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Recent advances in protein conformation sampling by combining machine learning with molecular simulation

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Chinese Physics B 2024年第3期33卷 80-87页

作者：唐一鸣杨中元姚逸飞周运谈圆王子超潘瞳熊瑞孙俊力韦广红 Department of Physics State Key Laboratory of Surface Physicsand Key Laboratory for Computational Physical Sciences (Ministry of Education)Shanghai 200438China

The rapid advancement and broad application of machine learning(ML)have driven a groundbreaking revolution in computational *** of the most cutting-edge and important applications of ML is its integration with molecular simulations to improve the sampling efficiency of the vast conformational space of large *** review focuses on recent studies that utilize ML-based techniques in the exploration of protein conformational *** first highlight the recent development of ML-aided enhanced sampling methods,including heuristic algorithms and neural networks that are designed to refine the selection of reaction coordinates for the construction of bias potential,or facilitate the exploration of the unsampled region of the energy ***,we review the development of autoencoder based methods that combine molecular simulations and deep learning to expand the search for protein ***,we discuss the cutting-edge methodologies for the one-shot generation of protein conformations with precise Boltzmann ***,this review demonstrates the promising potential of machine learning in revolutionizing our insight into the complex conformational ensembles of proteins.

关键词： machine learning molecular simulation protein conformational space enhanced sampling

A comparison of statistical learning of naturalistic textures between DCNNs and the human visual hierarchy

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Science China Technological sciences 2024年第8期67卷 2310-2318页

作者： LU XinCheng YUAN ZiQi ZHANG YiChi AI HaiLin CHENG SiYuan GE YiRan FANG Fang CHEN NiHong Department of Psychological and Cognitive sciences Tsinghua University Department of Computer Science and Technology Tsinghua University School of Psychological and Cognitive sciences and Beijing key laboratory of Behavior and Mental Health Peking University key laboratory of Machine Perception (Ministry of education) Peking University Peking-Tsinghua Center for Life sciences Peking University IDG/McGovern Institute for brain Research Peking University State key laboratory of brain and Cognitive Science Institute of Psychology Chinese Academy of Sciences IDG/McGovern Institute for brain Research Tsinghua University

The visual system continuously adapts to the statistical properties of the environment. Existing evidence shows a close resemblance between deep convolutional neural networks(CNNs) and primate visual stream in neural selectivity to naturalistic textures above the primary visual processing stage. This study delves into the mechanisms of perceptual learning in CNNs,focusing on how they assimilate the high-order statistics of natural textures. Our results show that a CNN model achieves a similar performance improvement as humans, as manifested in the learning pattern across different types of high-order image statistics. While L2 was the first stage exhibiting texture selectivity, we found that stages beyond L2 were critically involved in learning. The significant contribution of L4 to learning was manifested both in the modulations of texture-selective responses and in the consequences of training with frozen connection weights. Our findings highlight learning-dependent plasticity in the mid-to-high-level areas of the visual hierarchy. This research introduces an AI-inspired approach for studying learning-induced cortical plasticity, utilizing DCNNs as an experimental framework to formulate testable predictions for empirical brain studies.

关键词： CNN perceptual learning naturalistic texture psychophysics

Microplastic exposure disturbs sleep structure,reduces lifespan,and decreases ovary size in Drosophila melanogaster

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Zoological Research 2024年第4期45卷 805-820页

作者： Wei Yan Zi-Jie Li Zi-Yi Lin Shu-Qin Ji William Ka Fai Tse Zhi-Qiang Meng Chang Liu Lei Li Shenzhen-Hong Kong Institute of brain Science Shenzhen Institute of Advanced TechnologyChinese Academy of SciencesShenzhenGuangdong 518000China CAS key laboratory of brain Connectome and Manipulation the Brain Cognition and Brain Disease InstituteShenzhen Institute of Advanced TechnologyChinese Academy of SciencesShenzhenGuangdong 518000China laboratory of Developmental Disorders and Toxicology Center for Promotion of International Education and ResearchFaculty of AgricultureKyushu UniversityFukuokaFukuoka 819-0395Japan Shenzhen key laboratory of Drug Addiction the Brain Cognition and Brain Disease InstituteShenzhen Institute of Advanced TechnologyChinese Academy of SciencesShenzhenGuangdong 518000China Guangdong Provincial key laboratory of brain Connectome and Behavior Brain Cognition and Brain Disease InstituteShenzhen Institute of Advanced TechnologyChinese Academy of SciencesShenzhenGuangdong 518000China

The organ-specific toxicity resulting from microplastic(MP)exposure has been extensively explored,particularly concerning the gut,liver,testis,and ***,under natural conditions,these effects are not restricted to specific organs or *** whether MP exposure presents a systemic threat to an entire organism,impacting factors such as lifespan,sleep,and fecundity,is *** this study,we investigated the effects of dietary exposure to two different doses of MPs(1–5μm)using the terrestrial model organism Drosophila *** indicated that the particles caused gut damage and remained within the digestive *** MP exposure significantly shortened the lifespan of adult *** short-term exposure disrupted sleep patterns,increasing the length of daytime sleep ***,one week of MP exposure reduced ovary size,with a trend towards decreased egg-laying in mated *** MPs did not penetrate the brain or ovaries,transcriptome analysis revealed altered gene expression in these *** the ovary,Gene Ontology(GO)analysis indicated genotoxic effects impacting inflammation,circadian regulation,and metabolic processes,with significant impacts on extracellular structure-related *** the brain,GO analysis identified changes in pathways associated with proteolysis and carbohydrate ***,this study provides compelling evidence of the systemic negative effects of MP exposure,highlighting the urgent need to address and mitigate environmental MP pollution.

关键词： Microplastics Sleep Lifespan Reproduction Risk assessment Drosophila melanogaster

Rapid Unconscious Acquisition of Conditioned Fear with Low-Spatial-Frequency but Emotionally Neutral Stimuli

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Research 2024年第1期2023卷 753-762页

作者： Yujie Chen Si Chen Zhongju Sun Xilei Zhang Xiangyong Yuan Liang Wang Yi Jiang State key laboratory of brain and Cognitive sciences CAS Center for Excellence in Brain Science and Intelligence TechnologyInstitute of PsychologyChinese Academy of SciencesBeijing 100101China Department of Psychology University of Chinese Academy of SciencesBeijing 100049China Chinese Institute for brain Research Beijing 102206China CAS key laboratory of Mental Health Institute of PsychologyChinese Academy of SciencesBeijing 100101China

It has long been proposed that emotionally“prepared”(i.e.,fear-related)stimuli are privileged in the unconscious acquisition of conditioned ***,as fear processing is suggested to highly depend on the coarse,low-spatial-frequency(LSF)components of the fear-related stimuli,it is plausible that LSF may play a unique role in the unconscious fear conditioning even with emotionally neutral ***,we provided empirical evidence that,following classical fear conditioning,an invisible,emotionally neutral conditioned stimulus(CS+)with LSF,but not with high spatial frequency(HSF),can rapidly elicit stronger skin conductance responses(SCRs)and larger pupil diameters than its CS−*** comparison,consciously perceived emotionally neutral CS+with LSF and HSF elicited comparable *** together,these results support that the unconscious fear conditioning does not necessarily entail emotionally prepared stimuli but prioritizes LSF information processing and highlight the crucial distinctions between the unconscious and the conscious fear *** findings not only coincide with the postulation that a rapid,spatial-frequency-dependent subcortical route is engaged in unconscious fear processing but also suggest the existence of multiple routes for conscious fear processing.

关键词： neutral necessarily diameters

Bias distribution and regulation in photoelectrochemical overall water-splitting cells

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National Science Review 2024年第4期11卷 141-150页

作者： Kun Dang Siqin Liu Lei Wu Daojian Tang Jing Xue Jiaming Wang Hongwei Ji Chuncheng Chen Yuchao Zhang Jincai Zhao key laboratory of Photochemistry CAS ResearchEducation Center for Excellence in Molecular Sciences Institute of Chemistry Chinese Academy of Sciences University of Chinese Academy of sciences

The water oxidation half-reaction at anodes is always considered the rate-limiting step of overall water splitting（OWS）,but the actual bias distribution between photoanodes and cathodes of photoelectro chemical（PEC） OWS cells has not been investigated *** this work,we find that,for PEC cells consisting of photoanodes（nickel-modified n-Si [Ni/n-Si] and α-Fe2O3） with low photovoltage(Vph 1V,the bias required for cathode activation can be significantly reduced,exhibiting a kinetics-controlled *** investigations show that the bias distribution can be regulated by tuning the electrolyte pH and using alternative half-reaction ***,a volcano plot is presented for the rational design of the overall reactions and unbiased PEC *** by this,an unbiased PEC cell consisting of a simple Ni/n-Si photoanode and Pt cathode is assembled,delivering a photo current density of 5.3±0.2 mA cm-2.

关键词： photoelectrochemistry overall reaction cell bias distribution photoanode water splitting

Polymer: Non-fullerene acceptor heterojunction-based phototransistor for short-wave infrared photodetection

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Nano Research 2024年第4期17卷 3087-3095页

作者： Jing Li Weigang Zhu Yang Han Yanhou Geng Wenping Hu key laboratory of Organic Integrated Circuits of Ministry of education&key laboratory of Molecular Optoelectronic sciences School of Science&Collaborative Innovation Center of Chemical Science and Engineering(Tianjin)Tianjin UniversityTianjin 300072China key laboratory of Organic Integrated Circuits of Ministry of education&key laboratory of Molecular Optoelectronic sciences School of Materials Science and EngineeringTianjin UniversityTianjin 300072China

It remains full of challenge for extending short-wave infrared(SWIR)spectral response and weak-light detection in the context of broad spectral responses for *** this work,a novel poly(2,5-bis(4-hexyldodecyl)-2,5-dihydro-3,6-di-2-thienyl-pyrrolo[3,4-c]pyrrole-1,4-dione-alt-thiophene)(PDPPT3-HDO):COTIC-4F organic bulk-heterojunction is prepared as active layer for bulk heterojunction ***3-HDO serves as a hole transport material,while COTIC-4F enhances the absorption of SWIR light to 1020 *** a result,smooth and connected PDPPT3-HDO film is fabricated by blade coating method and exhibits high hole mobility up to 2.34 cm^(2)·V^(-1)·s^(-1) with a current on/off ratio of 4.72×10^(5) in organic thin film ***3-HDO:COTIC-4F heterojunction phototransistors exhibit high responsivity of 2680 A·W^(-1) to 900 nm and 815 A·W^(-1) to 1020 nm,with fast response time(rise time~20 ms and fall time~100 ms).The photosensitivity of the heterojunction phototransistor improves as the mass ratio of non-fullerene acceptors increases,resulting in an approximately two orders of magnitude enhancement compared to the bare polymer ***,the phototransistor exhibits decent responsivity even under ultra-weak light power of 43μW·cm^(-2) to 1020 *** work represents a highly effective and general strategy for fabricating efficient and sensitive SWIR light photodetectors.

关键词： photodetection phototransistor organic semiconductor heterojunction non-fullerene acceptor

Developmental Impairments of Synaptic Refinement in the Thalamus of a Mouse Model of Fragile X Syndrome

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Neuroscience Bulletin 2024年第4期40卷 439-450页

作者： Xiaotong Wu Yali Liu Xiaomeng Wang Lu Zheng Libiao Pan Hao Wang Department of Neurosurgery of Second Affiliated Hospital and School of brain Science and brain Medicine Key Laboratory for Biomedical Engineering of Education MinistryZhejiang University School of MedicineHangzhou310058China Nanhu brain-computer Interface Institute Hangzhou311100China NHC and CAMS key laboratory of Medical Neurobiology MOE Frontier Science Center for Brain Research and Brain Machine IntegrationKey Laboratory of Precise Treatment and Clinical Translational Research of Neurological DiseasesSchool of Brain Science and Brain MedicineZhejiang UniversityHangzhou310058China Lingang laboratory Shanghai200031China

While somatosensory over-reactivity is a common feature of autism spectrum disorders such as fragile X syndrome(FXS),the thalamic mechanisms underlying this remain ***,we found that the developmental elimination of synapses formed between the principal nucleus of V(PrV)and the ventral posterior medial nucleus(VPm)of the somatosensory system was delayed in fragile X mental retardation 1 gene knockout(Fmr1 KO)mice,while the developmental strengthening of these synapses was *** showed excessive VGluT2 puncta in mutants at P12–13,but not at P7–8 or P15–16,confirming a delay in somatic pruning of PrV-VPm *** synaptic function was associated with a reduction in the frequency of quantal AMPA events,as well as developmental deficits in presynaptic vesicle size and *** results uncovered the developmental impairment of thalamic relay synapses in Fmr1 KO mice and suggest that a thalamic contribution to the somatosensory over-reactivity in FXS should be considered.

关键词： Fragile X syndrome Synaptic refinement VPm Sensory over-reactivity

Long-term exposure to aryl hydrocarbon receptor agonist neburon induces reproductive toxicity in male zebrafish(Danio rerio)

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Journal of Environmental sciences 2024年第8期142卷 193-203页

作者： Fucong Zhang Chen Tang Yue Zhu Qian Wang Xin Huang Chunyan Yang Chengyong He Zhenghong Zuo key laboratory of the Ministry of education for Coastal and Wetland Ecosystems School of Life SciencesXiamen UniversityXiamen 361102China

Neburon is a phenylurea herbicide that is widely used worldwide,but its toxicity is poorly *** our previous study,we found that neburon has strong aryl hydrocarbon receptor(AhR)agonist activity,but whether it causes reproductive toxicity is not *** the present study,zebrafish were conducted as a model organism to evaluate whether environmental concentrations of neburon(0.1,1 and 10μg/L)induce reproductive disorder in *** exposure to neburon for 150 days from embryo to adult,that the average spawning egg number in high concentration group was 106.40,which was significantly lower than 193.00in control *** result was mainly due to the abnormal male reproductive behavior caused by abnormal transcription of genes associated with reproductive behavior in the brain,such as *** proportions of spermatozoa in the medium and high concentration groups were 82.40%and 83.84%,respectively,which were significantly lower than 89.45%in control *** result was mainly caused by hormonal disturbances and an increased proportion of apoptotic *** hormonal disruption was due to the significant changes in the transcription levels of key genes in the hypothalamus-pituitary-gonadal axis following neburon *** treatment also significantly activated the AhR signaling pathway,causing oxidative stress damage and eventually leading to a significant increase in apoptosis in the exposed ***,these data filled the currently more vacant profile of neburon toxicity and might provide information to assess the ecotoxicity of neburon on male reproduction at environmentally relevant concentrations.

关键词： Zebrafish Neburon Male reproductive toxicity HPG axis AhR agonist

Soil inorganic amendments produce safe rice by reducing the transfer of Cd and increasing key amino acids in brown rice

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Journal of Environmental sciences 2024年第2期136卷 121-132页

作者： Fanyi Kong Shenggao Lu Zhejiang Provincial key laboratory of Agricultural Resources and Environment Key Laboratory of Environmental Remediation and Ecosystem HealthMinistry of EducationCollege of Environmental and Resource SciencesZhejiang UniversityHangzhou 310058China

The digestibility of cadmium(Cd)in brown rice is directly related to amino acid metabolism in rice and human *** our field study,three kinds of alkaline calcium-rich soil inorganic amendments(SIAs)at three dosages were applied to produce safe rice and improve the quality of rice in Cd-contaminated *** the increased application of SIA,Cd content in iron plaque on rice root significantly increased,the transfer of Cd from rice root to grain significantly decreased,and then Cd content in brown rice decreased *** vitro digestibility of Cd in brown rice was estimated by a physiologically based extraction *** showed that more than 70%of Cd in brown rice could be digested by simulated gastrointestinal *** on the total and digestible Cd contents in brown rice to evaluate the health risk,the application of 2.25 ton SIA/ha could produce safe rice in acidic slightly Cd-contaminated paddy *** amino acids(AAs)in brown rice were determined by high-performance liquid *** contents of 5 key AAs(KAAs)that actively respond to environmental changes increased significantly with the increased application of *** structural equation model indicated that KAAs could be affected by the Cd translocation capacity from rice root to grain,and consequently altered the ratio of indigestible Cd in brown *** formation of indigestible KAAs-Cd complexes by combining KAAs(phenylalanine,leucine,histidine,glutamine,and asparagine)with Cd in brown rice could be considered a potential mechanism for reducing the digestibility of Cd.

关键词： Cadmium digestibility Soil inorganic amendments Safe rice Amino acid Priming effect Health risk