Fan Wang

Journal Article Anesthesiology · August 1, 2025 BACKGROUND: General anesthesia, such as isoflurane, induces analgesia (loss of pain) and loss of consciousness through mechanisms that are not fully understood. A distinct population of γ-aminobutyric acid-mediated neurons has been recently identified in t ... Full text Link to item Cite

PDAI: A green pesticide molecule design technology platform driven by high-performance computing and artificial intelligence

Journal Article Advanced Agrochem · June 1, 2025 Pesticides are integral to agricultural productivity and food security. Despite the notable advancements in Computer Aided Drug Design (CADD) and Artificial Intelligence Drug Discovery (AIDD) in pharmaceuticals, their application in the pesticide sector re ... Full text Cite

PE-GCL: Advancing pesticide ecotoxicity prediction with graph contrastive learning.

Journal Article J Hazard Mater · April 5, 2025 Ecotoxicity assessments, which rely on animal testing, face serious challenges, including high costs and ethical concerns. Computational toxicology presents a promising alternative; nevertheless, existing predictive models encounter difficulties such as li ... Full text Link to item Cite

Geometric deep learning with adaptive full-band spatial diffusion for accurate, efficient, and robust cortical parcellation.

Journal Article Med Image Anal · April 2025 Cortical parcellation delineates the cerebral cortex into distinct regions according to their distinctiveness in anatomy and/or function, which is a fundamental preprocess in brain cortex analysis and can influence the accuracy and specificity of subsequen ... Full text Link to item Cite

A Novel Hierarchical Cross-Stream Aggregation Neural Network for Semantic Segmentation of 3-D Dental Surface Models.

Journal Article IEEE Trans Neural Netw Learn Syst · April 2025 Accurate teeth delineation on 3-D dental models is essential for individualized orthodontic treatment planning. Pioneering works like PointNet suggest a promising direction to conduct efficient and accurate 3-D dental model analyses in end-to-end learnable ... Full text Link to item Cite

Deep and dynamic metabolic and structural imaging in living tissues.

Journal Article Sci Adv · December 13, 2024 Label-free imaging through two-photon autofluorescence of NAD(P)H allows for nondestructive, high-resolution visualization of cellular activities in living systems. However, its application to thick tissues has been restricted by its limited penetration de ... Full text Link to item Cite

Cryo-EM Structures Reveal the Unique Binding Modes of Metyltetraprole in Yeast and Porcine Cytochrome bc1 Complex Enabling Rational Design of Inhibitors.

Journal Article J Am Chem Soc · December 11, 2024 Cytochrome bc1 (complex III) represents a significant target for the discovery of both drugs and fungicides. Metyltetraprole (MET) is commonly classified as a quinone site inhibitor (QoI) that combats the G143A mutated isolate, which confers high resistanc ... Full text Link to item Cite

DigFrag as a digital fragmentation method used for artificial intelligence-based drug design

Journal Article Communications Chemistry · December 1, 2024 Fragment-Based Drug Design (FBDD) plays a pivotal role in the field of drug discovery and development. The construction of high-quality fragment libraries is a critical step in FBDD. Conventional fragmentation approaches often rely on rigid rules and chemi ... Full text Cite

New drug discovery and development from natural products: Advances and strategies.

Journal Article Pharmacol Ther · December 2024 Natural products (NPs) have a long history as sources for drug discovery, more than half of approved drugs are related to NPs, which also exhibit multifaceted advantages in the clinical treatment of complex diseases. However, bioactivity screening of NPs, ... Full text Link to item Cite

Melatonin mediates intestinal barrier dysfunction and systemic inflammation in moderate-severe OSA patients.

Journal Article Ann Med · December 2024 BACKGROUND: Intestinal barrier dysfunction and systemic inflammation are common in obstructive sleep apnoea (OSA). We aimed to investigate the role of melatonin, an anti-inflammatory mediator, in mediating the relationships between OSA, intestinal barrier ... Full text Link to item Cite

General anesthesia activates a central anxiolytic center in the BNST.

Journal Article Cell Rep · November 26, 2024 Low doses of general anesthetics like ketamine and dexmedetomidine have anxiolytic properties independent of their sedative effects, but the underlying mechanisms remain unclear. We discovered a population of GABAergic neurons in the oval division of the b ... Full text Link to item Cite

Improved Ensemble Model for Insecticide Recognition by Incorporating Insect Toxicity Data.

Journal Article J Agric Food Chem · November 6, 2024 Pesticide molecules, such as insecticides, play a critical role in modern agricultural production. Traditional pesticide development methods are often inefficient and expensive, while data-driven artificial intelligence (AI) techniques have emerged as a us ... Full text Link to item Cite

DBAII-Net with multiscale feature aggregation and cross-modal attention for enhancing infant brain injury classification in MRI.

Journal Article Phys Med Biol · October 14, 2024 Objectives.Magnetic resonance imaging (MRI) is pivotal in diagnosing brain injuries in infants. However, the dynamic development of the brain introduces variability in infant MRI characteristics, posing challenges for MRI-based classification in this popul ... Full text Link to item Cite

Reverse-engineering placebo analgesia.

Journal Article Curr Biol · September 23, 2024 Placebo analgesia is a widely observed clinical phenomenon. Establishing a robust mouse model of placebo analgesia is needed for careful dissection of the underpinning circuit mechanisms. However, previous studies failed to observe consistent placebo effec ... Full text Link to item Cite

Publisher Correction: An implantable piezoelectric ultrasound stimulator (ImPULS) for deep brain activation.

Journal Article Nat Commun · July 25, 2024 Full text Link to item Cite

Unilateral movement decoding of upper and lower limbs using magnetoencephalography

Journal Article Biomedical Signal Processing and Control · July 1, 2024 Problem: The effectiveness of distinguishing unilateral lower limb motor execution (ME) or imagery (MI) based on electroencephalogram (EEG) is limited by its low spatial resolution, since the somatotopies of bilateral lower limbs are close to each other. A ... Full text Cite

Unravelling biosynthesis and biodegradation potentials of microbial dark matters in hypersaline lakes

Journal Article Environmental Science and Ecotechnology · July 1, 2024 Biosynthesis and biodegradation of microorganisms critically underpin the development of biotechnology, new drugs and therapies, and environmental remediation. However, most uncultured microbial species along with their metabolic capacities in extreme envi ... Full text Cite

An implantable piezoelectric ultrasound stimulator (ImPULS) for deep brain activation.

Journal Article Nat Commun · June 4, 2024 Precise neurostimulation can revolutionize therapies for neurological disorders. Electrode-based stimulation devices face challenges in achieving precise and consistent targeting due to the immune response and the limited penetration of electrical fields. ... Full text Link to item Cite

GIaNt: Protein-Ligand Binding Affinity Prediction via Geometry-Aware Interactive Graph Neural Network

Journal Article IEEE Transactions on Knowledge and Data Engineering · May 1, 2024 Drug discovery often relies on the successful prediction of protein-ligand binding affinity. Recent advances have shown great promise in applying graph neural networks (GNNs) for better affinity prediction by learning the representations of protein-ligand ... Full text Cite

AquaticTox: A Web-Based Tool for Aquatic Toxicity Evaluation Based on Ensemble Learning to Facilitate the Screening of Green Chemicals

Journal Article Environment and Health · April 19, 2024 The widespread use of chemical products inevitably brings many side effects as environmental pollutants. Toxicological assessment of compounds to aquatic life plays an important role in protecting the environment from their hazards. However, in vivo animal ... Full text Cite

Introducing a Toxicological Perspective to View Chemicals: A Web-Based Class for Educating Green Molecular Design

Journal Article Journal of Chemical Education · April 9, 2024 Designing safer chemicals is an integral part of green chemistry that supports good health and well-being. The teaching of molecule design through relevant courses has important implications for the education of sustainable chemists. In these courses, trai ... Full text Cite

Brainstem control of vocalization and its coordination with respiration.

Journal Article Science · March 8, 2024 Phonation critically depends on precise controls of laryngeal muscles in coordination with ongoing respiration. However, the neural mechanisms governing these processes remain unclear. We identified excitatory vocalization-specific laryngeal premotor neuro ... Full text Link to item Cite

Spectral-temporal-spatial customization via modulating multimodal nonlinear pulse propagation.

Journal Article Nat Commun · March 6, 2024 Multimode fibers (MMFs) are gaining renewed interest for nonlinear effects due to their high-dimensional spatiotemporal nonlinear dynamics and scalability for high power. High-brightness MMF sources with effective control of the nonlinear processes would o ... Full text Link to item Cite

Pesti-DGI-Net: A multi-modal deep learning architecture based on dual interpretability for pesticide-likeness prediction

Journal Article Computers and Electronics in Agriculture · February 1, 2024 “Pesticide-likeness” represents an extension of the pharmaceutical concept of “drug-likeness” to the field of pesticides. The development of algorithmic tools for predicting pesticide-likeness holds great significance for the rational design of pesticide m ... Full text Cite

CellBoost: A pipeline for machine assisted annotation in neuroanatomy

Journal Article AI Open · January 1, 2024 One of the important yet labor intensive tasks in neuroanatomy is the identification of select populations of cells. Current high-throughput techniques enable marking cells with histochemical fluorescent molecules as well as through the genetic expression ... Full text Cite

Unveiling toxicity profile for food risk components: A manually curated toxicological databank of food-relevant chemicals.

Journal Article Crit Rev Food Sci Nutr · 2024 Rigorous risk assessment of chemicals in food and feed is essential to address the growing worldwide concerns about food safety. High-quality toxicological data on food-relevant chemicals are fundamental for risk modeling and assessment in the food safety ... Full text Link to item Cite

Weakly Supervised Tooth Instance Segmentation on 3D Dental Models with Multi-label Learning

Conference Lecture Notes in Computer Science Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics · January 1, 2024 Automatic tooth segmentation on 3D dental models is a fundamental task for computer-aided orthodontic treatment. Many deep learning methods aimed at precise tooth segmentation currently require meticulous point-wise annotations, which are extremely timecon ... Full text Cite

Towards Graph Neural Networks with Domain-Generalizable Explainability for fMRI-Based Brain Disorder Diagnosis

Conference Lecture Notes in Computer Science Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics · January 1, 2024 Graph neural networks (GNNs) represent a cutting-edge methodology in diagnosing brain disorders via fMRI data. Explainability and generalizability are two critical issues of GNNs for fMRI-based diagnoses, considering the high complexity of functional brain ... Full text Cite

Efficient Cortical Surface Parcellation via Full-Band Diffusion Learning at Individual Space

Conference Lecture Notes in Computer Science Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics · January 1, 2024 Cortical parcellation delineates the cerebral cortex into distinct regions based on anatomical and/or functional criteria, a process crucial for neuroscientific research and clinical applications. Conventional methods for cortical parcellation involve sphe ... Full text Cite

Learning to Select External Knowledge With Multi-Scale Negative Sampling

Journal Article IEEE ACM Transactions on Audio Speech and Language Processing · January 1, 2024 The Track-1 of DSTC9 aims to effectively answer user requests or questions during task-oriented dialogues, which are out of the scope of APIs/DB. By leveraging external knowledge resources, relevant information can be retrieved and encoded into the respons ... Full text Cite

Low- and high-level coordination of orofacial motor actions.

Journal Article Curr Opin Neurobiol · December 2023 Orofacial motor actions are movements that, in rodents, involve whisking of the vibrissa, deflection of the nose, licking and lapping with the tongue, and consumption through chewing. These actions, along with bobbing and turning of the head, coordinate to ... Full text Link to item Cite

Melatonin attenuates chronic intermittent hypoxia-induced intestinal barrier dysfunction in mice.

Journal Article Microbiol Res · November 2023 BACKGROUND AND PURPOSE: Chronic intermittent hypoxia (CIH) triggers subclinical intestinal barrier disruption prior to systemic low-grade inflammation. Increasing evidence suggests therapeutic effects of melatonin on systemic inflammation and gut microbiot ... Full text Link to item Cite

A method for multiple-sequence-alignment-free protein structure prediction using a protein language model

Journal Article Nature Machine Intelligence · October 1, 2023 Protein structure prediction pipelines based on artificial intelligence, such as AlphaFold2, have achieved near-experimental accuracy. These advanced pipelines mainly rely on multiple sequence alignments (MSAs) as inputs to learn the co-evolution informati ... Full text Cite

Longitudinal mapping of the development of cortical thickness and surface area in rhesus macaques during the first three years.

Journal Article Proc Natl Acad Sci U S A · August 8, 2023 Studying dynamic spatiotemporal patterns of early brain development in macaque monkeys is critical for understanding the cortical organization and evolution in humans, given the phylogenetic closeness between humans and macaques. However, due to huge chall ... Full text Link to item Cite

Fine-grained functional parcellation maps of the infant cerebral cortex.

Journal Article Elife · August 1, 2023 Resting-state functional MRI (rs-fMRI) is widely used to examine the dynamic brain functional development of infants, but these studies typically require precise cortical parcellation maps, which cannot be directly borrowed from adult-based functional parc ... Full text Link to item Cite

ACFIS 2.0: an improved web-server for fragment-based drug discovery via a dynamic screening strategy.

Journal Article Nucleic Acids Res · July 5, 2023 Drug discovery, which plays a vital role in maintaining human health, is a persistent challenge. Fragment-based drug discovery (FBDD) is one of the strategies for the discovery of novel candidate compounds. Computational tools in FBDD could help to identif ... Full text Link to item Cite

Improved 3D Markerless Mouse Pose Estimation Using Temporal Semi-Supervision.

Journal Article Int J Comput Vis · June 2023 Three-dimensional markerless pose estimation from multi-view video is emerging as an exciting method for quantifying the behavior of freely moving animals. Nevertheless, scientifically precise 3D animal pose estimation remains challenging, primarily due to ... Full text Link to item Cite

RLCharge: Imitative Multi-Agent Spatiotemporal Reinforcement Learning for Electric Vehicle Charging Station Recommendation

Journal Article IEEE Transactions on Knowledge and Data Engineering · June 1, 2023 Electric Vehicle (EV) has become a preferable choice in the modern transportation system due to its environmental and energy sustainability. However, in many large cities, EV drivers often fail to find the proper spots for charging, because of the limited ... Full text Cite

Rational Design of Esterase-Insensitive Fluorogenic Probes for In Vivo Imaging.

Journal Article ACS Sens · May 26, 2023 Small-molecule fluorogenic probes are indispensable tools for performing research in biomedical fields and chemical biology. Although numerous cleavable fluorogenic probes have been developed to investigate various bioanalytes, few of them meet the baselin ... Full text Link to item Cite

CIPDB: A biological structure databank for studying cation and π interactions.

Journal Article Drug Discov Today · May 2023 As major forces for modulating protein folding and molecular recognition, cation and π interactions are extensively identified in protein structures. They are even more competitive than hydrogen bonds in molecular recognition, thus, are vital in numerous b ... Full text Link to item Cite

Monitoring of thermal lesions in ultrasound using fully convolutional neural networks: A preclinical study.

Journal Article Ultrasonics · April 2023 Accurate monitoring of thermal ablation regions is an important guarantee for successful ablation treatment, which mainly depends on the subjective judgment of radiologists in current clinical practice. This work innovatively applied fully convolutional ne ... Full text Link to item Cite

Dynamic Cross-Task Representation Adaptation for Clinical Targets Co-Segmentation in CT Image-Guided Post-Prostatectomy Radiotherapy.

Journal Article IEEE Trans Med Imaging · April 2023 Adjuvant and salvage radiotherapy after radical prostatectomy requires precise delineations of prostate bed (PB), i.e., the clinical target volume, and surrounding organs at risk (OARs) to optimize radiotherapy planning. Segmenting PB is particularly chall ... Full text Link to item Cite

Toxicological data bank bridges the gap between environmental risk assessment and green organic chemical design in One Health world

Journal Article Green Chemistry · January 25, 2023 In the conceptual frame of “One Health”, the safety crisis caused by various toxicological issues due to chemical exposure is of great concern. The urgent demand for environmentally safe chemicals is increasing the awareness of the importance of designing ... Full text Cite

BloodNet: An attention-based deep network for accurate, efficient, and costless bloodstain time since deposition inference.

Journal Article Brief Bioinform · January 19, 2023 The time since deposition (TSD) of a bloodstain, i.e., the time of a bloodstain formation is an essential piece of biological evidence in crime scene investigation. The practical usage of some existing microscopic methods (e.g., spectroscopy or RNA analysi ... Full text Link to item Cite

Biaxial Magnetoencephalography Acquisition of Auditory Evoked Responses Using Optically Pumped Magnetometer: a Preliminary Study*

Journal Article Progress in Biochemistry and Biophysics · January 1, 2023 Objective Optically pumped magnetometer (OPM)-magnetoencephalography (MEG) is a rapidly developing new-generation brain function imaging technology compared to the traditional MEG. Due to the proximity of the detectors and the scalp, OPM-MEG offers higher ... Full text Cite

Dual Meta-Learning with Longitudinally Generalized Regularization for One-Shot Brain Tissue Segmentation Across the Human Lifespan

Conference Proceedings of the IEEE International Conference on Computer Vision · January 1, 2023 Brain tissue segmentation is essential for neuroscience and clinical studies. However, segmentation on longitudinal data is challenging due to dynamic brain changes across the lifespan. Previous researches mainly focus on self-supervision with regularizati ... Full text Cite

NeuroExplainer: Fine-Grained Attention Decoding to Uncover Cortical Development Patterns of Preterm Infants

Conference Lecture Notes in Computer Science Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics · January 1, 2023 In addition to model accuracy, current neuroimaging studies require more explainable model outputs to relate brain development, degeneration, or disorders to uncover atypical local alterations. For this purpose, existing approaches typically explicate netw ... Full text Cite

Punctate White Matter Lesion Segmentation in Preterm Infants Powered by Counterfactually Generative Learning

Conference Lecture Notes in Computer Science Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics · January 1, 2023 Accurate segmentation of punctate white matter lesions (PWMLs) are fundamental for the timely diagnosis and treatment of related developmental disorders. Automated PWMLs segmentation from infant brain MR images is challenging, considering that the lesions ... Full text Cite

Forensic Histopathological Recognition via a Context-Aware MIL Network Powered by Self-supervised Contrastive Learning

Conference Lecture Notes in Computer Science Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics · January 1, 2023 Forensic pathology is critical in analyzing death manner and time from the microscopic aspect to assist in the establishment of reliable factual bases for criminal investigation. In practice, even the manual differentiation between different postmortem org ... Full text Cite

Towards Boosting the Open-Domain Chatbot with Human Feedback

Conference Proceedings of the Annual Meeting of the Association for Computational Linguistics · January 1, 2023 Many open-domain dialogue models pre-trained with social media comments can generate coherent replies but have difficulties producing engaging responses. This phenomenon might mainly result from the deficiency of annotated human-human conversations and the ... Full text Cite

Query Enhanced Knowledge-Intensive Conversation via Unsupervised Joint Modeling

Conference Proceedings of the Annual Meeting of the Association for Computational Linguistics · January 1, 2023 In this paper, we propose an unsupervised query enhanced approach for knowledge-intensive conversations, namely QKConv. There are three modules in QKConv: a query generator, an off-the-shelf knowledge selector, and a response generator. QKConv is optimized ... Full text Cite

Changes in the oral and nasal microbiota in pediatric obstructive sleep apnea

Journal Article Journal of Oral Microbiology · January 1, 2023 Background: Several clinical studies have demonstrated that pediatric obstructive sleep apnea (OSA) is associated with dysbiosis of airway mucosal microbiota. However, how oral and nasal microbial diversity, composition, and structure are altered in pediat ... Full text Cite

Somatosensory cortical signature of facial nociception and vibrotactile touch-induced analgesia.

Journal Article Sci Adv · November 18, 2022 Pain relief by vibrotactile touch is a common human experience. Previous neurophysiological investigations of its underlying mechanism in animals focused on spinal circuits, while human studies suggested the involvement of supraspinal pathways. Here, we ex ... Full text Link to item Cite

Theory of hierarchically organized neuronal oscillator dynamics that mediate rodent rhythmic whisking.

Journal Article Neuron · November 16, 2022 Rodents explore their environment through coordinated orofacial motor actions, including whisking. Whisking can free-run via an oscillator of inhibitory neurons in the medulla and can be paced by breathing. Yet, the mechanics of the whisking oscillator and ... Full text Link to item Cite

Two-Stage Mesh Deep Learning for Automated Tooth Segmentation and Landmark Localization on 3D Intraoral Scans.

Journal Article IEEE Trans Med Imaging · November 2022 Accurately segmenting teeth and identifying the corresponding anatomical landmarks on dental mesh models are essential in computer-aided orthodontic treatment. Manually performing these two tasks is time-consuming, tedious, and, more importantly, highly de ... Full text Link to item Cite

The whisking oscillator circuit.

Journal Article Nature · September 2022 Central oscillators are primordial neural circuits that generate and control rhythmic movements1,2. Mechanistic understanding of these circuits requires genetic identification of the oscillator neurons and their synaptic connections to enable targeted elec ... Full text Link to item Cite

Evolving Decomposed Plasticity Rules for Information-Bottlenecked Meta-Learning

Journal Article Transactions on Machine Learning Research · September 1, 2022 Artificial neural networks (ANNs) are typically confined to accomplishing pre-defined tasks by learning a set of static parameters. In contrast, biological neural networks (BNNs) can adapt to various new tasks by continually updating the neural connections ... Cite

A structural MRI study of global developmental delay in infants (<2 years old)

Journal Article Frontiers in Neurology · August 18, 2022 Objective: To use structural magnetic resonance imaging (3D-MRI) to evaluate the abnormal development of the cerebral cortex in infants with global developmental delay (GDD). Methods: The GDD group includes 67 infants aged between 112 and 699 days with glo ... Full text Cite

Mapping developmental regionalization and patterns of cortical surface area from 29 post-menstrual weeks to 2 years of age.

Journal Article Proc Natl Acad Sci U S A · August 16, 2022 Surface area of the human cerebral cortex expands extremely dynamically and regionally heterogeneously from the third trimester of pregnancy to 2 y of age, reflecting the spatial heterogeneity of the underlying microstructural and functional development of ... Full text Link to item Cite

Exploring the kinase-inhibitor fragment interaction space facilitates the discovery of kinase inhibitor overcoming resistance by mutations.

Journal Article Brief Bioinform · July 18, 2022 Protein kinases play crucial roles in many cellular signaling processes, making them become important targets for drug discovery. But drug resistance mediated by mutation puts a barrier to the therapeutic effect of kinase inhibitors. Fragment-based drug di ... Full text Link to item Cite

BatchDTA: implicit batch alignment enhances deep learning-based drug-target affinity estimation.

Journal Article Brief Bioinform · July 18, 2022 Candidate compounds with high binding affinities toward a target protein are likely to be developed as drugs. Deep neural networks (DNNs) have attracted increasing attention for drug-target affinity (DTA) estimation owning to their efficiency. However, the ... Full text Link to item Cite

HelixADMET: a robust and endpoint extensible ADMET system incorporating self-supervised knowledge transfer.

Journal Article Bioinformatics · June 27, 2022 MOTIVATION: Accurate ADMET (an abbreviation for 'absorption, distribution, metabolism, excretion and toxicity') predictions can efficiently screen out undesirable drug candidates in the early stage of drug discovery. In recent years, multiple comprehensive ... Full text Link to item Cite

Distinct networks coupled with parietal cortex for spatial representations inside and outside the visual field.

Journal Article Neuroimage · May 15, 2022 Our mental representation of egocentric space is influenced by the disproportionate sensory perception of the body. Previous studies have focused on the neural architecture for egocentric representations within the visual field. However, the space represen ... Full text Link to item Cite

Trans-Seq maps a selective mammalian retinotectal synapse instructed by Nephronectin.

Journal Article Nat Neurosci · May 2022 The mouse visual system serves as an accessible model to understand mammalian circuit wiring. Despite rich knowledge in retinal circuits, the long-range connectivity map from distinct retinal ganglion cell (RGC) types to diverse brain neuron types remains ... Full text Link to item Cite

Reinforcement Learning with Evolutionary Trajectory Generator: A General Approach for Quadrupedal Locomotion

Journal Article IEEE Robotics and Automation Letters · April 1, 2022 Recently reinforcement learning (RL) has emerged as a promising approach for quadrupedal locomotion, which can save the manual effort in conventional approaches such as designing skill-specific controllers. However, due to the complex nonlinear dynamics in ... Full text Cite

Virtual intracranial EEG signals reconstructed from MEG with potential for epilepsy surgery.

Journal Article Nat Commun · February 22, 2022 Modelling the interactions that arise from neural dynamics in seizure genesis is challenging but important in the effort to improve the success of epilepsy surgery. Dynamical network models developed from physiological evidence offer insights into rapidly ... Full text Link to item Cite

A flexible summary statistics-based colocalization method with application to the mucin cystic fibrosis lung disease modifier locus.

Journal Article Am J Hum Genet · February 3, 2022 Mucus obstruction is a central feature in the cystic fibrosis (CF) airways. A genome-wide association study (GWAS) of lung disease by the CF Gene Modifier Consortium (CFGMC) identified a significant locus containing two mucin genes, MUC20 and MUC4. Express ... Full text Link to item Cite

Effects of Chronic Intermittent Hypoxia and Chronic Sleep Fragmentation on Gut Microbiome, Serum Metabolome, Liver and Adipose Tissue Morphology

Journal Article Frontiers in Endocrinology · February 1, 2022 Chronic intermittent hypoxia (CIH) and chronic sleep fragmentation (CSF) are two cardinal pathological features of obstructive sleep apnea (OSA). Dietary obesity is a crucial risk intermediator for OSA and metabolic disorders. Gut microbiota affect hepatic ... Full text Cite

Transcranial Ultrasound Estimation of Viscoelasticity and Fluidity of the Soft Matter

Journal Article Physical Review Applied · February 1, 2022 In the fields of geology, materials and biomedical engineering, the noninvasive and accurate estimation of the dynamic mechanical properties of the soft matter enclosed in a rigid shell induced by a low-frequency vibration is worthy of exploration. The add ... Full text Cite

Geometry-enhanced molecular representation learning for property prediction

Journal Article Nature Machine Intelligence · February 1, 2022 Effective molecular representation learning is of great importance to facilitate molecular property prediction. Recent advances for molecular representation learning have shown great promise in applying graph neural networks to model molecules. Moreover, a ... Full text Cite

Existence of Functional Connectome Fingerprint during Infancy and Its Stability over Months.

Journal Article J Neurosci · January 19, 2022 The functional connectome fingerprint is a cluster of individualized brain functional connectivity patterns that are capable of distinguishing one individual from others. Although its existence has been demonstrated in adolescents and adults, whether such ... Full text Link to item Cite

PTMdyna: exploring the influence of post-translation modifications on protein conformational dynamics.

Journal Article Brief Bioinform · January 17, 2022 Protein post-translational modifications (PTM) play vital roles in cellular regulation, modulating functions by driving changes in protein structure and dynamics. Exploring comprehensively the influence of PTM on conformational dynamics can facilitate the ... Full text Link to item Cite

Metabolomics Analysis on Obesity-Related Obstructive Sleep Apnea After Weight Loss Management: A Preliminary Study

Journal Article Frontiers in Endocrinology · January 3, 2022 Objective: Roux-en-Y gastric bypass (RYGB) surgery is an effective type of weight loss management and may improve obesity-related obstructive sleep apnea (OSA). Obese subjects who meet the criteria for surgery with OSA were enrolled. We investigated the me ... Full text Cite

Using Viral Vectors to Visualize Pain-Related Neural Circuits in Mice

Chapter · January 1, 2022 Neural circuit tracing methods that take advantage of viral vectors and transgenic mice provide opportunities to gain insight into functional connectivity. Here we describe several protocols for identifying synaptic connections made by projection neurons, ... Full text Cite

G-quadruplexes in genomes of viruses infecting eukaryotes or prokaryotes are under different selection pressures from hosts.

Journal Article J Genet Genomics · January 2022 G-quadruplexes in viral genomes can be applied as the targets of antiviral therapies, which has attracted wide interest. However, it is still not clear whether the pervasive number of such elements in the viral world is the result of natural selection for ... Full text Link to item Cite

PLATO-XL: Exploring the Large-scale Pre-training of Dialogue Generation

Conference 2nd Conference of the Asia Pacific Chapter of the Association for Computational Linguistics and the 12th International Joint Conference on Natural Language Processing Findings of the Association for Computational Linguistics Aacl Ijcnlp 2022 · January 1, 2022 To explore the limit of dialogue generation pretraining, we present the models of PLATO-XLwith up to 11 billion parameters, trained onboth Chinese and English social media conversations. To train such large models, weadopt the architecture of unified trans ... Cite

Q-TOD: A Query-driven Task-oriented Dialogue System

Conference Proceedings of the 2022 Conference on Empirical Methods in Natural Language Processing Emnlp 2022 · January 1, 2022 Existing pipelined task-oriented dialogue systems usually have difficulties adapting to unseen domains, whereas end-to-end systems are plagued by large-scale knowledge bases in practice. In this paper, we introduce a novel query-driven task-oriented dialog ... Full text Cite

HelixMO: Sample-Efficient Molecular Optimization in Scene-Sensitive Latent Space

Conference Proceedings 2022 IEEE International Conference on Bioinformatics and Biomedicine Bibm 2022 · January 1, 2022 Efficient exploration of the chemical space to search the candidate drugs that satisfy various constraints is a fundamental task of drug discovery. Advanced deep generative methods attempt to optimize the molecules in the compact latent space instead of th ... Full text Cite

Metagenomics analysis revealing the occurrence of antibiotic resistome in salt lakes.

Journal Article Sci Total Environ · October 10, 2021 Although antimicrobial resistance genes (ARGs) in dozens of environments have been well documented, the distribution of ARGs in salt lake ecosystems has been less intensively investigated. In this study, the broad-spectrum ARG profiles, microbial community ... Full text Link to item Cite

HISNAPI: a bioinformatic tool for dynamic hot spot analysis in nucleic acid-protein interface with a case study.

Journal Article Brief Bioinform · September 2, 2021 Protein-nucleic acid interactions play essential roles in many biological processes, such as transcription, replication and translation. In protein-nucleic acid interfaces, hotspot residues contribute the majority of binding affinity toward molecular recog ... Full text Link to item Cite

A novel tumor suppressor CECR2 down regulation links glutamine metabolism contributes tumor growth in laryngeal squamous cell carcinoma.

Journal Article Clin Transl Oncol · September 2021 PURPOSE: Glutamine plays an important role in tumor metabolism and progression. This research aimed to find out how Gln exert their effects on laryngeal squamous cell carcinoma (LSCC). METHODS: Cell proliferation was measured by CCK8 and EdU assay, mitocho ... Full text Link to item Cite

Structure-aware Interactive Graph Neural Networks for the Prediction of Protein-Ligand Binding Affinity

Conference Proceedings of the ACM SIGKDD International Conference on Knowledge Discovery and Data Mining · August 14, 2021 Drug discovery often relies on the successful prediction of protein-ligand binding affinity. Recent advances have shown great promise in applying graph neural networks (GNNs) for better affinity prediction by learning the representations of protein-ligand ... Full text Cite

SSML: Self-Supervised Meta-Learner for en Route Travel Time Estimation at Baidu Maps

Conference Proceedings of the ACM SIGKDD International Conference on Knowledge Discovery and Data Mining · August 14, 2021 Travel time estimation (TTE) is one of the most critical modules at Baidu Maps, which plays a vital role in intelligent transportation services such as route planning and navigation. During the driving en route, the navigation system of Baidu Maps can prov ... Full text Cite

ABCnet: Adversarial bias correction network for infant brain MR images.

Journal Article Med Image Anal · August 2021 Automatic correction of intensity nonuniformity (also termed as the bias correction) is an essential step in brain MR image analysis. Existing methods are typically developed for adult brain MR images based on the assumption that the image intensities with ... Full text Link to item Cite

S3Reg: Superfast Spherical Surface Registration Based on Deep Learning.

Journal Article IEEE Trans Med Imaging · August 2021 Cortical surface registration is an essential step and prerequisite for surface-based neuroimaging analysis. It aligns cortical surfaces across individuals and time points to establish cross-sectional and longitudinal cortical correspondences to facilitate ... Full text Link to item Cite

Cloud 3D-QSAR: a web tool for the development of quantitative structure-activity relationship models in drug discovery.

Journal Article Brief Bioinform · July 20, 2021 Effective drug discovery contributes to the treatment of numerous diseases but is limited by high costs and long cycles. The Quantitative Structure-Activity Relationship (QSAR) method was introduced to evaluate the activity of a large number of compounds v ... Full text Link to item Cite

Intelligent electric vehicle charging recommendation based on multi-agent reinforcement learning

Conference Web Conference 2021 Proceedings of the World Wide Web Conference Www 2021 · June 3, 2021 Electric Vehicle (EV) has become a preferable choice in the modern transportation system due to its environmental and energy sustainability. However, in many large cities, EV drivers often fail to find the proper spots for charging, because of the limited ... Full text Cite

Geometric deep learning enables 3D kinematic profiling across species and environments.

Journal Article Nat Methods · May 2021 Comprehensive descriptions of animal behavior require precise three-dimensional (3D) measurements of whole-body movements. Although two-dimensional approaches can track visible landmarks in restrictive environments, performance drops in freely moving anima ... Full text Link to item Cite

Constructing an adult orofacial premotor atlas in Allen mouse CCF.

Journal Article Elife · April 27, 2021 Premotor circuits in the brainstem project to pools of orofacial motoneurons to execute essential motor action such as licking, chewing, breathing, and in rodent, whisking. Previous transsynaptic tracing studies only mapped orofacial premotor circuits in n ... Full text Link to item Cite

HerbiPAD: a free web platform to comprehensively analyze constitutive property and herbicide-likeness to estimate chemical bioavailability.

Journal Article Pest Manag Sci · March 2021 BACKGROUND: Herbicides, as efficient weed control measures, play a crucial role in ensuring food security. The emergence of herbicide-resistant weeds has negatively affected food security and promoted the demand for new and improved herbicides. The balance ... Full text Link to item Cite

Constructing An Adult Orofacial Premotor Atlas In Allen Mouse CCF

Journal Article · February 19, 2021 AbstractPremotor circuits in the brainstem control pools of orofacial motoneurons to execute essential functions such as drinking, eating, breathing, and in rodent, whisking. Previous transsynaptic tracing studies only mapp ... Full text Cite

The Associations Between Sleep Architecture and Metabolic Parameters in Patients With Obstructive Sleep Apnea: A Hospital-Based Cohort Study

Journal Article Frontiers in Neurology · February 10, 2021 Background and Objectives: The associations between objective sleep architecture and metabolic parameters have been rarely studied in patients with obstructive sleep apnea (OSA). Here, we evaluated the associations between objective sleep measures derived ... Full text Cite

PlantSPEAD: a web resource towards comparatively analysing stress-responsive expression of splicing-related proteins in plant.

Journal Article Plant Biotechnol J · February 2021 Full text Link to item Cite

PIIMS Server: A Web Server for Mutation Hotspot Scanning at the Protein-Protein Interface.

Journal Article J Chem Inf Model · January 25, 2021 Protein-protein interactions (PPIs) play vital roles in regulating biological processes, such as cellular and signaling pathways. Hotspots are certain residues located at protein-protein interfaces that contribute more in protein-protein binding than other ... Full text Link to item Cite

Erratum to: LARMD: integration of bioinformatic resources to profile ligand-driven protein dynamics with a case on the activation of estrogen receptor.

Journal Article Brief Bioinform · January 18, 2021 Full text Link to item Cite

Vertebrate Evolution Conserves Hindbrain Circuits despite Diverse Feeding and Breathing Modes.

Journal Article eNeuro · 2021 Feeding and breathing are two functions vital to the survival of all vertebrate species. Throughout the evolution, vertebrates living in different environments have evolved drastically different modes of feeding and breathing through using diversified orof ... Full text Link to item Cite

MULTIMODAL PRE-TRAINING MODEL FOR SEQUENCE-BASED PREDICTION OF PROTEIN-PROTEIN INTERACTION

Conference Proceedings of Machine Learning Research · January 1, 2021 Protein-protein interactions (PPIs) are essentials for many biological processes where two or more proteins physically bind together to achieve their functions. Modeling PPIs is useful for many biomedical applications, such as vaccine design, antibody ther ... Cite

PLATO-KAG: Unsupervised Knowledge-Grounded Conversation via Joint Modeling

Conference Nlp for Conversational AI Nlp4convai 2021 Proceedings of the 3rd Workshop · January 1, 2021 Large-scale conversation models are turning to leveraging external knowledge to improve the factual accuracy in response generation. Considering the infeasibility to annotate the external knowledge for large-scale dialogue corpora, it is desirable to learn ... Cite

Association of Hypertriglyceridemic Waist Phenotype with Obstructive Sleep Apnea: A Cross-Sectional Study

Journal Article Nature and Science of Sleep · January 1, 2021 Objective: Hypertriglyceridemic waist (HTGW) phenotype is an independent risk factor for metabolic disorders. Although obstructive sleep apnea (OSA) is associated with metabolic disorders, it is unclear whether there is an association between HTGW phenotyp ... Full text Cite

Proactive Interaction Framework for Intelligent Social Receptionist Robots

Conference Proceedings IEEE International Conference on Robotics and Automation · January 1, 2021 Proactive human-robot interaction (HRI) allows the receptionist robots to actively greet people and offer services based on vision, which has been found to improve acceptability and customer satisfaction. Existing approaches are either based on multi-stage ... Full text Cite

Docking-based Virtual Screening with Multi-Task Learning

Conference Proceedings 2021 IEEE International Conference on Bioinformatics and Biomedicine Bibm 2021 · January 1, 2021 Machine learning shows great potential in virtual screening for drug discovery. Current efforts on accelerating docking-based virtual screening do not consider using existing data of other previously developed targets. To make use of the knowledge of the o ... Full text Cite

Amendable Generation for Dialogue State Tracking

Conference Nlp for Conversational AI Nlp4convai 2021 Proceedings of the 3rd Workshop · January 1, 2021 In task-oriented dialogue systems, recent dialogue state tracking methods tend to perform one-pass generation of the dialogue state based on the previous dialogue state. The mistakes of these models made at the current turn are prone to be carried over to ... Cite

PLATO-2: Towards Building an Open-Domain Chatbot via Curriculum Learning

Conference Findings of the Association for Computational Linguistics Acl Ijcnlp 2021 · January 1, 2021 To build a high-quality open-domain chatbot, we introduce the effective training process of PLATO-2 via curriculum learning. There are two stages involved in the learning process. In the first stage, a coarse-grained generation model is trained to learn re ... Full text Cite

Action Set Based Policy Optimization for Safe Power Grid Management

Conference Lecture Notes in Computer Science Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics · January 1, 2021 Maintaining the stability of the modern power grid is becoming increasingly difficult due to fluctuating power consumption, unstable power supply coming from renewable energies, and unpredictable accidents such as man-made and natural disasters. As the ope ... Full text Cite

Circuit and synaptic organization of forebrain-to-midbrain pathways that promote and suppress vocalization.

Journal Article Elife · December 29, 2020 Animals vocalize only in certain behavioral contexts, but the circuits and synapses through which forebrain neurons trigger or suppress vocalization remain unknown. Here, we used transsynaptic tracing to identify two populations of inhibitory neurons that ... Full text Link to item Cite

LARMD: integration of bioinformatic resources to profile ligand-driven protein dynamics with a case on the activation of estrogen receptor.

Journal Article Brief Bioinform · December 1, 2020 Protein dynamics is central to all biological processes, including signal transduction, cellular regulation and biological catalysis. Among them, in-depth exploration of ligand-driven protein dynamics contributes to an optimal understanding of protein func ... Full text Link to item Cite

Disentangled-Multimodal Adversarial Autoencoder: Application to Infant Age Prediction With Incomplete Multimodal Neuroimages.

Journal Article IEEE Trans Med Imaging · December 2020 Effective fusion of structural magnetic resonance imaging (sMRI) and functional magnetic resonance imaging (fMRI) data has the potential to boost the accuracy of infant age prediction thanks to the complementary information provided by different imaging mo ... Full text Link to item Cite

LocusFocus: Web-based colocalization for the annotation and functional follow-up of GWAS.

Journal Article PLoS Comput Biol · October 2020 Genome-wide association studies (GWAS) have primarily identified trait-associated loci in the non-coding genome. Colocalization analyses of SNP associations from GWAS with expression quantitative trait loci (eQTL) evidence enable the generation of hypothes ... Full text Link to item Cite

ConSTGAT: Contextual Spatial-Temporal Graph Attention Network for Travel Time Estimation at Baidu Maps

Conference Proceedings of the ACM SIGKDD International Conference on Knowledge Discovery and Data Mining · August 23, 2020 The task of travel time estimation (TTE), which estimates the travel time for a given route and departure time, plays an important role in intelligent transportation systems such as navigation, route planning, and ride-hailing services. This task is challe ... Full text Cite

Viral vectors for neuronal cell type-specific visualization and manipulations.

Journal Article Curr Opin Neurobiol · August 2020 Characterizing neuronal cell types demands efficient strategies for specific labeling and manipulation of individual subtypes to dissect their connectivity and functions. Recombinant viral technology offers a powerful toolbox for targeted transgene express ... Full text Link to item Cite

Graph attention convolutional neural network model for chemical poisoning of honey bees’ prediction

Journal Article Science Bulletin · July 30, 2020 The impact of pesticides on insect pollinators has caused worldwide concern. Both global bee decline and stopping the use of pesticides may have serious consequences for food security. Automated and accurate prediction of chemical poisoning of honey bees i ... Full text Cite

Recurrent circuitry is required to stabilize piriform cortex odor representations across brain states.

Journal Article Elife · July 14, 2020 Pattern completion, or the ability to retrieve stable neural activity patterns from noisy or partial cues, is a fundamental feature of memory. Theoretical studies indicate that recurrently connected auto-associative or discrete attractor networks can perfo ... Full text Open Access Link to item Cite

General anesthetics activate a potent central pain-suppression circuit in the amygdala.

Journal Article Nat Neurosci · July 2020 General anesthesia (GA) can produce analgesia (loss of pain) independent of inducing loss of consciousness, but the underlying mechanisms remain unclear. We hypothesized that GA suppresses pain in part by activating supraspinal analgesic circuits. We disco ... Full text Open Access Link to item Cite

Auto In Silico Ligand Directing Evolution to Facilitate the Rapid and Efficient Discovery of Drug Lead

Journal Article Iscience · June 26, 2020 Pharmaceutical Science; Chemistry; Computational Chemistry ... Full text Cite

AIMMS suite: a web server dedicated for prediction of drug resistance on protein mutation.

Journal Article Brief Bioinform · January 17, 2020 Drug resistance is one of the most intractable issues for successful treatment in current clinical practice. Although many mutations contributing to drug resistance have been identified, the relationship between the mutations and the related pharmacologica ... Full text Link to item Cite

The bottom-up and top-down processing of faces in the human occipitotemporal cortex.

Journal Article Elife · January 14, 2020 Although face processing has been studied extensively, the dynamics of how face-selective cortical areas are engaged remains unclear. Here, we uncovered the timing of activation in core face-selective regions using functional Magnetic Resonance Imaging and ... Full text Link to item Cite

Interrelationships among common predictors of cardiovascular diseases in patients of OSA: A large-scale observational study.

Journal Article Nutr Metab Cardiovasc Dis · January 3, 2020 BACKGROUND AND AIMS: The apolipoprotein B/apolipoprotein A-I (ApoB/ApoA-I) and insulin resistance has been recognized as common cardiovascular diseases (CVD) risk factors. However, whether they were biomarkers for 10-year CVD risk in obstructive sleep apne ... Full text Link to item Cite

Axon maintenance and degeneration

Chapter · January 1, 2020 In this chapter, we will first introduce several key molecular cellular mechanisms that are involved in maintaining axonal integrity during postnatal growth and throughout an animal's entire life span. These include both neuronal-intrinsic mechanisms, such ... Full text Cite

PLATO: Pre-trained dialogue generation model with discrete latent variable

Conference Proceedings of the Annual Meeting of the Association for Computational Linguistics · January 1, 2020 Pre-training models have been proved effective for a wide range of natural language processing tasks. Inspired by this, we propose a novel dialogue generation pre-training framework to support various kinds of conversations, including chit-chat, knowledge ... Cite

Multi-task Dynamic Transformer Network for Concurrent Bone Segmentation and Large-Scale Landmark Localization with Dental CBCT

Conference Lecture Notes in Computer Science Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics · January 1, 2020 Accurate bone segmentation and anatomical landmark localization are essential tasks in computer-aided surgical simulation for patients with craniomaxillofacial (CMF) deformities. To leverage the complementarity between the two tasks, we propose an efficien ... Full text Cite

Construction of Spatiotemporal Infant Cortical Surface Functional Templates

Conference Lecture Notes in Computer Science Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics · January 1, 2020 Infant cortical surface templates play an essential role in spatial normalization of cortical surfaces across individuals in pediatric neuroimaging analysis. However, existing infant surface templates have two major limitations in functional MRI analysis. ... Full text Cite

Disentangled Intensive Triplet Autoencoder for Infant Functional Connectome Fingerprinting

Conference Lecture Notes in Computer Science Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics · January 1, 2020 Functional connectome “fingerprint” is a highly characterized brain pattern that distinguishes one individual from others. Although its existence has been demonstrated in adults, an unanswered but fundamental question is whether such individualized pattern ... Full text Cite

Know more about each other: Evolving dialogue strategy via compound assessment

Conference Acl 2019 57th Annual Meeting of the Association for Computational Linguistics Proceedings of the Conference · January 1, 2020 In this paper, a novel Generation-Evaluation framework is developed for multi-turn conversations with the objective of letting both participants know more about each other. For the sake of rational knowledge utilization and coherent conversation flow, a di ... Cite

Mapping hemispheric asymmetries of the macaque cerebral cortex during early brain development.

Journal Article Hum Brain Mapp · January 2020 Studying cortical hemispheric asymmetries during the dynamic early postnatal stages in macaque monkeys (with close phylogenetic relationship to humans) would increase our limited understanding on the possible origins, developmental trajectories, and evolut ... Full text Link to item Cite

Association between Upper-airway Surgery and Ameliorative Risk Markers of Endothelial Function in Obstructive Sleep Apnea.

Journal Article Sci Rep · December 27, 2019 The objective of our study was to evaluate the effects of upper-airway surgery on improvement of endothelial function-related markers in patients with obstructive sleep apnea (OSA). Subjects with moderate to severe OSA who underwent upper-airway surgery, w ... Full text Link to item Cite

ACID: a free tool for drug repurposing using consensus inverse docking strategy

Journal Article Journal of Cheminformatics · November 27, 2019 Drug repurposing offers a promising alternative to dramatically shorten the process of traditional de novo development of a drug. These efforts leverage the fact that a single molecule can act on multiple targets and could be beneficial to indications wher ... Full text Cite

Fetal cortical surface atlas parcellation based on growth patterns.

Journal Article Hum Brain Mapp · September 2019 Defining anatomically and functionally meaningful parcellation maps on cortical surface atlases is of great importance in surface-based neuroimaging analysis. The conventional cortical parcellation maps are typically defined based on anatomical cortical fo ... Full text Link to item Cite

The association between obstructive sleep apnea syndrome and metabolic syndrome: a confirmatory factor analysis.

Journal Article Sleep Breath · September 2019 BACKGROUND: Growing evidence suggests an independent relationship between obstructive sleep apnea syndrome (OSAS) and metabolic syndrome (MS). Patients with OSAS always show clustering of metabolic components. However, the understanding of interplay betwee ... Full text Link to item Cite

A Specialized Neural Circuit Gates Social Vocalizations in the Mouse.

Journal Article Neuron · August 7, 2019 Vocalizations are fundamental to mammalian communication, but the underlying neural circuits await detailed characterization. Here, we used an intersectional genetic method to label and manipulate neurons in the midbrain periaqueductal gray (PAG) that are ... Full text Link to item Cite

Developmental topography of cortical thickness during infancy.

Journal Article Proc Natl Acad Sci U S A · August 6, 2019 During the first 2 postnatal years, cortical thickness of the human brain develops dynamically and spatially heterogeneously and likely peaks between 1 and 2 y of age. The striking development renders this period critical for later cognitive outcomes and v ... Full text Link to item Cite

A Common Neuroendocrine Substrate for Diverse General Anesthetics and Sleep.

Journal Article Neuron · June 5, 2019 How general anesthesia (GA) induces loss of consciousness remains unclear, and whether diverse anesthetic drugs and sleep share a common neural pathway is unknown. Previous studies have revealed that many GA drugs inhibit neural activity through targeting ... Full text Link to item Cite

Construction of 4d neonatal cortical surface atlases using wasserstein distance

Conference Proceedings International Symposium on Biomedical Imaging · April 1, 2019 Spatiotemporal (4D) neonatal cortical surface atlases with densely sampled ages are important tools for understanding the dynamic early brain development. Conventionally, after non-linear co-registration, surface atlases are constructed by simple Euclidean ... Full text Cite

Charting development-based joint parcellation maps of human and macaque brains during infancy

Conference Proceedings International Symposium on Biomedical Imaging · April 1, 2019 Comparative characterization of early brain development between human and macaque using neuroimaging data is crucial to understand the mechanisms of brain development and evolution. To this end, joint cortical parcellation maps of human and macaque infant ... Full text Cite

Cortical foldingprints for infant identification

Conference Proceedings International Symposium on Biomedical Imaging · April 1, 2019 Cortical folding of the adult brain is highly convoluted and encodes inter-subject variable characteristics. Recent studies suggest that it is useful for individual identification in adults. However, little is known about whether the infant cortical foldin ... Full text Cite

Benchmark on Automatic 6-month-old Infant Brain Segmentation Algorithms: The iSeg-2017 Challenge.

Journal Article IEEE Trans Med Imaging · February 27, 2019 Accurate segmentation of infant brain magnetic resonance (MR) images into white matter (WM), gray matter (GM), and cerebrospinal fluid (CSF) is an indispensable foundation for early studying of brain growth patterns and morphological changes in neurodevelo ... Full text Link to item Cite

InsectiPAD: A Web Tool Dedicated to Exploring Physicochemical Properties and Evaluating Insecticide-Likeness of Small Molecules.

Journal Article J Chem Inf Model · February 25, 2019 The concept of insecticide-likeness is valuable to select more promising lead candidates during the early stages of drug discovery. We analyzed the physicochemical properties of commercial insecticides and optimized available drug-likeness scoring function ... Full text Link to item Cite

FungiPAD: A Free Web Tool for Compound Property Evaluation and Fungicide-Likeness Analysis.

Journal Article J Agric Food Chem · February 20, 2019 The increasing prevalence of fungal diseases, continual development of resistance, and stringent environmental regulations have revealed an urgent need to develop more selective, safer, resistance-breaking, and cost-effective fungicides. However, most new ... Full text Link to item Cite

Genetic association and transcriptome integration identify contributing genes and tissues at cystic fibrosis modifier loci.

Journal Article PLoS Genet · February 2019 Cystic Fibrosis (CF) exhibits morbidity in several organs, including progressive lung disease in all patients and intestinal obstruction at birth (meconium ileus) in ~15%. Individuals with the same causal CFTR mutations show variable disease presentation w ... Full text Link to item Cite

A System for Learning Atoms Based on Long Short-Term Memory Recurrent Neural Networks

Conference Proceedings 2018 IEEE International Conference on Bioinformatics and Biomedicine Bibm 2018 · January 21, 2019 In recent years, researchers in the fields of bioinformatics and cheminformatics have attempted to utilize machine learning methods for molecule modeling, bioactivity prediction, chemical property prediction, biology analysis, etc. In this paper, we presen ... Full text Cite

Computational neuroanatomy of baby brains: A review.

Journal Article Neuroimage · January 15, 2019 The first postnatal years are an exceptionally dynamic and critical period of structural, functional and connectivity development of the human brain. The increasing availability of non-invasive infant brain MR images provides unprecedented opportunities fo ... Full text Link to item Cite

Identifying Parabrachial Neurons Selectively Regulating Satiety for Highly Palatable Food in Mice.

Journal Article eNeuro · 2019 Food consumption is necessary for organisms to maintain metabolic homeostasis. Both extrinsic and intrinsic processes, relayed via intricate neural circuitry, orchestrate the initiation and termination of food intake. More specifically, there are functiona ... Full text Link to item Cite

Observing the steady-state visual evoked potentials with a compact quad-channel spin exchange relaxation-free magnetometer

Journal Article Chinese Physics B · January 1, 2019 We observed the steady-state visually evoked potential (SSVEP) from a healthy subject using a compact quad-channel potassium spin exchange relaxation-free (SERF) optically pumped magnetometer (OPM). To this end, 30 s of data were collected, and SSVEP-relat ... Full text Cite

Molecular-scale structures of uranyl surface complexes on hematite facets

Journal Article Environmental Science Nano · January 1, 2019 As the fate, transport and bioavailability of U(vi) in subsurface environments are strongly influenced by its adsorption structures on iron minerals such as hematite, we systematically studied the molecular-scale structures of U(vi) complexes formed at the ... Full text Cite

Revealing Developmental Regionalization of Infant Cerebral Cortex Based on Multiple Cortical Properties

Conference Lecture Notes in Computer Science Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics · January 1, 2019 The human brain develops dynamically and regionally heterogeneously during the first two postnatal years. Cortical developmental regionalization, i.e., the landscape of cortical heterogeneity in development, reflects the organization of underlying microstr ... Full text Cite

Learning to select knowledge for response generation in dialog systems

Conference Ijcai International Joint Conference on Artificial Intelligence · January 1, 2019 End-to-end neural models for intelligent dialogue systems suffer from the problem of generating uninformative responses. Various methods were proposed to generate more informative responses by leveraging external knowledge. However, few previous work has f ... Full text Cite

Generating multiple diverse responses with multi-mapping and posterior mapping selection

Conference Ijcai International Joint Conference on Artificial Intelligence · January 1, 2019 In human conversation an input post is open to multiple potential responses, which is typically regarded as a one-to-many problem. Promising approaches mainly incorporate multiple latent mechanisms to build the one-to-many relationship. However, without ac ... Full text Cite

A computational method for longitudinal mapping of orientation-specific expansion of cortical surface in infants.

Journal Article Med Image Anal · October 2018 The cortical surface of the human brain expands dynamically and regionally heterogeneously during the first postnatal year. As all primary and secondary cortical folds as well as many tertiary cortical folds are well established at term birth, the cortical ... Full text Link to item Cite

PADFrag: A Database Built for the Exploration of Bioactive Fragment Space for Drug Discovery.

Journal Article J Chem Inf Model · September 24, 2018 Structural analyses of drugs and pesticides can enable the identification of new bioactive compounds with novel and diverse scaffolds as well as improve our understanding of the bioactive fragment space. The Pesticide And Drug Fragments (PADFrag) database ... Full text Link to item Cite

MIN1PIPE: A Miniscope 1-Photon-Based Calcium Imaging Signal Extraction Pipeline.

Journal Article Cell Rep · June 19, 2018 In vivo calcium imaging using a 1-photon-based miniscope and a microendoscopic lens enables studies of neural activities in freely behaving animals. However, the high and fluctuating background, the inevitable movements and distortions of imaging field, an ... Full text Link to item Cite

Publisher Correction: A craniofacial-specific monosynaptic circuit enables heightened affective pain.

Journal Article Nat Neurosci · June 2018 In the version of this article initially published, ORCID links were missing for authors Erica Rodriguez, Koji Toda and Fan Wang. The error has been corrected in the HTML and PDF versions of the article. ... Full text Link to item Cite

Fetal cortical parcellation based on growth patterns

Conference Proceedings International Symposium on Biomedical Imaging · May 23, 2018 Dividing the human cerebral cortex into structurally and functionally distinct regions is important in many neuroimaging studies. Although many parcellations have been created for adults, they are not applicable for fetal studies, due to dramatic differenc ... Full text Cite

A computational method for longitudinal mapping of orientation-specific expansion of cortical surface area in infants

Conference Proceedings International Symposium on Biomedical Imaging · May 23, 2018 The dynamic expansion of the human cortical surface during infancy is largely driven by the increase of surface area in two orthogonal directions: 1) the expansion parallel to the folding orientation (i.e., increasing the lengths of folds) and 2) the expan ... Full text Cite

Construction of spatiotemporal infant cortical surface atlas of rhesus macaque

Conference Proceedings International Symposium on Biomedical Imaging · May 23, 2018 As a widely used animal model in MR imaging studies, rhesus macaque helps to better understand both normal and abnormal neural development in the human brain. However, the available adult macaque brain atlases are not well suitable for study of brain devel ... Full text Cite

Vibrissa sensory neurons: Linking distinct morphology to specific physiology and function.

Journal Article Neuroscience · January 1, 2018 Rodents use an array of long tactile facial hairs, the vibrissae, to locate and discriminate objects. Each vibrissa is densely innervated by multiple different types of trigeminal (TG) sensory neurons. Based on the sensory ending morphology, there are at l ... Full text Link to item Cite

Circuits in the rodent brainstem that control whisking in concert with other orofacial motor actions.

Journal Article Neuroscience · January 1, 2018 The world view of rodents is largely determined by sensation on two length scales. One is within the animal's peri-personal space; sensorimotor control on this scale involves active movements of the nose, tongue, head, and vibrissa, along with sniffing to ... Full text Link to item Cite

Central nervous system pain pathways

Chapter · January 1, 2018 Cite

Intervention Aided Reinforcement Learning for Safe and Practical Policy Optimization in Navigation

Conference Proceedings of Machine Learning Research · January 1, 2018 Combining deep neural networks with reinforcement learning has shown great potential in the next-generation intelligent control. However, there are challenges in terms of safety and cost in practical applications. In this paper, we propose the Intervention ... Cite

A craniofacial-specific monosynaptic circuit enables heightened affective pain.

Journal Article Nat Neurosci · December 2017 Humans often rank craniofacial pain as more severe than body pain. Evidence suggests that a stimulus of the same intensity induces stronger pain in the face than in the body. However, the underlying neural circuitry for the differential processing of facia ... Full text Open Access Link to item Cite

Sodium channel NaV1.3 is important for enterochromaffin cell excitability and serotonin release.

Journal Article Sci Rep · November 15, 2017 In the gastrointestinal (GI) epithelium, enterochromaffin (EC) cells are enteroendocrine cells responsible for producing >90% of the body's serotonin (5-hydroxytryptamine, 5-HT). However, the molecular mechanisms of EC cell function are poorly understood. ... Full text Link to item Cite

Perceptual integration rapidly activates dorsal visual pathway to guide local processing in early visual areas.

Journal Article PLoS Biol · November 2017 Rapidly grouping local elements into an organized object (i.e., perceptual integration) is a fundamental yet challenging task, especially in noisy contexts. Previous studies demonstrate that ventral visual pathway, which is widely known to mediate object r ... Full text Link to item Cite

Parallel Inhibitory and Excitatory Trigemino-Facial Feedback Circuitry for Reflexive Vibrissa Movement.

Journal Article Neuron · August 2, 2017 Animals employ active touch to optimize the acuity of their tactile sensors. Prior experimental results and models lead to the hypothesis that sensory inputs are used in a recurrent manner to tune the position of the sensors. A combination of electrophysio ... Full text Link to item Cite

Parallel Inhibitory and Excitatory Trigemino-Facial Feedback Circuitry for Reflexive Vibrissa Movement.

Journal Article Neuron · August 2, 2017 Full text Link to item Cite

Mechanosensitive ion channel Piezo2 is important for enterochromaffin cell response to mechanical forces.

Journal Article J Physiol · January 1, 2017 KEY POINTS: The gastrointestinal epithelial enterochromaffin (EC) cell synthesizes the vast majority of the body's serotonin. As a specialized mechanosensor, the EC cell releases this serotonin in response to mechanical forces. However, the molecular mecha ... Full text Link to item Cite

Capturing and Manipulating Activated Neuronal Ensembles with CANE Delineates a Hypothalamic Social-Fear Circuit.

Journal Article Neuron · November 23, 2016 Featured Publication We developed a technology (capturing activated neuronal ensembles [CANE]) to label, manipulate, and transsynaptically trace neural circuits that are transiently activated in behavioral contexts with high efficiency and temporal precision. CANE consists of ... Full text Open Access Link to item Cite

Supratrigeminal Bilaterally Projecting Neurons Maintain Basal Tone and Enable Bilateral Phasic Activation of Jaw-Closing Muscles.

Journal Article J Neurosci · July 20, 2016 UNLABELLED: Anatomical studies have identified brainstem neurons that project bilaterally to left and right oromotor pools, which could potentially mediate bilateral muscle coordination. We use retrograde lentiviruses combined with a split-intein-mediated ... Full text Link to item Cite

Altered mGluR5-Homer scaffolds and corticostriatal connectivity in a Shank3 complete knockout model of autism.

Journal Article Nat Commun · May 10, 2016 Human neuroimaging studies suggest that aberrant neural connectivity underlies behavioural deficits in autism spectrum disorders (ASDs), but the molecular and neural circuit mechanisms underlying ASDs remain elusive. Here, we describe a complete knockout m ... Full text Open Access Link to item Cite

Inhibition, Not Excitation, Drives Rhythmic Whisking.

Journal Article Neuron · April 20, 2016 Sniffing and whisking typify the exploratory behavior of rodents. These actions involve separate oscillators in the medulla, located respectively in the pre-Bötzinger complex (preBötC) and the vibrissa-related region of the intermediate reticular formation ... Full text Open Access Link to item Cite

Inhibition of mechanical allodynia in neuropathic pain by TLR5-mediated A-fiber blockade.

Journal Article Nat Med · November 2015 Mechanical allodynia, induced by normally innocuous low-threshold mechanical stimulation, represents a cardinal feature of neuropathic pain. Blockade or ablation of high-threshold, small-diameter unmyelinated group C nerve fibers (C-fibers) has limited eff ... Full text Link to item Cite

Identifying local and descending inputs for primary sensory neurons.

Journal Article J Clin Invest · October 1, 2015 Primary pain and touch sensory neurons not only detect internal and external sensory stimuli, but also receive inputs from other neurons. However, the neuronal derived inputs for primary neurons have not been systematically identified. Using a monosynaptic ... Full text Link to item Cite

Spine pruning drives antipsychotic-sensitive locomotion via circuit control of striatal dopamine.

Journal Article Nat Neurosci · June 2015 Psychiatric and neurodevelopmental disorders may arise from anomalies in long-range neuronal connectivity downstream of pathologies in dendritic spines. However, the mechanisms that may link spine pathology to circuit abnormalities relevant to atypical beh ... Full text Link to item Cite

Feedback in the brainstem: an excitatory disynaptic pathway for control of whisking.

Journal Article J Comp Neurol · April 15, 2015 Sensorimotor processing relies on hierarchical neuronal circuits to mediate sensory-driven behaviors. In the mouse vibrissa system, trigeminal brainstem circuits are thought to mediate the first stage of vibrissa scanning control via sensory feedback that ... Full text Link to item Cite

Lack of evidence for ectopic sprouting of genetically labeled Aβ touch afferents in inflammatory and neuropathic trigeminal pain.

Journal Article Mol Pain · April 10, 2015 BACKGROUND: Mechanical and in particular tactile allodynia is a hallmark of chronic pain in which innocuous touch becomes painful. Previous cholera toxin B (CTB)-based neural tracing experiments and electrophysiology studies had suggested that aberrant axo ... Full text Open Access Link to item Cite

Neuroepithelial circuit formed by innervation of sensory enteroendocrine cells.

Journal Article J Clin Invest · February 2015 Satiety and other core physiological functions are modulated by sensory signals arising from the surface of the gut. Luminal nutrients and bacteria stimulate epithelial biosensors called enteroendocrine cells. Despite being electrically excitable, enteroen ... Full text Open Access Link to item Cite

Presynaptic Inputs to Any CNS Projection Neuron Identified by Dual Recombinant Virus Infection.

Journal Article PLoS One · 2015 Although neuroanatomical tracing studies have defined the origin and targets of major projection neurons (PN) of the central nervous system (CNS), there is much less information about the circuits that influence these neurons. Recently, genetic approaches ... Full text Open Access Link to item Cite

TRPV4 is necessary for trigeminal irritant pain and functions as a cellular formalin receptor.

Journal Article Pain · December 2014 Detection of external irritants by head nociceptor neurons has deep evolutionary roots. Irritant-induced aversive behavior is a popular pain model in laboratory animals. It is used widely in the formalin model, where formaldehyde is injected into the roden ... Full text Open Access Link to item Cite

Genetic interactions between Shox2 and Hox genes during the regional growth and development of the mouse limb.

Journal Article Genetics · November 2014 The growth and development of the vertebrate limb relies on homeobox genes of the Hox and Shox families, with their independent mutation often giving dose-dependent effects. Here we investigate whether Shox2 and Hox genes function together during mouse lim ... Full text Link to item Cite

State-dependent architecture of thalamic reticular subnetworks.

Journal Article Cell · August 14, 2014 Behavioral state is known to influence interactions between thalamus and cortex, which are important for sensation, action, and cognition. The thalamic reticular nucleus (TRN) is hypothesized to regulate thalamo-cortical interactions, but the underlying fu ... Full text Link to item Cite

How the brainstem controls orofacial behaviors comprised of rhythmic actions.

Journal Article Trends Neurosci · July 2014 Mammals perform a multitude of well-coordinated orofacial behaviors such as breathing, sniffing, chewing, licking, swallowing, vocalizing, and in rodents, whisking. The coordination of these actions must occur without fault to prevent fatal blockages of th ... Full text Link to item Cite

More than a rhythm of life: breathing as a binder of orofacial sensation.

Journal Article Nat Neurosci · May 2014 When rodents engage in the exploration of novel stimuli, breathing occurs at an accelerated rate that is synchronous with whisking. We review the recently observed relationships between breathing and the sensations of smell and vibrissa-based touch. We con ... Full text Link to item Cite

Monosynaptic premotor circuit tracing reveals neural substrates for oro-motor coordination.

Journal Article Elife · April 30, 2014 Feeding behaviors require intricately coordinated activation among the muscles of the jaw, tongue, and face, but the neural anatomical substrates underlying such coordination remain unclear. In this study, we investigate whether the premotor circuitry of j ... Full text Link to item Cite

The Brainstem Oscillator for Whisking and the Case for Breathing as the Master Clock for Orofacial Motor Actions.

Journal Article Cold Spring Harb Symp Quant Biol · 2014 Whisking and sniffing are predominant aspects of exploratory behavior in rodents. We review evidence that these motor rhythms are coordinated by the respiratory patterning circuitry in the ventral medulla. A recently described region in the intermediate re ... Full text Link to item Cite

The organization of submodality-specific touch afferent inputs in the vibrissa column.

Journal Article Cell Rep · October 17, 2013 The rodent tactile vibrissae are innervated by several different types of touch sensory neurons. The central afferents of all touch neurons from one vibrissa collectively project to a columnar structure called a barrelette in the brainstem. Delineating how ... Full text Link to item Cite

A circuit for motor cortical modulation of auditory cortical activity.

Journal Article J Neurosci · September 4, 2013 Normal hearing depends on the ability to distinguish self-generated sounds from other sounds, and this ability is thought to involve neural circuits that convey copies of motor command signals to various levels of the auditory system. Although such interac ... Full text Link to item Cite

Axon Maintenance and Degeneration

Journal Article · August 29, 2013 Full text Cite

Loss of NR1 subunit of NMDARs in primary sensory neurons leads to hyperexcitability and pain hypersensitivity: involvement of Ca(2+)-activated small conductance potassium channels.

Journal Article J Neurosci · August 14, 2013 It is well established that activation of NMDARs plays an essential role in spinal cord synaptic plasticity (i.e., central sensitization) and pain hypersensitivity after tissue injury. Despite prominent expression of NMDARs in DRG primary sensory neurons, ... Full text Link to item Cite

Temporomandibular joint pain: a critical role for Trpv4 in the trigeminal ganglion.

Journal Article Pain · August 2013 Temporomandibular joint disorder (TMJD) is known for its mastication-associated pain. TMJD is medically relevant because of its prevalence, severity, chronicity, the therapy-refractoriness of its pain, and its largely elusive pathogenesis. Against this bac ... Full text Open Access Link to item Cite

New modules are added to vibrissal premotor circuitry with the emergence of exploratory whisking.

Journal Article Neuron · January 23, 2013 Rodents begin to use bilaterally coordinated, rhythmic sweeping of their vibrissae ("whisking") for environmental exploration around 2 weeks after birth. Whether (and how) the vibrissal control circuitry changes after birth is unknown, and the relevant pre ... Full text Link to item Cite

Regulation of mammalian autophagy by class II and III PI 3-kinases through PI3P synthesis.

Journal Article PLoS One · 2013 Synthesis of phosphatidylinositol-3-phosphate (PI3P) by Vps34, a class III phosphatidylinositol 3-kinase (PI3K), is critical for the initial steps of autophagosome (AP) biogenesis. Although Vps34 is the sole source of PI3P in budding yeast, mammalian cells ... Full text Link to item Cite

Sexually dimorphic BDNF signaling directs sensory innervation of the mammary gland.

Journal Article Science · December 7, 2012 How neural circuits associated with sexually dimorphic organs are differentially assembled during development is unclear. Here, we report a sexually dimorphic pattern of mouse mammary gland sensory innervation and the mechanism of its formation. Brain-deri ... Full text Link to item Cite

Generation and characterization of Tmeff2 mutant mice.

Journal Article Biochem Biophys Res Commun · August 24, 2012 TMEFF2 is a single-transmembrane protein containing one EGF-like and two follistatin-like domains. Some studies implicated TMEFF2 as a tumor suppressor for prostate and other cancers, whereas others reported TMEFF2 functioning as a growth factor for neuron ... Full text Link to item Cite

The calcium-activated chloride channel anoctamin 1 acts as a heat sensor in nociceptive neurons.

Journal Article Nat Neurosci · May 27, 2012 Nociceptors are a subset of small primary afferent neurons that respond to noxious chemical, thermal and mechanical stimuli. Ion channels in nociceptors respond differently to noxious stimuli and generate electrical signals in different ways. Anoctamin 1 ( ... Full text Link to item Cite

Distinct Nav1.7-dependent pain sensations require different sets of sensory and sympathetic neurons.

Journal Article Nat Commun · April 24, 2012 Human acute and inflammatory pain requires the expression of voltage-gated sodium channel Nav1.7 but its significance for neuropathic pain is unknown. Here we show that Nav1.7 expression in different sets of mouse sensory and sympathetic neurons underlies ... Full text Link to item Cite

Axonally translated SMADs link up BDNF and retrograde BMP signaling.

Journal Article Neuron · April 12, 2012 Axonal target-derived BMP and neurotrophin signaling are both known to regulate neuronal gene expression, differentiation, and axon growth. In this issue of Neuron, Ji and Jaffrey (2012) discovered that BMP-signaling endosomes depend on BDNF-induced axonal ... Full text Link to item Cite

Guidelines for the use and interpretation of assays for monitoring autophagy.

Journal Article Autophagy · April 2012 In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have ... Full text Link to item Cite

Sodium channels and mammalian sensory mechanotransduction.

Journal Article Mol Pain · March 26, 2012 BACKGROUND: Members of the degenerin/epithelial (DEG/ENaC) sodium channel family are mechanosensors in C elegans, and Nav1.7 and Nav1.8 voltage-gated sodium channel knockout mice have major deficits in mechanosensation. β and γENaC sodium channel subunits ... Full text Link to item Cite

Sodium channels and mammalian sensory mechanotransduction

Journal Article Molecular Pain · 2012 Background: Members of the degenerin/epithelial (DEG/ENaC) sodium channel family are mechanosensors in C elegans, and Nav1.7 and Nav1.8 voltage-gated sodium channel knockout mice have major deficits in mechanosensation. β and γENaC sodium channel subunits ... Full text Cite

Intersectional Cre driver lines generated using split-intein mediated split-Cre reconstitution.

Journal Article Sci Rep · 2012 Tissue and cell type highly specific Cre drivers are very rare due to the fact that most genes or promoters used to direct Cre expressions are generally expressed in more than one tissues and/or in multiple cell types. We developed a split-intein based spl ... Full text Link to item Cite

Temporal control of gene deletion in sensory ganglia using a tamoxifen-inducible Advillin-Cre-ERT2 recombinase mouse.

Journal Article Mol Pain · December 21, 2011 BACKGROUND: Tissue-specific gene deletion has proved informative in the analysis of pain pathways. Advillin has been shown to be a pan-neuronal marker of spinal and cranial sensory ganglia. We generated BAC transgenic mice using the Advillin promoter to dr ... Full text Link to item Cite

The class III kinase Vps34 promotes T lymphocyte survival through regulating IL-7Rα surface expression.

Journal Article J Immunol · November 15, 2011 IL-7Rα-mediated signals are essential for naive T lymphocyte survival. Recent studies show that IL-7Rα is internalized and either recycled to cell surface or degraded. However, how the intracellular process of IL-7Rα trafficking is regulated is unclear. In ... Full text Link to item Cite

Ectopic myelinating oligodendrocytes in the dorsal spinal cord as a consequence of altered semaphorin 6D signaling inhibit synapse formation.

Journal Article Development · September 2011 Different types of sensory neurons in the dorsal root ganglia project axons to the spinal cord to convey peripheral information to the central nervous system. Whereas most proprioceptive axons enter the spinal cord medially, cutaneous axons typically do so ... Full text Link to item Cite

Transcription factor short stature homeobox 2 is required for proper development of tropomyosin-related kinase B-expressing mechanosensory neurons.

Journal Article J Neurosci · May 4, 2011 Dorsal root ganglia (DRG) contain somatosensory neurons of diverse sensory modalities. Among these different types of sensory neurons, the molecular mechanisms that regulate the development and specification of touch neurons are the least well understood. ... Full text Link to item Cite

Proper formation of whisker barrelettes requires periphery-derived Smad4-dependent TGF-beta signaling.

Journal Article Proc Natl Acad Sci U S A · February 22, 2011 Mammalian somatosensory topographic maps contain specialized neuronal structures that precisely recapitulate the spatial pattern of peripheral sensory organs. In the mouse, whiskers are orderly mapped onto several brainstem nuclei as a set of modular struc ... Full text Link to item Cite

Retrograde neural circuit specification by target-derived neurotrophins and growth factors.

Journal Article Curr Opin Neurobiol · February 2011 Neural circuit assembly during development involves a series of highly regulated steps. While genetically pre-determined programs play key roles in the early steps including neurogenesis, migration, and initial growth and guidance of axons; increasing evid ... Full text Link to item Cite

The mammalian class 3 PI3K (PIK3C3) is required for early embryogenesis and cell proliferation.

Journal Article PLoS One · January 20, 2011 The Pik3c3 gene encodes an 887 amino acid lipid kinase, phosphoinositide-3-kinase class 3 (PIK3C3). PIK3C3 is known to regulate various intracellular membrane trafficking events. However, little is known about its functions during early embryogenesis in ma ... Full text Link to item Cite

Pik3c3 deletion in pyramidal neurons results in loss of synapses, extensive gliosis and progressive neurodegeneration.

Journal Article Neuroscience · January 13, 2011 The lipid kinase PIK3C3 (also known as VPS34) regulates multiple aspects of endo-membrane trafficking processes. PIK3C3 is widely expressed by neurons in the CNS, and its catalytic product PI3P is enriched in dendritic spines. Here we generated a line of c ... Full text Link to item Cite

Activity-induced remodeling of olfactory bulb microcircuits revealed by monosynaptic tracing.

Journal Article PLoS One · 2011 The continued addition of new neurons to mature olfactory circuits represents a remarkable mode of cellular and structural brain plasticity. However, the anatomical configuration of newly established circuits, the types and numbers of neurons that form new ... Full text Link to item Cite

BMP signaling in the development of the mouse esophagus and forestomach.

Journal Article Development · December 2010 The stratification and differentiation of the epidermis are known to involve the precise control of multiple signaling pathways. By contrast, little is known about the development of the mouse esophagus and forestomach, which are composed of a stratified s ... Full text Open Access Link to item Cite

Mammalian target of rapamycin (mTOR) activation increases axonal growth capacity of injured peripheral nerves.

Journal Article J Biol Chem · September 3, 2010 Unlike neurons in the central nervous system (CNS), injured neurons in the peripheral nervous system (PNS) can regenerate their axons and reinnervate their targets. However, functional recovery in the PNS often remains suboptimal, especially in cases of se ... Full text Link to item Cite

Effects of neuronal PIK3C3/Vps34 deletion on autophagy and beyond.

Journal Article Autophagy · August 2010 PIK3C3/Vps34 plays important roles in the endocytic and autophagic pathways, both of which are essential for maintaining neuronal integrity. However, it is unclear how inactivating PIK3C3 may affect neuronal endosomal versus autophagic processes in vivo. W ... Full text Open Access Link to item Cite

Deletion of PIK3C3/Vps34 in sensory neurons causes rapid neurodegeneration by disrupting the endosomal but not the autophagic pathway.

Journal Article Proc Natl Acad Sci U S A · May 18, 2010 The lipid kinase PIK3C3 (also called Vps34) regulates both the endosomal and autophagic pathways. However, the effect of inactivating PIK3C3 on neuronal endosomal versus autophagic processes in vivo has not been studied. We generated mice in which Pik3c3 w ... Full text Link to item Cite

The role of Scgb1a1+ Clara cells in the long-term maintenance and repair of lung airway, but not alveolar, epithelium.

Journal Article Cell Stem Cell · June 5, 2009 To directly test the contribution of Scgb1a1(+) Clara cells to postnatal growth, homeostasis, and repair of lung epithelium, we generated a Scgb1a1-CreER "knockin" mouse for lineage-tracing these cells. Under all conditions tested, the majority of Clara ce ... Full text Link to item Cite

Erratum: N-myc alters the fate of preneoplastic cells in a mouse model of medulloblastoma (Genes and Development (2009) 23 (157-170))

Journal Article Genes and Development · February 15, 2009 Cite

N-myc alters the fate of preneoplastic cells in a mouse model of medulloblastoma.

Journal Article Genes Dev · January 15, 2009 Studying the early stages of cancer can provide important insight into the molecular basis of the disease. We identified a preneoplastic stage in the patched (ptc) mutant mouse, a model for the brain tumor medulloblastoma. Preneoplastic cells (PNCs) are fo ... Full text Link to item Cite

Class III phosphatidylinositol 3-kinase (Vps34) is essential for radial neuronal migration in the developing neocortex

Journal Article Neuroscience Research · January 2009 Full text Cite

Axon Guidance: Building Pathways with Molecular Cues in Vertebrate Sensory Systems

Journal Article · January 1, 2009 In this article, we briefly review the axon guidance molecules that work in concert to orchestrate the pathfinding processes that lead to the formation of sensory systems. We focus on the visual and the olfactory systems, outline key axon guidance processe ... Full text Cite

Visualizing mechanosensory endings of TrkC-expressing neurons in HS3ST-2-hPLAP mice.

Journal Article J Comp Neurol · December 1, 2008 Somatosensory neurons are classified into three main types according to their modalities: nociceptive, thermal, and mechanosensory. Within each modality group, neurons can be further divided into morphologically and functionally distinct subclasses. Here w ... Full text Link to item Cite

Mesothelium contributes to vascular smooth muscle and mesenchyme during lung development.

Journal Article Proc Natl Acad Sci U S A · October 28, 2008 During mouse development, the sophisticated vascular network of the lung is established from embryonic day (E) approximately 10.5 and continues to develop postnatally. This network is composed of endothelial cells enclosed by vascular smooth muscle, pericy ... Full text Link to item Cite

Analyzing somatosensory axon projections with the sensory neuron-specific Advillin gene

Journal Article NEUROSCIENCE RESEARCH · January 1, 2008 Link to item Cite

Analyzing somatosensory axon projections with the sensory neuron-specific Advillin gene.

Journal Article J Neurosci · December 26, 2007 Peripheral sensory neurons detect diverse physical stimuli and transmit the information into the CNS. At present, the genetic tools for specifically studying the development, plasticity, and regeneration of the sensory axon projections are limited. We foun ... Full text Link to item Cite

Retrograde BMP signaling regulates trigeminal sensory neuron identities and the formation of precise face maps.

Journal Article Neuron · August 16, 2007 Somatosensory information from the face is transmitted to the brain by trigeminal sensory neurons. It was previously unknown whether neurons innervating distinct areas of the face possess molecular differences. We have identified a set of genes differentia ... Full text Link to item Cite

Unc-51-like kinase 1/2-mediated endocytic processes regulate filopodia extension and branching of sensory axons.

Journal Article Proc Natl Acad Sci U S A · April 3, 2007 The molecular mechanism and significance of endocytic processes involved in directional axon elongation are not well understood. The Unc-51 family of serine/threonine kinases was shown to be important for axon growth and was also linked to endocytosis, pro ... Full text Link to item Cite

Calcineurin/NFAT Signaling in Development and Function of the Nervous System

Journal Article · May 22, 2006 The four genes that encode the cytoplasmic subunits of NFAT-transcription complexes (NFATc proteins) are both transcription factors and signaling molecules. Calcium stimuli in neurons lead to the activation of calcineurin (CaN) phosphatase activity and the ... Full text Cite

Steering growth cones with a CaMKII/calcineurin switch.

Journal Article Neuron · September 16, 2004 Calcium can regulate and induce both attractive and repulsive turnings by growth cones. In this issue of Neuron, Wen et al. report that differential activations of CaMKII and calcineurin (CaN) act as the read out for distinct patterns of intracellular calc ... Full text Link to item Cite

SLIT2-mediated ROBO2 signaling restricts kidney induction to a single site.

Journal Article Dev Cell · May 2004 Kidney development occurs in a stereotypic position along the body axis. It begins when a single ureteric bud emerges from the nephric duct in response to GDNF secreted by the adjacent nephrogenic mesenchyme. Posterior restriction of Gdnf expression is con ... Full text Link to item Cite

Neurotrophins and netrins require calcineurin/NFAT signaling to stimulate outgrowth of embryonic axons.

Journal Article Cell · May 30, 2003 Axon outgrowth is the first step in the formation of neuronal connections, but the pathways that regulate axon extension are still poorly understood. We find that mice deficient in calcineurin-NFAT signaling have dramatic defects in axonal outgrowth, yet h ... Full text Link to item Cite

Formation of precise connections in the olfactory bulb occurs in the absence of odorant-evoked neuronal activity.

Journal Article Neuron · April 2000 Olfactory neurons expressing the same odorant receptor converge to a small number of glomeruli in the olfactory bulb. In turn, mitral and tufted cells receive and relay this information to higher cortical regions. In other sensory systems, correlated neuro ... Full text Link to item Cite

An olfactory sensory map develops in the absence of normal projection neurons or GABAergic interneurons.

Journal Article Neuron · December 1998 Olfactory sensory neurons expressing a given odorant receptor project to two topographically fixed glomeruli in the olfactory bulb. We have examined the contribution of different cell types in the olfactory bulb to the establishment of this topographic map ... Full text Link to item Cite

Odorant receptors govern the formation of a precise topographic map.

Journal Article Cell · April 3, 1998 Olfactory neurons expressing a given odorant receptor project with precision to 2 of the 1800 glomeruli within the olfactory bulb to create a topographic map of odor quality. We demonstrate that deletions or nonsense mutations in the P2 odorant receptor ge ... Full text Link to item Cite

Visualizing an olfactory sensory map.

Journal Article Cell · November 15, 1996 We have developed a genetic approach to visualize axons from olfactory sensory neurons expressing a given odorant receptor, as they project to the olfactory bulb. Neurons expressing a specific receptor project to only two topographically fixed loci among t ... Full text Link to item Cite

The molecular biology of olfactory perception.

Journal Article Cold Spring Harb Symp Quant Biol · 1996 Link to item Cite