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  1. Article ; Online: Deep language models for interpretative and predictive materials science

    Yiwen Hu / Markus J. Buehler

    APL Machine Learning, Vol 1, Iss 1, Pp 010901-010901-

    2023  Volume 18

    Abstract: Machine learning (ML) has emerged as an indispensable methodology to describe, discover, and predict complex physical phenomena that efficiently help us learn underlying functional rules, especially in cases when conventional modeling approaches cannot ... ...

    Abstract Machine learning (ML) has emerged as an indispensable methodology to describe, discover, and predict complex physical phenomena that efficiently help us learn underlying functional rules, especially in cases when conventional modeling approaches cannot be applied. While conventional feedforward neural networks are typically limited to performing tasks related to static patterns in data, recursive models can both work iteratively based on a changing input and discover complex dynamical relationships in the data. Deep language models can model flexible modalities of data and are capable of learning rich dynamical behaviors as they operate on discrete or continuous symbols that define the states of a physical system, yielding great potential toward end-to-end predictions. Similar to how words form a sentence, materials can be considered as a self-assembly of physically interacted building blocks, where the emerging functions of materials are analogous to the meaning of sentences. While discovering the fundamental relationships between building blocks and function emergence can be challenging, language models, such as recurrent neural networks and long-short term memory networks, and, in particular, attention models, such as the transformer architecture, can solve many such complex problems. Application areas of such models include protein folding, molecular property prediction, prediction of material failure of complex nonlinear architected materials, and also generative strategies for materials discovery. We outline challenges and opportunities, especially focusing on extending the deep-rooted kinship of humans with symbolism toward generalizable artificial intelligence (AI) systems using neuro-symbolic AI, and outline how tools such as ChatGPT and DALL·E can drive materials discovery.
    Keywords Physics ; QC1-999 ; Electronic computers. Computer science ; QA75.5-76.95
    Subject code 006
    Language English
    Publishing date 2023-03-01T00:00:00Z
    Publisher AIP Publishing LLC
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article ; Online: Individual differences in the neural architecture in semantic processing

    Xin Liu / Yiwen Hu / Yaokun Hao / Liu Yang

    Scientific Reports, Vol 14, Iss 1, Pp 1-

    2024  Volume 16

    Abstract: Abstract Neural mechanisms underlying semantic processing have been extensively studied by using functional magnetic resonance imaging, nevertheless, the individual differences of it are yet to be unveiled. To further our understanding of functional and ... ...

    Abstract Abstract Neural mechanisms underlying semantic processing have been extensively studied by using functional magnetic resonance imaging, nevertheless, the individual differences of it are yet to be unveiled. To further our understanding of functional and anatomical brain organization underlying semantic processing to the level of individual humans, we used out-of-scanner language behavioral data, T1, resting-state, and story comprehension task-evoked functional image data in the Human Connectome Project, to investigate individual variability in the task-evoked semantic processing network, and attempted to predict individuals’ language skills based on task and intrinsic functional connectivity of highly variable regions, by employing a machine-learning framework. Our findings first confirmed that individual variability in both functional and anatomical markers were heterogeneously distributed throughout the semantic processing network, and that the variability increased towards higher levels in the processing hierarchy. Furthermore, intrinsic functional connectivities among these highly variable regions were found to contribute to predict individual reading decoding abilities. The contributing nodes in the overall network were distributed in the left superior, inferior frontal, and temporo-parietal cortices. Our results suggested that the individual differences of neurobiological markers were heterogeneously distributed in the semantic processing network, and that neurobiological markers of highly variable areas are not only linked to individual variability in language skills, but can predict language skills at the individual level.
    Keywords Medicine ; R ; Science ; Q
    Subject code 150
    Language English
    Publishing date 2024-01-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article ; Online: Individual differences in the neural architecture in semantic processing.

    Liu, Xin / Hu, Yiwen / Hao, Yaokun / Yang, Liu

    Scientific reports

    2024  Volume 14, Issue 1, Page(s) 170

    Abstract: Neural mechanisms underlying semantic processing have been extensively studied by using functional magnetic resonance imaging, nevertheless, the individual differences of it are yet to be unveiled. To further our understanding of functional and ... ...

    Abstract Neural mechanisms underlying semantic processing have been extensively studied by using functional magnetic resonance imaging, nevertheless, the individual differences of it are yet to be unveiled. To further our understanding of functional and anatomical brain organization underlying semantic processing to the level of individual humans, we used out-of-scanner language behavioral data, T1, resting-state, and story comprehension task-evoked functional image data in the Human Connectome Project, to investigate individual variability in the task-evoked semantic processing network, and attempted to predict individuals' language skills based on task and intrinsic functional connectivity of highly variable regions, by employing a machine-learning framework. Our findings first confirmed that individual variability in both functional and anatomical markers were heterogeneously distributed throughout the semantic processing network, and that the variability increased towards higher levels in the processing hierarchy. Furthermore, intrinsic functional connectivities among these highly variable regions were found to contribute to predict individual reading decoding abilities. The contributing nodes in the overall network were distributed in the left superior, inferior frontal, and temporo-parietal cortices. Our results suggested that the individual differences of neurobiological markers were heterogeneously distributed in the semantic processing network, and that neurobiological markers of highly variable areas are not only linked to individual variability in language skills, but can predict language skills at the individual level.
    MeSH term(s) Humans ; Semantics ; Individuality ; Brain/diagnostic imaging ; Brain/physiology ; Language ; Brain Mapping/methods ; Connectome/methods ; Magnetic Resonance Imaging/methods
    Language English
    Publishing date 2024-01-02
    Publishing country England
    Document type Journal Article
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/s41598-023-49538-8
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Mesoporous black TiO

    Hu, Yiwen / Yan, Zhiyao / Du, Lianghui / Yu, Yongliu / Huang, Wanxia / Shi, Qiwu

    Optics express

    2023  Volume 31, Issue 21, Page(s) 33883–33897

    Abstract: ... Black ... ...

    Abstract Black TiO
    Language English
    Publishing date 2023-10-19
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1491859-6
    ISSN 1094-4087 ; 1094-4087
    ISSN (online) 1094-4087
    ISSN 1094-4087
    DOI 10.1364/OE.503344
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: The relationship between family communication and family resilience in Chinese parents of depressed adolescents: a serial multiple mediation of social support and psychological resilience.

    Zhang, Yinying / Hu, Yiwen / Yang, Min

    BMC psychology

    2024  Volume 12, Issue 1, Page(s) 33

    Abstract: Background: Family resilience plays a crucial role in helping depressed adolescents overcome challenges. However, studies examining family resilience in depressed adolescents are currently scarce. This study, guided by the family resilience framework, ... ...

    Abstract Background: Family resilience plays a crucial role in helping depressed adolescents overcome challenges. However, studies examining family resilience in depressed adolescents are currently scarce. This study, guided by the family resilience framework, aimed to investigate the serial-multiple mediation of social support and psychological resilience between family communication and family resilience in Chinese families of depressed adolescents.
    Methods: In 229 parents of adolescents with major depressive disorder, 20.1% comprises of fathers, while 79.9% comprises of mothers. The mean age of depressed adolescents was 14.84 (±1.76) years, and the mean age of parents of these depressed adolescents was 43.24 (±4.67) years. The Family Resilience Assessment Scale (FRAS), the Psychological Resilience of Parents of Special Children Questionnaire, and the Social Support Rating Scale, Family Assessment Device (FAD) were used to collected data. Descriptive, univariate, and Pearson correlation analyses were used in preliminary analyses. To explore mediation, we employed a serial-multiple mediation model (PROCESS model 6).
    Results: Family communication was positively correlated with family resilience, social support, and psychological resilience. Mediation analysis revealed indirect effects of family communication on family resilience, which were mediated solely by either social support or psychological resilience, or through multiple mediation pathways involving both social support and psychological resilience.
    Conclusions: Family communication positively and directly affects the family resilience of depressed adolescents, and a higher level of social support and psychological resilience can help improve family resilience. These findings not only provide empirical evidence supporting the family resilience framework but also have practical implications for future family interventions targeting depressed adolescents.
    MeSH term(s) Child ; Female ; Humans ; Adolescent ; Adult ; Middle Aged ; Resilience, Psychological ; Depressive Disorder, Major ; Family Health ; Parents/psychology ; Social Support ; Communication ; China
    Language English
    Publishing date 2024-01-18
    Publishing country England
    Document type Journal Article
    ZDB-ID 2705921-2
    ISSN 2050-7283 ; 2050-7283
    ISSN (online) 2050-7283
    ISSN 2050-7283
    DOI 10.1186/s40359-023-01514-7
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Recent advances in developing modified C14 side chain pleuromutilins as novel antibacterial agents.

    Liu, Yue / Zhou, Qinjiang / Huo, Yiwen / Sun, Xiujuan / Hu, Jinxing

    European journal of medicinal chemistry

    2024  Volume 269, Page(s) 116313

    Abstract: Owing to the increasing resistance to most existing antimicrobial drugs, research has shifted towards developing novel antimicrobial agents with mechanisms of action distinct from those of current clinical options. Pleuromutilins are antibiotics known ... ...

    Abstract Owing to the increasing resistance to most existing antimicrobial drugs, research has shifted towards developing novel antimicrobial agents with mechanisms of action distinct from those of current clinical options. Pleuromutilins are antibiotics known for their distinct mechanism of action, inhibiting bacterial protein synthesis by binding to the peptidyl transferase center of the ribosome. Recent studies have revealed that pleuromutilin derivatives can disrupt bacterial cell membranes, thereby enhancing antibacterial efficacy. Both marketed pleuromutilin derivatives and those in clinical trials have been developed by structurally modifying the pleuromutilin C14 side chain to improve their antimicrobial activity. Therefore, this review aims to review advancement in the chemical structural characteristics, antibacterial activities, and structure-activity relationship studies of pleuromutilins, specifically focusing on modifications made to the C14 side chain in recent years. These findings provide a valuable reference for future research and development of pleuromutilins.
    MeSH term(s) Pleuromutilins ; Anti-Bacterial Agents/pharmacology ; Anti-Bacterial Agents/chemistry ; Diterpenes/pharmacology ; Diterpenes/chemistry ; Polycyclic Compounds/pharmacology ; Structure-Activity Relationship ; Microbial Sensitivity Tests
    Chemical Substances Pleuromutilins ; Anti-Bacterial Agents ; Diterpenes ; Polycyclic Compounds
    Language English
    Publishing date 2024-03-15
    Publishing country France
    Document type Journal Article ; Review
    ZDB-ID 188597-2
    ISSN 1768-3254 ; 0009-4374 ; 0223-5234
    ISSN (online) 1768-3254
    ISSN 0009-4374 ; 0223-5234
    DOI 10.1016/j.ejmech.2024.116313
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Internal Concentration Polarization in the Polyamide Active Layer of Thin-Film Composite Membranes.

    Zhou, Zongyao / Wang, Qun / Qin, Yiwen / Hu, Yunxia

    Environmental science & technology

    2023  Volume 57, Issue 14, Page(s) 5999–6007

    Abstract: A free-standing polyamide (PA) film is fabricated via in situ release from a thin-film composite (TFC) membrane achieved through the removal of the polysulfone support. The structure ... ...

    Abstract A free-standing polyamide (PA) film is fabricated via in situ release from a thin-film composite (TFC) membrane achieved through the removal of the polysulfone support. The structure parameter
    MeSH term(s) Nylons/chemistry ; Membranes, Artificial ; Osmosis ; Water/chemistry ; Water Purification/methods
    Chemical Substances Nylons ; Membranes, Artificial ; Water (059QF0KO0R)
    Language English
    Publishing date 2023-03-30
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 1520-5851
    ISSN (online) 1520-5851
    DOI 10.1021/acs.est.2c09009
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Nanomechanical analysis of SARS-CoV-2 variants and predictions of infectiousness and lethality.

    Hu, Yiwen / Buehler, Markus J

    Soft matter

    2022  Volume 18, Issue 31, Page(s) 5833–5842

    Abstract: As variants of the pathogen that causes COVID-19 spread around the world, estimates of infectiousness and lethality of newly emerging strains are important. Here we report a predictive model that associates molecular motions and vibrational patterns of ... ...

    Abstract As variants of the pathogen that causes COVID-19 spread around the world, estimates of infectiousness and lethality of newly emerging strains are important. Here we report a predictive model that associates molecular motions and vibrational patterns of the virus spike protein with infectiousness and lethality. The key finding is that most SARS-CoV-2 variants are predicted to be more infectious and less lethal compared to the original spike protein. However, lineage B.1.351 (Beta variant) is predicted to be less infectious and more lethal, and lineage B.1.1.7 (Alpha variant) is predicted to have both higher infectivity and lethality, showing the potential of the virus to mutate towards different performance regimes. The relatively more recent lineage B.1.617.2 (Delta variant), although contains a few key spike mutations other than D614G, behaves quite similar to the single D614G mutation in both vibrational and predicted epidemiological aspects, which might explain its rapid circulation given the prevalence of D614G. This work may provide a tool to estimate the epidemiological effects of new variants, and offer a pathway to screen mutations against high threat levels. Moreover, the nanomechanical approach, as a novel tool to predict virus-cell interactions, may further open up the door towards better understanding other viruses.
    MeSH term(s) COVID-19 ; Humans ; Mutation ; SARS-CoV-2/genetics ; Spike Glycoprotein, Coronavirus/genetics
    Chemical Substances Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2
    Language English
    Publishing date 2022-08-10
    Publishing country England
    Document type Journal Article
    ZDB-ID 2191476-X
    ISSN 1744-6848 ; 1744-683X
    ISSN (online) 1744-6848
    ISSN 1744-683X
    DOI 10.1039/d1sm01181b
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: End-to-End Protein Normal Mode Frequency Predictions Using Language and Graph Models and Application to Sonification.

    Hu, Yiwen / Buehler, Markus J

    ACS nano

    2022  Volume 16, Issue 12, Page(s) 20656–20670

    Abstract: The prediction of mechanical and dynamical properties of proteins is an important frontier, especially given the greater availability of proteins structures. Here we report a series of models that provide end-to-end predictions of nanodynamical ... ...

    Abstract The prediction of mechanical and dynamical properties of proteins is an important frontier, especially given the greater availability of proteins structures. Here we report a series of models that provide end-to-end predictions of nanodynamical properties of proteins, focused on high-throughput normal mode predictions directly from the amino acid sequence. Using neural network models within the family of Natural Language Processing and graph-based methods, we offer atomistically based mechanistic predictions of key protein mechanical features. The models include an end-to-end long short-term memory (LSTM) model, an end-to-end transformer model, a graph-based transformer model, and an equivariant graph neural network. All four models show exceptional performance, with the graph-based transformer architecture offering the best results but at the cost of requiring a graph structure as input. Conversely, the LSTM and transformer models offer end-to-end sequence-to-property prediction capabilities, providing efficient avenues for protein engineering, analysis, and design. We compare our results against published data based on a Principal Neighborhood Aggregation graph neural network, revealing that the transformer model offers better performance while also being able to predict a large set of the first 64 normal mode frequencies, simultaneously. The use of the end-to-end transformer model may facilitate other downstream applications through the use of transfer learning, and it offers a comprehensive prediction of dynamical properties without any structural knowledge, directly from the amino acid sequence. We demonstrate a potential application in scientific sonification, where the normal mode frequencies are transposed to generate audible signals for a detailed analysis of subtle changes of protein sequences.
    MeSH term(s) Neural Networks, Computer ; Proteins/chemistry ; Amino Acid Sequence ; Learning
    Chemical Substances Proteins
    Language English
    Publishing date 2022-11-23
    Publishing country United States
    Document type Journal Article ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, N.I.H., Extramural
    ISSN 1936-086X
    ISSN (online) 1936-086X
    DOI 10.1021/acsnano.2c07681
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Thermal Decomposition Mechanism of Ammonium Nitrate on the Main Crystal Surface of Ferric Oxide: Experimental and Theoretical Studies.

    Lu, Qiangqiang / Hu, Yiwen / Yang, Junqing / Yang, Hongyu / Xiao, Lei / Zhao, Fengqi / Gao, Hongxu / Jiang, Wei / Hao, Gazi

    Langmuir : the ACS journal of surfaces and colloids

    2024  Volume 40, Issue 4, Page(s) 2198–2209

    Abstract: Understanding the decomposition process of ammonium nitrate (AN) on catalyst surfaces is crucial for the development of practical and efficient catalysts in AN-based propellants. In this study, two types of nano- ... ...

    Abstract Understanding the decomposition process of ammonium nitrate (AN) on catalyst surfaces is crucial for the development of practical and efficient catalysts in AN-based propellants. In this study, two types of nano-Fe
    Language English
    Publishing date 2024-01-19
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2005937-1
    ISSN 1520-5827 ; 0743-7463
    ISSN (online) 1520-5827
    ISSN 0743-7463
    DOI 10.1021/acs.langmuir.3c03230
    Database MEDical Literature Analysis and Retrieval System OnLINE

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