Lin Gao
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View article: Integrative Genomics and Multi-Tissue Transcriptomics Identify Key Loci and Pathways for Hypoxia Tolerance in Grass Carp
Integrative Genomics and Multi-Tissue Transcriptomics Identify Key Loci and Pathways for Hypoxia Tolerance in Grass Carp Open
Hypoxia is a critical environmental stressor in aquaculture, significantly affecting the survival and growth performance of cultured fish. To explore the genetic basis of hypoxia tolerance in grass carp (Ctenopharyngodon idella), we integr…
View article: Probing the Critical Point (CritPt) of AI Reasoning: a Frontier Physics Research Benchmark
Probing the Critical Point (CritPt) of AI Reasoning: a Frontier Physics Research Benchmark Open
While large language models (LLMs) with reasoning capabilities are progressing rapidly on high-school math competitions and coding, can they reason effectively through complex, open-ended challenges found in frontier physics research? And …
View article: Voxtral
Voxtral Open
We present Voxtral Mini and Voxtral Small, two multimodal audio chat models. Voxtral is trained to comprehend both spoken audio and text documents, achieving state-of-the-art performance across a diverse range of audio benchmarks, while pr…
View article: CellLoop: Identifying single-cell 3D genome chromatin loops
CellLoop: Identifying single-cell 3D genome chromatin loops Open
Single-cell 3D genome technologies provide unprecedented views of chromatin architecture, but the extreme sparsity and noise of contact maps limit robust detection of chromatin loops at the individual cell level. Here we present CellLoop, …
View article: Aging and lung cancer: the role of macrophages
Aging and lung cancer: the role of macrophages Open
Lung cancer remains one of the leading causes of cancer-related deaths worldwide, with a significant increase in incidence among the elderly population. Tumor-associated macrophages (TAMs) are a unique subset of macrophages that play a cru…
View article: Airway microbiota associated D-phenylalanine promotes non-small cell lung cancer metastasis through epithelial mesenchymal transition
Airway microbiota associated D-phenylalanine promotes non-small cell lung cancer metastasis through epithelial mesenchymal transition Open
The airway microbiota associated D-phenylalanine could promote lung cancer metastasis via EMT, which could be a new predictor for the diagnosis of tumor metastasis in NSCLC patients.
View article: The carotid body oxygen sensor
The carotid body oxygen sensor Open
Carotid body (CB) chemoreceptor glomus cells sense hypoxia through the inhibition of plasmalemmal K+ channels, which leads to the opening of Ca2+ channels, Ca2+ influx, and neurotransmitter release. The mec…
View article: Acute oxygen sensing by arterial chemoreceptors with a mutant mitochondrial complex I <scp>ND6</scp> subunit lacking reverse electron transport
Acute oxygen sensing by arterial chemoreceptors with a mutant mitochondrial complex I <span>ND6</span> subunit lacking reverse electron transport Open
Carotid body glomus cells are essential for stimulating breathing in response to hypoxia. They contain specialized mitochondria in which hypoxia induces the accumulation of NADH and H 2 O 2 that modulate membrane ion channel activity. We i…
View article: Intracellular signalling in arterial chemoreceptors during acute hypoxia and glucose deprivation: role of ATP
Intracellular signalling in arterial chemoreceptors during acute hypoxia and glucose deprivation: role of ATP Open
The carotid body (CB) is the main oxygen (O 2 ) sensing organ that mediates reflex hyperventilation and increased cardiac output in response to hypoxaemia. Acute O 2 sensing is an intrinsic property of CB glomus cells, which contain specia…
View article: Control Signature of Nodes in Biological Networks
Control Signature of Nodes in Biological Networks Open
View article: Combining Simple Deformations to Elicit Complex Motions and Directed Swimming of Smart Organic Crystals with Controllable Thickness
Combining Simple Deformations to Elicit Complex Motions and Directed Swimming of Smart Organic Crystals with Controllable Thickness Open
The lack of control over the crystal growth in a systematic way currently stands as an unsurmountable impediment to the preparation of dynamic crystals as soft robots; in effect, the mechanical effects of molecular crystals have become a s…
View article: Combining Simple Deformations to Elicit Complex Motions and Directed Swimming of Smart Organic Crystals with Controllable Thickness
Combining Simple Deformations to Elicit Complex Motions and Directed Swimming of Smart Organic Crystals with Controllable Thickness Open
The lack of control over the crystal growth in a systematic way currently stands as an unsurmountable impediment to the preparation of dynamic crystals as soft robots; in effect, the mechanical effects of molecular crystals have become a s…
View article: SciCode: A Research Coding Benchmark Curated by Scientists
SciCode: A Research Coding Benchmark Curated by Scientists Open
Since language models (LMs) now outperform average humans on many challenging tasks, it has become increasingly difficult to develop challenging, high-quality, and realistic evaluations. We address this issue by examining LMs' capabilities…
View article: Unsupervised and supervised discovery of tissue cellular neighborhoods from cell phenotypes
Unsupervised and supervised discovery of tissue cellular neighborhoods from cell phenotypes Open
It is poorly understood how different cells in a tissue organize themselves to support tissue functions. We describe the CytoCommunity algorithm for the identification of tissue cellular neighborhoods (TCNs) based on cell phenotypes and th…
View article: Beaconet: A Reference-Free Method for Integrating Multiple Batches of Single-Cell Transcriptomic Data in Original Molecular Space
Beaconet: A Reference-Free Method for Integrating Multiple Batches of Single-Cell Transcriptomic Data in Original Molecular Space Open
The analysis code, the visualization of all correction results of benchmark methods, the preprocessed benchmark datasets in the paper "Beaconet: A Reference-Free Method for Integrating Multiple Batches of Single-Cell Transcriptomic Data in…
View article: IL-17A promotes tumorigenesis and upregulates PD-L1 expression in non-small cell lung cancer
IL-17A promotes tumorigenesis and upregulates PD-L1 expression in non-small cell lung cancer Open
Background The tumor microenvironment plays a key role in non-small cell lung cancer (NSCLC) development and also influences the effective response to immunotherapy. The pro-inflammatory factor interleukin-17A mediates important immune res…
View article: Case report: Coexistence of triple-seronegative myasthenia gravis and pathology-proven cryptogenic organizing pneumonia
Case report: Coexistence of triple-seronegative myasthenia gravis and pathology-proven cryptogenic organizing pneumonia Open
Objective Emerging evidence shows that patients with myasthenia gravis (MG) were at a higher risk for the co-occurrence of other autoimmune diseases, which reflects phenotypic heterogeneity in MG. The coexistence of MG and cryptogenic orga…
View article: Defining and identifying cell sub-crosstalk pairs for characterizing cell–cell communication patterns
Defining and identifying cell sub-crosstalk pairs for characterizing cell–cell communication patterns Open
Current cell–cell communication analysis focuses on quantifying intercellular interactions at cell type level. In the tissue microenvironment, one type of cells could be divided into multiple cell subgroups that function differently and co…
View article: Mitochondrial integrated stress response controls lung epithelial cell fate
Mitochondrial integrated stress response controls lung epithelial cell fate Open
View article: Real-time scheduling for dynamic workshops with random new job insertions by using deep reinforcement learning
Real-time scheduling for dynamic workshops with random new job insertions by using deep reinforcement learning Open
Dynamic real-time workshop scheduling on job arrival is critical for effective production. This study proposed a dynamic shop scheduling method integrating deep reinforcement learning and convolutional neural network (CNN). In this method,…
View article: Efficient Generation of Paired Single‐Cell Multiomics Profiles by Deep Learning
Efficient Generation of Paired Single‐Cell Multiomics Profiles by Deep Learning Open
Recent advances in single‐cell sequencing technology have made it possible to measure multiple paired omics simultaneously in a single cell such as cellular indexing of transcriptomes and epitopes by sequencing (CITE‐seq) and single‐nucleu…
View article: High Expression Level of BRD4 Is Associated with a Poor Prognosis and Immune Infiltration in Esophageal Squamous Cell Carcinoma
High Expression Level of BRD4 Is Associated with a Poor Prognosis and Immune Infiltration in Esophageal Squamous Cell Carcinoma Open
BRD4 is associated with poor prognosis and immune infiltration in ESCC, and may be a potential biomarker for prognosis and immunotherapy application.
View article: Transgenic NADH dehydrogenase restores oxygen regulation of breathing in mitochondrial complex I-deficient mice
Transgenic NADH dehydrogenase restores oxygen regulation of breathing in mitochondrial complex I-deficient mice Open
View article: Thymoquinone Attenuates Inflammation in C. albicans Keratitis by Activating Nrf2/HO-1 Signaling Pathway and Reducing Fungal Load
Thymoquinone Attenuates Inflammation in C. albicans Keratitis by Activating Nrf2/HO-1 Signaling Pathway and Reducing Fungal Load Open
View article: Zyxin promotes hepatocellular carcinoma progression via the activation of AKT/mTOR signaling pathway
Zyxin promotes hepatocellular carcinoma progression via the activation of AKT/mTOR signaling pathway Open
Hepatocellular carcinoma (HCC) is a common malignancy that is driven by multiple genes and pathways. The aim of this study was to investigate the role and specific mechanism of the actin-interacting protein zyxin (ZYX) in HCC. We found tha…
View article: Generic sensitivity: customizing context-sensitive pointer analysis for generics
Generic sensitivity: customizing context-sensitive pointer analysis for generics Open
Generic programming has been extensively used in object-oriented programs such as Java. However, existing context-sensitive pointer analyses perform poorly in analyzing generics. This paper introduces \emph{generic sensitivity}, a new cont…
View article: Learning predictive models of tissue cellular neighborhoods from cell phenotypes with graph pooling
Learning predictive models of tissue cellular neighborhoods from cell phenotypes with graph pooling Open
It remains poorly understood how different cell types organize and coordinate with each other to support tissue functions. We describe CytoCommunity for identification of tissue cellular neighborhoods (TCNs) based on cell phenotypes and th…
View article: Single-cell sequencing reveals effects of chemotherapy on the immune landscape and TCR/BCR clonal expansion in a relapsed ovarian cancer patient
Single-cell sequencing reveals effects of chemotherapy on the immune landscape and TCR/BCR clonal expansion in a relapsed ovarian cancer patient Open
Cancer recurrence and chemoresistance are the leading causes of death in high-grade serous ovarian cancer (HGSOC) patients. However, the unique role of the immune environment in tumor progression for relapsed chemo-resistant patients remai…
View article: Oxygen regulation of breathing is abolished in mitochondrial complex III-deficient arterial chemoreceptors
Oxygen regulation of breathing is abolished in mitochondrial complex III-deficient arterial chemoreceptors Open
Acute oxygen (O 2 ) sensing is essential for adaptation of organisms to hypoxic environments or medical conditions with restricted exchange of gases in the lung. The main acute O 2 -sensing organ is the carotid body (CB), which contains ne…
View article: Conserved Control Path in Multilayer Networks
Conserved Control Path in Multilayer Networks Open
The determination of directed control paths in complex networks is important because control paths indicate the structure of the propagation of control signals through edges. A challenging problem is to identify them in complex networked s…