopt a facile dry ball milling method to synthesize lead-free Cs3Cu2X5(X=I,CI)perovskites with photoluminescence(PL)quantum yield up to 60%.The optical features including broad emission spectrum,large Stokes shift,and long PL lifetime can be attributed to self-trapped exciton recombination.The as-synthesized blue emissive Cs3Cu2I5 and green emissive Cs3Cu2Cl5 lead-free perovskite powders have good thermal stability and photostability.Furthermore,UV-pumped phosphor-converted light-emitting diodes were obtained by using Cs3Cu2I5 and Cs3Cu2Cl5 as phosphors.展开更多
Kirsten rat sarcoma viral oncogene homolog(namely KRAS)is a key biomarker for prognostic analysis and targeted therapy of colorectal cancer.Recently,the advancement of machine learning,especially deep learning,has gre...Kirsten rat sarcoma viral oncogene homolog(namely KRAS)is a key biomarker for prognostic analysis and targeted therapy of colorectal cancer.Recently,the advancement of machine learning,especially deep learning,has greatly promoted the development of KRAS mutation detection from tumor phenotype data,such as pathology slides or radiology images.However,there are still two major problems in existing studies:inadequate single-modal feature learning and lack of multimodal phenotypic feature fusion.In this paper,we propose a Disentangled Representation-based Multimodal Fusion framework integrating Pathomics and Radiomics(DRMF-PaRa)for KRAS mutation detection.Specifically,the DRMF-PaRa model consists of three parts:(1)the pathomics learning module,which introduces a tissue-guided Transformer model to extract more comprehensive and targeted pathological features;(2)the radiomics learning module,which captures the generic hand-crafted radiomics features and the task-specific deep radiomics features;(3)the disentangled representation-based multimodal fusion module,which learns factorized subspaces for each modality and provides a holistic view of the two heterogeneous phenotypic features.The proposed model is developed and evaluated on a multi modality dataset of 111 colorectal cancer patients with whole slide images and contrast-enhanced CT.The experimental results demonstrate the superiority of the proposed DRMF-PaRa model with an accuracy of 0.876 and an AUC of 0.865 for KRAS mutation detection.展开更多
Electron Tomography （ET） is an important method for studying cell ultrastructure in three-dimensional （3D） space. By combining cryo-electron tomography of frozen-hydrated samples （cryo-ET） and a sub-tomogram ave...Electron Tomography （ET） is an important method for studying cell ultrastructure in three-dimensional （3D） space. By combining cryo-electron tomography of frozen-hydrated samples （cryo-ET） and a sub-tomogram averaging approach, ET has recently reached sub-nanometer resolution, thereby realizing the capability for gaining direct insights into function and mechanism. To obtain a high-resolution 3D ET reconstruction, alignment and geometry determination of the ET tilt series are necessary. However, typical methods for determining geometry require human intervention, which is not only subjective and easily introduces errors, but is also labor intensive for high-throughput tomographic reconstructions. To overcome these problems, we have developed an automatic geometry-determination method, called AutoGDeterm. By taking advantage of the high-contrast re-projections of the Iterative Compressed-sensing Optimized Non-Uniform Fast Fourier Transform （NUFFT） reconstruction （ICON） and a series of numerical analysis methods, AutoGDeterm achieves high-precision fully automated geometry determination. Experimental results on simulated and resin-embedded datasets show that the accuracy of AutoGDeterm is high and comparable to that of the typical ＂manual positioning＂ method. We have made AutoGDeterm available as software, which can be freely downloaded from our website http：//ear.ict.ac.cn.展开更多
Super-resolution microscopy techniques have overcome the limit of optical diffraction. Recently, the Bayesian analysis of Bleaching and Blinking data （3B） method has emerged as an important tool to obtain super-reso...Super-resolution microscopy techniques have overcome the limit of optical diffraction. Recently, the Bayesian analysis of Bleaching and Blinking data （3B） method has emerged as an important tool to obtain super-resolution fluorescence images. 3B uses the change in information caused by adding or removing fiuorophores in the cell to fit the date. When adding a new fluorophore, 3B selects a random initial position, optimizes this position and then determines its reliability. However, the fluorophores are not evenly distributed in the entire image region, and the fluorescence intensilty at a given position positively correlates with the probability of observing a fluorophore at this position. In this paper, we present a Bayesian analysis of Bleaching and Blinking microscopy method based on fluorescence intensity distribution （FID3B）. We utilize the intensity distribution to select more reliable positions as the initial positions of fluorophores. This approach can improve the reconstruction results and significantly reduce the computational time. We validate the perfor. mance of our method using both simulated date and experimental date from cellular structures. The results confirm the effectiveness of our method.展开更多
As a weak non-covalent interaction,hydrogen bond(H-bond)is highly susceptible to the environmental interference.However,the direct quantification of a single H-bond under an interference-free condition is still a chal...As a weak non-covalent interaction,hydrogen bond(H-bond)is highly susceptible to the environmental interference.However,the direct quantification of a single H-bond under an interference-free condition is still a challenge.Herein,the intramolecular H-bond in a model system,poly(N-isopropylacrylamide),is studied in high vacuum by single-molecule atomic force microscopy and steered molecular dynamics simulations,which allows the precise quantification of H-bond strength in an interference-free state.Control experiments show that the H-bond is significantly weakened in nonpolar solvent,even if the dielectric constant is very close to vacuum.If a polar solvent is used as the environment,the H-bond will be further weaker or even broken.These results imply that for experiments in any liquid environment,the H-bond strength(△G)will be only -50% or even less of that measured in vacuum.Further analysis shows that in liquid environments,AG decays in a quasi-linear way with the increase of the dielectric constant(ε).For H-bond studies in future,the result measured in vacuum can be set as the standard value,namely,the inherent strength.This approach will provide fundamental insights into the H-bond participated nano-structures and materials in different environments.展开更多
The rapid advancement of high-throughput sequencing technologies and the explosive growth of biological data have revolutionized the field of bioinformatics and biomedical computing[1-4].The generation of vast amounts...The rapid advancement of high-throughput sequencing technologies and the explosive growth of biological data have revolutionized the field of bioinformatics and biomedical computing[1-4].The generation of vast amounts of genomic,transcriptomic,proteomic,and metabolomic data has created unprecedented opportunities for understanding the complexities of biological systems and their implications for human health[5-6].Moreover,the emergence of spatial omics technologies,such as spatial transcriptomics and spatial proteomics,has added a new dimension to our understanding of the spatial organization and heterogeneity of biological systems.These cutting-edge technologies enable the mapping of molecular information at a high spatial resolution,providing valuable insights into the tissue microenvironment and the interplay between cells in various physiological and pathological conditions[7-10].展开更多
Recent years have witnessed exponential growth in both the volume and complexity of biomedical data generated,which encompasses a diverse array of sources,including genomic sequences,clinical imaging,electronic health...Recent years have witnessed exponential growth in both the volume and complexity of biomedical data generated,which encompasses a diverse array of sources,including genomic sequences,clinical imaging,electronic health records,and real-time biometric sensing.This deluge of data has surpassed our traditional methods'abilities to efficiently process,analyze,store,and interpret,posing substantial challenges across the biomedical and healthcare sectors.展开更多
基金supported by Science and Technology Plan of Luzhou under Grant No.2024JYJ039.
文摘This review systematically summarizes recent advancements in the design of antibacterial hydrogels and the surface-related factors influencing microbial adhesion to polymeric materials.Hydrogels,characterized by their three-dimensional porous architecture and ultra-high water content,serve as ideal platforms for incorporating antibacterial agents(e.g.,metal ions,natural polymers)through physical/chemical interactions,enabling sustained release and enhanced antibacterial efficacy.For traditional polymers,surface properties(e.g.,roughness,charge,superhydrophobicity,free energy,nanoforce gradients)play critical roles in microbial adhesion.Modifying the surface properties of polymers through surface treatment can regulate antibacterial performance.In particular,by referencing the micro/nanostructures found on natural surfaces such as lotus leaves and cicada wings,antibacterial surfaces with multiple superior functions can be fabricated.Collectively,these findings provide a theoretical basis for the rational design of multifunctional antibacterial materials,offering material-based solutions to address complex infection scenarios and advance infection management strategies.
基金the financial support from the National Natural Science Foundation of China(62274088,62288102)the Project funded by China Postdoctoral Science Foundation(2023M741657)+1 种基金the Jiangsu Funding Program for Excellent Postdoctoral Talent(2023ZB554)the Jiangsu Specially-Appointed Professor program。
文摘Artificial skin should embody a softly functional film that is capable of self-powering,healing and sensing with neuromorphic processing.However,the pursuit of a bionic skin that combines high flexibility,self-healability,and zero-powered photosynaptic functionality remains elusive.In this study,we report a self-powered and self-healable neuromorphic vision skin,featuring silver nanoparticle-doped ionogel heterostructure as photoacceptor.The localized surface plasmon resonance induced by light in the nanoparticles triggers temperature fluctuations within the heterojunction,facilitating ion migration for visual sensing with synaptic behaviors.The abundant reversible hydrogen bonds in the ionogel endow the skin with remarkable mechanical flexibility and self-healing properties.We assembled a neuromorphic visual skin equipped with a 5×5 photosynapse array,capable of sensing and memorizing diverse light patterns.
文摘目的探讨可视穿刺针式肾镜治疗特殊类型肾结石的临床疗效及安全性。方法 2016年6月-2017年8月,采用F4.8铂立可视穿刺针式肾镜对46例特殊类型肾结石患者进行钬激光碎石术,其中肾盏憩室内结石8例,肾下盏结石[肾盂肾下盏漏斗夹角(IPA)<30°]7例,输尿管软镜治疗失败4例,集合系统无扩张肾结石17例,儿童肾结石4例,乙状结肠直肠膀胱术(Mainz-Ⅱ)术后并发肾结石6例。结石大小<1.5 cm 28例、大小>1.5 cm 18例,结石平均直径(1.6±0.4)cm。位于肾下盏、中盏、上盏、肾盂合并肾盏结石分别为20、10、5和11例。术中均"一针见石"建立经皮肾手术通道后碎石。结果术中所有患者均采用单通道,35例F4.8可视肾镜钬激光碎石,11例较大铸型结石术中再扩至F20行钬激光或超声碎石清石术,手术时间为25~50 min,平均为(37.4±9.2)min,术后35例完全无管化、11例留置肾造瘘管或双J管,术后所有患者均未出现活动性出血,3例患者出现发热,经常规抗感染治疗后,症状很快消失,术后住院时间为(2.4±0.8)d,术后1个月结石清除率为91.3%(42/46)。4例有残石患者辅助予以体外冲击波碎石、物理振动及药物促进排石治疗,再随访1个月结石均排净。结论 F4.8可视穿刺针式肾镜治疗特殊类型肾结石更加安全有效,成功率高,清石率高,且并发症低,近似无出血手术,患者恢复快,值得临床推广应用。
基金supported by the National Key R&D Program of China(Grant Nos.2021YFF0704300 and 2020YFA0712400)the National Natural Science Foundation of China(Grant Nos.62072280,61771009,61932018,62072441,32241027,and T2225007)+1 种基金the open project of BGI-Shenzhen,Shenzhen 518000,China(Grant No.BGIRSZ20220005)the Natural Science Foundation of Ningxia Province,China(Grant No.2023AAC05036).
文摘The release of AlphaFold2 has sparked a rapid expansion in protein model databases.Efficient protein structure retrieval is crucial for the analysis of structure models,while measuring the similarity between structures is the key challenge in structural retrieval.Although existing structure alignment algorithms can address this challenge,they are often time-consuming.Currently,the state-of-the-art approach involves converting protein structures into three-dimensional(3D)Zernike descriptors and assessing similarity using Euclidean distance.However,the methods for computing 3D Zernike descriptors mainly rely on structural surfaces and are predominantly web-based,thus limiting their application in studying custom datasets.To overcome this limitation,we developed FP-Zernike,a user-friendly toolkit for computing different types of Zernike descriptors based on feature points.Users simply need to enter a single line of command to calculate the Zernike descriptors of all structures in customized datasets.FP-Zernike outperforms the leading method in terms of retrieval accuracy and binary classification accuracy across diverse benchmark datasets.In addition,we showed the application of FP-Zernike in the construction of the descriptor database and the protocol used for the Protein Data Bank(PDB)dataset to facilitate the local deployment of this tool for interested readers.Our demonstration contained 590,685 structures,and at this scale,our system required only 4-9 s to complete a retrieval.The experiments confirmed that it achieved the state-of-the-art accuracy level.FP-Zernike is an open-source toolkit,with the source code and related data accessible at https://ngdc.cncb.ac.cn/biocode/tools/BT007365/releases/0.1,as well as through a webserver at http://www.structbioinfo.cn/.
文摘It is our great honor to announce the publication of this special section on AI and big data analytics in biology and medicine in the Journal of Computing Science and Technology(JCST).As more and more modern biological and medical data are produced,artificial intelligence(AI)and big data analytics are playing an increasingly important role in helping to draw meaningful and logical conclusions about biology and medicine.
基金National Natural Science Foundation of China(Nos.32370021 and 31860008)the Innovative team program of the Department of Education of Guangdong Province(Nos.2022KCXTD015 and 2022ZDJS020)+75 种基金the Project of Fungi Investigation in Tomur Mountains National Nature Reserve(2021-01-139-2)the National Natural Science Foundation of China(No.32100012)the Science and Technology Bureau of Guangzhou City(202201011618)to acknowledge Zhongkai University of Agriculture and Engineering,talent funding(Grant number KA210319288)the Guangzhou Science and Technology Plan Project(2023A04J1427)the Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China,Guangdong(KA21031C502)Zhongkai University of Agriculture and Engineering,Guangzhou,Guangdong,China(KA22016B746)for financial research supportthe UP System Balik PhD Program(OVPAA-BPhD-2022-02)Yunnan Department of Sciences and Technology of China(Grant No:202101AS070045,202205AM070007,202302AE090023,202303AP140001)the financial support provided by the Distinguished Scientist Fellowship Program(DSFP)at King Saud University in Riyadh,Saudi ArabiaScience&Engineering Research Board(SERB),Department of Science&Technology(DST)Govt.of India(Scheme No.CRG/2020/006053)Institution of Eminence(IoE)Scheme,Ministry of Human Resource and Development(MHRD),Govt.of India(No.R/Dev/D/IoE/Incentive/2021-22/32387)for providing financial supportGenivaldo Alves-Silva,Elisandro R.Drechsler-Santos,Rosa M.B.da Silveira,and Aristóteles Góes-Neto are supported by Conselho Nacional de Desenvolvimento Científico e Tecnológico(CNPq)(Grant No.153025/2022-0,310150/2022-1,308122/2019-4,308880/2022-6,respectively)the CNPq and FAPESC under the PROTAX program(Grant No.FAPESC 2021TR390,Grant No.CNPq 441821/2020-0)and M.E.Engels for collectionsde Desenvolvimento Científico e Tecnológico(CNPq),Brazil,that provided research grants to B.T.Goto(proc.306632/2022-5)support from the National Science and Technology Council is acknowledged(101-2621-B-019-001-MY3)supported by Prof.Dr.M.Schnittler(University of Greifswald,Germany),through the DFG project RESPONSE(RTG2010)study by Ralaiveloarisoa Asupported by the Today’s Flora for Tomorrow project funded by a generous donor through the Kew Foundation,and by a grant from the Bentham-Moxon Trustsupported by the Bulgarian National Science Fund(Grant no.KP-06-N51/10/16.11.2021)the herbarium at the Botanic Garden and Botanical Museum Berlin received support from the SYNTHESYS Plus Project http://www.synthesys.info,which is financed by the H2020 Research Infrastructures Programme(Grant no.DE-TAF-8193)providing tuition fee scholarship.The Center for Yunnan Plateau Biological Resources Protection and Utilization,College of Biological Resource and Food Engineering,Qujing Normal University is thanked for the facilities provided for the research worksupported by the National Natural Science Foundation of China(No.32060012)Muhammad Usman and Abdul Nasir Khalid would like to thank Dr.Kamran Habib,Dr.Muhammad Ali,Mr.Mohammad Aijaz Ahmad and Mr.Muhammad Shafiq for accompanying during the collection surveythe Science and Engineering Research Board(SERB)the Department of Science and Technology,Government of India,for their financial support through CRG/2020/000668 projectthe MACS Agharkar Research Institute in Pune,for providing the lab resources and motivating us in our research workFunding Scheme for Research and Innovation grant for the project“Discovery of new antivirals using cultures of filamentous fungi collected in Europe and Thailand as compound sources(JFS20ST-127 Antiviralfun,P2150844)”BIOTEC-Novartis collaboration for microbial bioprospecting project(P20-52031)to CSIR-HRDG,India,for providing her with financial assistance as part of the JRF fellowship(09/0670(13602)/2022-EMR-I)to Javier Etayo(Pamplona)for his valuable suggestionsNational Science Foundation of China(No.31870528)support from Iran National Science Foundation(INSF,no.4000655)Coordenação de Aperfeiçoamento de Pessoal de Nível Superior-Brasil(CAPES)-Finance Code 001 who provided a visiting professorship to the first authorsupporting this work with a PhD’s scholarship to LAS(140847/2019-7)a research grant to MESC(307569/2019-5)and for financial support in the Universal project(Process:437097/2018-8ERDF-A way of making Europe(Grant PID2021-128068NB-100)the Department of Biotechnology(DBT),Government of India(Grant no.BT/PR/0054/NDB/52/94/2007)support under the project‘Establishment of Microbial Culture Collection(NCMR-NCCS).’Gajanan Mane is thankful to the University Grants Commission,Delhi(India)for the senior research fellowship(File No.16-6(Dec.2017)/2018(NET/CSIR)Rohit Sharma thanks the Department of Biotechnology(DBT),Government of India(Grant no.BT/PR25490/NER/95/1220/2017 dated 28.06.2018),for financial supportthe grant from the Guangdong Rural Science and Technology Commissioner project(KTP20210313)the Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China,Guangdong(KA21031C501)the Innovative Team program of the Department of Education of Guangdong Province(2023KCXTD018/2022KCXTD015)Extramural Research-SERB,DST(EMR/2016/003078)Government of India for the financial assistanceto‘The PCCF’of the Tamil Nadu Forest Department for providing permission(E2/20458/2017)assistance and support during field visit in the Eastern Ghats.Malarvizhi Kaliyaperumal and Kezhocuyi Kezo thank RUSA 2.0(Theme-1,Group-1/2021/49)for providing grantthe Tamil Nadu State Council for Higher Education,Chennai(RGP/2019-20/MU/HECP-0040)for financial assistancethe National Science Foundation of China(No.31870528)support under statutory funds from the W.Szafer Institute of Botany,Polish Academy of Sciencesto ICMBio(Instituto Chico Mendes de Conservação da Biodiversidade)and IF(Instituto Florestal)for the collecting permits#38466-2 and#260108-001.102/2015,respectivelyinanced in part by Coordination of Improvement of Higher Education Personnel-Brazil(CAPES)-Finance Code 001 and by the National Council for Scientific and Technological Development(to LFPG and Proc.305269/2018-6 to AR)to LFPG and Proc.305269/2018-6 to AR)the Program CAPES-PrInt,process number 88887.310463/2018-00Mobility numbers#88887.468939/2019-00 and#88887.571230/2020-00the Coordenação de Aperfeiçoamento de Pessoal de Nível Superior CAPES(processes numbers CAPES 88887.360774/2019-00)Conselho Nacional Desenvolvimento Científico e Tecnológico CNPq(ONDACBC:465764/2014-2 and NEXUS:441305/2017-2)the Fundação de AmparoàCiência e Tecnologia de Pernambuco-FACEPE(BFP-0046-5.01/20,APQ-0350-2.12/19 and APQ 1527-5.01/22)the Conselho Nacional de Desenvolvimento Científico e Tecnológico-CNPq(Proc.312606/2022-2)the National Natural Science Foundation of China(Project ID:32060005)and the Yunnan Fundamental Research Project(202201AW070001)the National Natural Science Foundation of China(No.32260004)Yunnan Revitalization Talents Support Plan(High-End Foreign Experts Program)the Key Laboratory of Yunnan Provincial Department of Education of the Deep-Time Evolution on Biodiversity from the Origin of the Pearl River for their support.Xing-Can Peng and Ting-Chi Wen acknowledge the support by the National Natural Science Foundation of China(No.32060012)Department of Sciences and Technology of China(No.202202AE090091)the National Natural Science Foundation of China(Grant No.32200015)the foundation of the Guangzhou bureau of science and technology(Grant No.2023A04J1425)Thailand Science Research and Innovation(TSRI)for the grant“Biodiversity,taxonomy,phylogeny and evolution of Colletotrichum on Avocado,Citrus,Durian and Mango in northern Thailand”(Grant no.652A01003)the National Natural Science Foundation of China(No.NSFC 32260004)and the Yunnan Revitalization Talents Support Plan(Young Talents Program and High-End Foreign Experts Program)The Center for Yunnan Plateau Biological Resources Protection and Utilization,College of Biological Resource and Food Engineering,Qujing Normal University for the facilities provided for the research workthe National Natural Science Foundation of China(Grant no.31600019)the Modern Agricultural Industry Technology System Flower Innovation Team of Guangdong Province(Grant no.2023KJ121)the Project of Educational Commission of Guangdong Province of China(Grant no.2021KTSCX045)the research productivity fellowship(Grant No.303834/2020-0)the Eminent scholar offered by Kyun Hee Universitythe Chinese Research Fund,Grant number E1644111K1,titled“Flexible introduction of the high-level expert program,Kunming Institute of Botany,Chinese Academy of Sciences”for financial supportthe Italian National Antarctic Research Program for funding Antarctic campaingssupport to the Mycological Section of the MNA and the Culture Collection of Antarctic fungi(MNA-CCFEE),University of Tuscia,Italy.
文摘This article is the 17th in the Fungal Diversity Notes series which allows the researchers to publish fungal collections with updated reports of fungus-host and fungus-geography.Herein we report 97 taxa with four new genera distributed in three phyla(Ascomycota,Glomeromycota and Mucoromycota),11 classes,38 orders and 62 families collected from various regions worldwide.This collection is further classified into taxa from 69 genera with four novel genera namely Jinshana,Lithophyllospora,Parapolyplosphaeria and Stegonsporiicola.Furthermore,71 new species,21 new records,one new combination and four novel phylogenetic placements are provided.The new species comprise Acrocalymma estuarinum,Aggregatorygma isidiatum,Alleppeysporonites elsikii,Amphibambusa aquatica,Apiospora hongheensis,Arthrobotrys tachengensis,Calonectria potisiana,Collariella hongheensis,Colletotrichum squamosae,Corynespora chengduensis,Diaporthe beijingensis,Dicellaesporites plicatus,Dicellaesporites verrucatus,Dictyoarthrinium endophyticum,Distoseptispora chiangraiensis,Dothiora eucalypti,Epicoccum indicum,Exesisporites chandrae,Fitzroyomyces pseudopandanicola,Fomitiporia exigua,Fomitiporia rondonii,Fulvifomes subthailandicus,Gigaspora siqueirae,Gymnopus ailaoensis,Hyalorbilia yunnanensis,Hygrocybe minimiholatra,H.mitsinjoensis,H.parviholatra,H.solis,H.vintsy,Helicogermslita kunmingensis,Jinshana tangtangiae,Kirschsteiniothelia dujuanhuensis,Lamproderma subcristatum,Leucoagaricus madagascarensis,Leucocoprinus mantadiaensis,Lithophyllospora australis,Marasmius qujingensis,Melomastia aquilariae,Monoporisporites jansoniusii,M.pattersonii,Monoporisporites valdiyae,Mucispora maesotensis,Mucor soli,Muyocopron yunnanensis,Nigrospora tomentosae,Ocellularia psorirregularis,Ophiocordyceps duyunensis,Oxneriaria nigrodisca,Oxydothis aquatica,O.filiforme,Phacidiella xishuangbannaensis,Phlebiopsis subgriseofuscescens,Pleurothecium takense,Pleurotus tuber-regium,Pseudochaetosphaeronema puerensis,Pseudodactylaria guttulate,Racheliella chinensis,Rhexoacrodictys fangensis,Roussoella neoaquatica,Rubroboletus pruinosus,Sanghuangporus subzonatus,Scytalidium assmuthi,Shrungabeeja kudremukhensis,Spirographa skorinae,Stanjehughesia bambusicola,Stegonsporiicola aurantiaca,Umbelopsis hingganensis,Vararia tenuata,Verruconis pakchongensis,Wongia bandungensis,and Zygosporium cymodoceae.The new combination is Parapolyplosphaeria thailandica(≡Polyplosphaeria thailandica).The 21 new hosts,geographical and habitat records comprise Acrocalymma fici,Apiculospora spartii,Aspergillus subramanianii,Camposporium ramosum,Clonostachys rogersoniana,Colletotrichum brevisporum,C.plurivorum,Collybiopsis gibbosa,Dictyosporium tratense,Distoseptispora adscendens,Exosporium livistonae,Ganoderma gibbosum,Graphis mikuraensis,Gymnosporangium paraphysatum,Lasiodiplodia thailandica,Moesziomyces bullatus,Penicillium cremeogriseum,P.echinulonalgiovense,P.javanicum,P.lanosocoeruleum,P.polonicum,and Pleurotus tuber-regium.Graphis chlorotica,G.panhalensis and G.parilis are given as novel phylogenetic placements.In addition,we provide the morphology of Tarzetta tibetensis which was missing in the previous Fungal Diversity Notes 1611–1716.Identification of characterization of all these taxa are supported by morphological and multigene phylogenetic analyses.
基金supported by the Strategic Priority Research Program of the Chinese Academy of Sciences(Grant No.XDB0810000)the Beijing Municipal Science and Technology Project,China(Grant No.Z241100007724009).
文摘(S)-Pregabalin(S-PGB)is extensively employed in analgesic therapy.One of the current chemical processes used to produce S-PGB involves the Hofmann rearrangement of(R)-3-isobutyl glutaric acid monoamide(R-IBM).However,the chemical resolution of R-IBM is inefficient and environmentally unsustainable.In this study,we established an enzyme-catalyzed route to R-IBM that proceeds with exceptional optical purity and yield.We successfully resculpted the substrate-binding pocket of D-hydantoinase by attenuating the steric hindrance and enhancing hydrophilicity,resulting in accelerated substrate transport and restricted side-chain rotation during the asymmetric hydrolysis process.Notably,both optical purity and yield for the generation of R-IBM from the prochiral substrate 3-isobutyl glutarimide(IBI)were enhanced for the M3(L64A/F66H/C318T)mutant;the enantiomeric excess increased from 65.51%±5.85%to 98.62%±0.28%(ee_(p))and k_(cat)/K_(m) increased from 14.92 to 207.06 s^(-1)·M^(-1).The ancestral sequence reconstruction(ASR)and consensus analyses guided further engineering of the flexible C-terminal region of D-hydantoinase to enhance the thermostability of the enzyme.The final mutant,M6(L64A/F66H/C318T/R99G/A265P/G466N/E470A),demonstrated a remarkable improvement in R-IBM production efficiency;thus,500 mM IBI was completely transformed into R-IBM in 24 h.This study therefore showcases a new enzyme that offers a green,enzymatic route for R-IBM production.
基金supported by the National Key Research and Development Program of China under Grant No.2021YFF0704300the National Natural Science Foundation of China under Grant Nos.32241027,62072441,and 62072283.
文摘Advances in cryo-electron tomography(cryo-ET)have enabled the visualization of molecules within their native cellular environments in three-dimensions(3D).These visualizations are essential for studying the functions of biological entities in their natural conditions.Recently,deep learning techniques have shown significant success in tackling the challenge of particle detection in cryo-ET data.However,accurately identifying and classifying multi-class molecules remain challenging due to factors like low signal-to-noise ratios and the wide range of particle sizes.In this study,we introduce a novel framework CFNPicker for 3D object detection applied to cryo-ET analysis.A major advantage of our method is the design of central feature network(CFN)to integrate central features across multiple scales,allowing for the accurate detection of both small(⩽200)and large(⩾600)molecules.Additionally,we propose an adaptive weighted sampling training strategy to distinguish the complex noise distribution in the background,reducing false positive particles.We also construct the localization label to explicitly utilize the size and position variations of multi-class protein structures.Compared with existing methods,CFN improves the F1 score for classification by 3.6%,7.3%,6.6%,and 5.1%for the four smallest molecules tested respectively,while preserving similar or higher F1 scores for other molecules analyzed.
文摘Single particle analysis, which can be regarded as an average of signals from thousands or even millions of particle projections, is an efficient method to study the three-dimensional structures of biological macro- molecules. An intrinsic assumption in single particle analysis is that all the analyzed particles must have identical composition and conformation. Thus specimen heterogeneity in either composition or conformation has raised great challenges for high-resolution analysis. For particles with multiple conformations, inaccurate align- ments and orientation parameters will yield an averaged map with diminished resolution and smeared density. Besides extensive classification approaches, here based on the assumption that the macromolecular complex is made up of multiple rigid modules whose relative orien- tations and positions are in slight fluctuation around equilibriums, we propose a new method called as local optimization refinement to address this conformational heterogeneity for an improved resolution. The key idea is to optimize the orientation and shift parameters of each rigid module and then reconstruct their three-dimen- sional structures individually. Using simulated data of 80S/70S ribosomes with relative fluctuations between the large （60S/50S） and the small （40S/30S） subunits, we tested this algorithm and found that the resolutions of both subunits are significantly improved. Our method provides a proof-of-principle solution for high-resolutionsingle particle analysis of macromolecular complexes with dynamic conformations.
基金National Key R&D Program of China(2017YFB1002900)National Natural Science Foundation of China(51602024,61420106014,61574017,61775019)+2 种基金Beijing Nova Program(Z171100001117047)Bejing Outstanding Young Scientist Program(BJJWZYJH01201910007022)Opened Fund of the State Key Laboratory on Integrated.Optoelectronics(IOSKL2017KF13).
文摘Lead halide perovskites have drawn extensive attention over recent decades owing to their outstanding photo-electric performances.However,their toxicity and instability are big issues that need to be solved for further commercialization.Herein,we adopt a facile dry ball milling method to synthesize lead-free Cs3Cu2X5(X=I,CI)perovskites with photoluminescence(PL)quantum yield up to 60%.The optical features including broad emission spectrum,large Stokes shift,and long PL lifetime can be attributed to self-trapped exciton recombination.The as-synthesized blue emissive Cs3Cu2I5 and green emissive Cs3Cu2Cl5 lead-free perovskite powders have good thermal stability and photostability.Furthermore,UV-pumped phosphor-converted light-emitting diodes were obtained by using Cs3Cu2I5 and Cs3Cu2Cl5 as phosphors.
基金supported by the National Natural Science Foundation of China(Nos.61932018,32241027,62072441,62272326,62132015,and U22A2037)the Beijing Municipal Administration of Hospitals Incubating Program(No.PX2021013).
文摘Kirsten rat sarcoma viral oncogene homolog(namely KRAS)is a key biomarker for prognostic analysis and targeted therapy of colorectal cancer.Recently,the advancement of machine learning,especially deep learning,has greatly promoted the development of KRAS mutation detection from tumor phenotype data,such as pathology slides or radiology images.However,there are still two major problems in existing studies:inadequate single-modal feature learning and lack of multimodal phenotypic feature fusion.In this paper,we propose a Disentangled Representation-based Multimodal Fusion framework integrating Pathomics and Radiomics(DRMF-PaRa)for KRAS mutation detection.Specifically,the DRMF-PaRa model consists of three parts:(1)the pathomics learning module,which introduces a tissue-guided Transformer model to extract more comprehensive and targeted pathological features;(2)the radiomics learning module,which captures the generic hand-crafted radiomics features and the task-specific deep radiomics features;(3)the disentangled representation-based multimodal fusion module,which learns factorized subspaces for each modality and provides a holistic view of the two heterogeneous phenotypic features.The proposed model is developed and evaluated on a multi modality dataset of 111 colorectal cancer patients with whole slide images and contrast-enhanced CT.The experimental results demonstrate the superiority of the proposed DRMF-PaRa model with an accuracy of 0.876 and an AUC of 0.865 for KRAS mutation detection.
基金supported by the National Natural Science Foundation of China (Nos. U1611263, U1611261, 61232001, 61472397, 61502455, and 61672493)the Special Program for Applied Research on Super Computation of the NSFC-Guangdong Joint Fund (the second phase)+1 种基金the Strategic Priority Research Program of Chinese Academy of Sciences (No. XDB08030202)the National Key Research and Development Program of China (No. 2017YFA0504702)
文摘Electron Tomography （ET） is an important method for studying cell ultrastructure in three-dimensional （3D） space. By combining cryo-electron tomography of frozen-hydrated samples （cryo-ET） and a sub-tomogram averaging approach, ET has recently reached sub-nanometer resolution, thereby realizing the capability for gaining direct insights into function and mechanism. To obtain a high-resolution 3D ET reconstruction, alignment and geometry determination of the ET tilt series are necessary. However, typical methods for determining geometry require human intervention, which is not only subjective and easily introduces errors, but is also labor intensive for high-throughput tomographic reconstructions. To overcome these problems, we have developed an automatic geometry-determination method, called AutoGDeterm. By taking advantage of the high-contrast re-projections of the Iterative Compressed-sensing Optimized Non-Uniform Fast Fourier Transform （NUFFT） reconstruction （ICON） and a series of numerical analysis methods, AutoGDeterm achieves high-precision fully automated geometry determination. Experimental results on simulated and resin-embedded datasets show that the accuracy of AutoGDeterm is high and comparable to that of the typical ＂manual positioning＂ method. We have made AutoGDeterm available as software, which can be freely downloaded from our website http：//ear.ict.ac.cn.
文摘Super-resolution microscopy techniques have overcome the limit of optical diffraction. Recently, the Bayesian analysis of Bleaching and Blinking data （3B） method has emerged as an important tool to obtain super-resolution fluorescence images. 3B uses the change in information caused by adding or removing fiuorophores in the cell to fit the date. When adding a new fluorophore, 3B selects a random initial position, optimizes this position and then determines its reliability. However, the fluorophores are not evenly distributed in the entire image region, and the fluorescence intensilty at a given position positively correlates with the probability of observing a fluorophore at this position. In this paper, we present a Bayesian analysis of Bleaching and Blinking microscopy method based on fluorescence intensity distribution （FID3B）. We utilize the intensity distribution to select more reliable positions as the initial positions of fluorophores. This approach can improve the reconstruction results and significantly reduce the computational time. We validate the perfor. mance of our method using both simulated date and experimental date from cellular structures. The results confirm the effectiveness of our method.
基金supported by the National Natural Science Foundation of China(No.21774102).
文摘As a weak non-covalent interaction,hydrogen bond(H-bond)is highly susceptible to the environmental interference.However,the direct quantification of a single H-bond under an interference-free condition is still a challenge.Herein,the intramolecular H-bond in a model system,poly(N-isopropylacrylamide),is studied in high vacuum by single-molecule atomic force microscopy and steered molecular dynamics simulations,which allows the precise quantification of H-bond strength in an interference-free state.Control experiments show that the H-bond is significantly weakened in nonpolar solvent,even if the dielectric constant is very close to vacuum.If a polar solvent is used as the environment,the H-bond will be further weaker or even broken.These results imply that for experiments in any liquid environment,the H-bond strength(△G)will be only -50% or even less of that measured in vacuum.Further analysis shows that in liquid environments,AG decays in a quasi-linear way with the increase of the dielectric constant(ε).For H-bond studies in future,the result measured in vacuum can be set as the standard value,namely,the inherent strength.This approach will provide fundamental insights into the H-bond participated nano-structures and materials in different environments.
文摘The rapid advancement of high-throughput sequencing technologies and the explosive growth of biological data have revolutionized the field of bioinformatics and biomedical computing[1-4].The generation of vast amounts of genomic,transcriptomic,proteomic,and metabolomic data has created unprecedented opportunities for understanding the complexities of biological systems and their implications for human health[5-6].Moreover,the emergence of spatial omics technologies,such as spatial transcriptomics and spatial proteomics,has added a new dimension to our understanding of the spatial organization and heterogeneity of biological systems.These cutting-edge technologies enable the mapping of molecular information at a high spatial resolution,providing valuable insights into the tissue microenvironment and the interplay between cells in various physiological and pathological conditions[7-10].
文摘Recent years have witnessed exponential growth in both the volume and complexity of biomedical data generated,which encompasses a diverse array of sources,including genomic sequences,clinical imaging,electronic health records,and real-time biometric sensing.This deluge of data has surpassed our traditional methods'abilities to efficiently process,analyze,store,and interpret,posing substantial challenges across the biomedical and healthcare sectors.
