Li Li

• Dr.
• Chinese Academy of Sciences

Salinity is a key environmental factor influencing the survival of aquatic organisms, and transcriptional plasticity is a crucial emergency response to environmental changes. However, most transcriptomic studies on salinity responses have not explored the expression patterns and regulatory mechanisms across different tissues. The Suminoe oyster (Cr...

Chemoresistance is the most significant challenge affecting the clinical efficacy of the treatment of patients with gastric cancer (GC). Here we reported that transmembrane protein 160 (TMEM160) suppressed ferroptosis and induced chemoresistance in GC cells. Mechanistically, TMEM160 recruited the E3 ligase TRIM37 to promote K48-linked ubiquitinatio...

Emaciation syndrome due to starvation is a significant cause of mortality in marine animals, yet the underlying mechanisms in non-feeding and weak/no-mobility marine bivalves remain poorly understood. This study investigated nutrient utilization and transcriptional responses in oysters subjected to a 44-day starvation period. Nutrient analysis reve...

Radiation-induced structural abnormalities in white matter (WM) have been reported in patients with nasopharyngeal carcinoma (NPC); however, the alterations in functional domain were insufficiently investigated. A total of 111 NPC patients were included and these patients, based on whether completed radiation therapy (RT) or not, were divided into...

Tetraploid oysters are used to cross with diploids to produce triploid oysters that have become an important part of the oyster aquaculture industry worldwide. Although most tetraploid oysters are artificially induced autotetraploids, allotetraploids can be produced between closely related species, providing new opportunities for polyploid breeding...

Clock genes regulate physiological and metabolic processes by responding to changes in environmental light and temperature, and genetic variations in these genes may facilitate environmental adaptation, offering opportunities for resilience to climate change. However, the genetic and molecular mechanisms remain unclear in marine organisms. In this...

Network-on-Chip (NoC) is a scalable on-chip communication architecture widely used in neural network accelerators. However, data-intensive applications like machine learning place significant demands on the NoC’s communication and computation, and often have a degree of resilience to data noise, which allows to use approximation techniques to reduc...

Phenotypic plasticity plays an essential role in adaptive evolution. However, the molecular mechanisms of how genotype‐by‐environment interaction (G × E) effects shape phenotypic plasticity in marine organisms remain poorly understood. The crucial temperature‐responsive trait triacylglycerol (TAG) content and its major gene adipose triglyceride lip...

Background The possible nonlinear association with therapeutic outcomes in ulcerative colitis may contribute to the inconclusive cutoff values of fecal calprotectin (FC). We aimed to explore the nonlinear association between FC levels and long-term therapeutic outcomes in patients with ulcerative colitis and establish a clinically applicable FC ind...

Long-chain polyunsaturated fatty acids (LC-PUFAs) are crucial for human health and cannot be produced internally. Bivalves, such as oysters, serve as valuable sources of high-quality PUFAs. The enzyme fatty acid desaturase (FADS) plays a key role in the metabolism of LC-PUFAs. In this study, we conducted a thorough genome-wide analysis of the genes...

AI-based breast cancer detection can improve the sensitivity and specificity of detection, especially for small lesions, which has clinical value in realizing early detection and treatment so as to reduce mortality. The two-stage detection network performs well; however, it adopts an imprecise ROI during classification, which can easily include sur...

Background Radiation-induced brain injury (RBI) is a common complication in patients with nasopharyngeal carcinoma (NPC) who have undergone radiotherapy (RT), which is characterized by significant cognitive and psychological impairments. Although radiation-induced regional structural abnormalities have been well-reported, the effects of RT on the w...

The Suminoe oyster Crassostrea ariakensis (Fujita, 1913) is one of the most important ecological and fishery bivalve mollusks with a worldwide distribution. Here, we reported an improved high-quality chromosomal-level genome assembly of C. ariakensis inhabiting the South China Sea, using Nanopore technology, Illumina sequencing, and high-throughput...

Background Several studies have confirmed the potential value of applying radiomics to predict prognosis of breast cancer. However, the tumor segmentation in these studies depended on delineation or annotation of breast cancer by radiologist, which is often laborious, tedious, and vulnerable to inter- and intra-observer variability. Automatic segme...

Phosphorylation of Ser32 and Ser36 controls the degradation of IκBα is the conserved cascade mechanisms of immune core signaling pathway, NF-κB pathway in metazoans, but it’s response to abiotic stress and the presence of novel phosphorylation mechanisms in other species remain unclear. Herein, we reported a novel heat-induced phosphorylation site...

Cysteine-aspartic proteases (caspases) are critical drivers of apoptosis, exhibiting expansion and domain shuffling in mollusks. However, the functions and regulatory mechanisms of these caspases remain unclear. In this study, we identified a group of Caspase-3/6/7 in Bivalvia and Gastropoda with a long inter-subunit linker (IL) that inhibits cleav...

In NoC-based neural network accelerators, many-to-one and many-to-many are prevalent traffic patterns. In these traffic patterns, there exists a need for communication synchronization between Processing Elements (PEs) of adjacent layers to optimize latency. The last received packet will determine the end time of a layer’s computation. The Communica...

Oysters are of the most economically important bivalves worldwide. It has high nutritional value and is regarded as a good source of proteins, lipids, glycogen, and amino acids. C. gigas and C. angulata are allopatric congeneric dominant oysters that are widely cultivated in the northern and southern coast of China, and have shown remarkable differ...

Objective Serum amyloid A (SAA) was found to be positively correlated with the activity of Crohn’s disease (CD); however, its prognostic value remains uncertain. Here, we examined its predictive ability in newly diagnosed CD and explored genetic association. Methods This retrospective cohort study included patients newly diagnosed as CD at the Fir...

Microorganisms are vital for the health of marine invertebrates, and their assembly is driven by both deterministic and stochastic factors that regulate residents (innate to the host) and transients (from ambient water). However, the role of water microbiota and the significance of deterministic and stochastic processes in aquatic hosts facing mort...

Background Lymphocytes play a key role in the pathogenesis of inflammatory bowel disease (IBD) and are widely explored as promising prognostic indicators. We aimed to outline the existing evidences on the capability of lymphocyte subpopulations to predict disease progression and treatment response in patients with IBD. Methods The protocol for thi...

Mucus injury associated with goblet cell (GC) depletion constitutes an early event in inflammatory bowel disease (IBD). Using single-cell sequencing to detect critical events in mucus dysfunction, we discover that the Kazal-type serine protease inhibitor SPINK4 is dynamically regulated in colitic intestine in parallel with disease activities. Under...

Global warming drives adaptive evolution by influencing natural selection and exploiting temperature-related phenotypic plasticity. However, predicting how phenotypic plasticity will evolve under climate change remains a challenge, urging the need for understanding underlying genetic and molecular mechanisms. In this study, we focus on the expressi...

Pyruvate kinase (PK), as a key rate-limiting enzyme in glycolysis, has been widely used to assess the stress tolerance and sensitivity of organisms. However, its phosphorylation regulatory mechanisms mainly focused on human cancer research, with no reports in marine organisms. In this study, we firstly reported a conserved PK Ser11 phosphorylation...

Network-on-Chip (NoC) is a scalable on-chip communication architecture for the NN accelerator, but with the increase in the number of nodes, the communication delay becomes higher. Applications such as machine learning have a certain resilience to noisy/erroneous transmitted data. Therefore, approximate communication becomes a promising solution to...

Phosphorylation of IkappaBalpha at Ser32 and Ser36 by IKKs during biotic stress triggers its ubiquitin-proteasome degradation, causing to the nuclear translocation of REL, representing a key cascade mechanism in metazoans conserved and immune core signaling pathway, NF-kappaB. However, studies on its response to abiotic stress and signal transducti...

Background The effectiveness of anti-programmed cell death protein 1(PD-1)/programmed cell death 1 ligand 1(PD-L1) therapy in treating certain types of cancer is associated with the level of PD-L1. However, this relationship has not been observed in colorectal cancer (CRC), and the underlying regulatory mechanism of PD-L1 in CRC remains unclear. M...

Background. Tenapanor is a locally acting selective sodium-hydrogen exchanger 3 inhibitor with the potential to treat sodium/phosphorus and fluid overload in various cardiac-renal diseases, which has been approved for constipation-predominant irritable bowel syndrome in the US. The pharmacokinetics (PK) of tenapanor and its metabolite tenapanor-M1...

Anaplastic lymphoma kinase (ALK) rearrangement is a well-known driver oncogene detected in approximately 5% of non–small cell lung cancer. However, ALK rearrangement is much less frequent in other solid tumors outside the lungs, such as colorectal cancer (CRC); thus, the optimal management of CRC with ALK rearrangements has yet to be established. I...

Radiation encephalopathy (RE) refers to radiation-induced brain necrosis and is a life-threatening complication in patients with nasopharyngeal carcinoma (NPC) after radiotherapy (RT), and radiation-induced pre-symptomatic glymphatic alterations have not yet been investigated. We used diffusion tensor image analysis along the perivascular space (DT...

Homomorphic encryption (HE) enables third-party servers to perform computations on encrypted user data while preserving privacy. Although conceptually attractive, the speed of software implementations of HE is almost impractical. To address this challenge, various domain-specific architectures have been proposed to accelerate homomorphic evaluation...

Spiking neural networks (SNNs) use discrete binary spikes to transfer information between neurons, which is different from artificial neural networks (ANNs). Although event-based characteristics bring potential computation power and efficiency to SNNs, the long processing time window of discrete spikes leads to high latency. In this brief, a spike...

Background Clinical remission (CR) is the principal short‐term treatment target in patients with ulcerative colitis (UC). However, whether rapidly achieving CR indicates better outcomes remains unclear. Objectives We aimed to explore the associations between the timing of CR and therapeutic outcomes in UC. Methods This study included UC patients...

As the world’s largest farmed marine animal, oysters have enormous economic and ecological value. However, mass summer mortality caused by high temperature poses a significant threat to the oyster industry. To investigate the molecular mechanisms underlying heat adaptation and improve the heat tolerance ability in the oyster, we conducted genome-wi...

Stanniocalcin‐1 (STC1) is upregulated by inflammation and modulates oxidative stress‐induced cell death. Herein, the function of STC1 in colitis and stress‐induced parthanatos, a newly identified type of programmed necrotic cell death dependent on the activation of poly‐ADP ribose polymerase‐1 (PARP1) is investigated. Results show that STC1 express...

The excessive storage overhead and the lack of sparsity-aware design hinder the development of NoC-based spatial DNN accelerators. To address them, first, we propose a memory-friendly dataflow which reduces the memory overhead compared with Tianjic by 86.6% for VGG16. Second, we propose a mask-based consecutive sparse activations skipping method wh...

Inflammatory bowel disease (IBD) is a chronic, recurrent inflammatory disease of the gastrointestinal tract. In addition to digestive symptoms, patients with IBD may also develop extra-intestinal manifestations (EIMs), the etiology of which remains undefined. The gut microbiota has been reported to exert a critical role in the pathogenesis of IBD,...

Background The Portuguese oyster Crassostrea angulata and the Pacific oyster C. gigas are two major Crassostrea species that are naturally distributed along the Northwest Pacific coast and possess great ecological and economic value. Here, we report the construction and comparative analysis of the chromosome-level haplotype-resolved genomes of the...

Objectives To investigate the characteristics and prognostic value of fecal lactoferrin trajectories in ulcerative colitis (UC). Methods This study used data from the UNIFI trial and included patients who received ustekinumab during induction for trajectory modeling (n=637). Patients who received ustekinumab during maintenance therapy were used fo...

High-temperature stress caused by global climate change poses a significant threat to marine ectotherms. This study investigated the role of protein phosphorylation modifications in the molecular regulation network under heat stress in oysters, which are representative intertidal organisms that experience considerable temperature changes. Firstly,...

Background Intestinal barrier dysfunction plays a central role in the pathological onset of Crohn’s disease. We identify the cadherin superfamily member protocadherin 20 (PCDH20) as a crucial factor in Crohn’s disease. Here we describe the function of PCDH20 and its mechanisms in gut homeostasis, barrier integrity, and Crohn’s disease development....

Regulatory variants in gene expression serve as bridges linking genetic variation and phenotypic plasticity. Environmental conditions typically influence the effects of regulatory variants on phenotypic plasticity; however, such genotype-by-environment interactions (G × E) are poorly understood. This study aimed to investigate the genetic basis of...

Background and Aims Prophylaxis of postoperative recurrence is an intractable problem for clinicians and patients with Crohn’s disease. Prognostic models are effective tools for patient stratification and personalised management. This systematic review aimed to provide an overview and critically appraise the existing models for predicting postopera...

Jinjiang oyster Crassostrea ariakensis, a species with economic and ecological value, is distributed along the estuaries and coasts of East Asia. With the decline in natural resources, the conservation and aquaculture of this species is urgent. However, studies characterizing their shell shape remain scarce. We investigated the morphological differ...

Background: Fecal lactoferrin (FL) is associated with disease activity and relapse in ulcerative colitis. However, whether FL could early predict long-term outcomes in ulcerative colitis is poorly understood. Methods: This post-hoc analysis included participants who received biologics and had available data of FL concentration at week 4 from the...

Transcriptional plasticity interacts with natural selection in complex ways and is crucial for the survival of species under rapid climate change. How 3D genome architecture affects transcriptional plasticity and its interaction with genetic adaptation are unclear. We transplanted estuarine oysters to a new environment and found that genes located...

Inflammatory bowel diseases (IBD) is featured by gastrointestinal inflammation and a disease course with alternating recurrence and remission. The global burden caused by IBD has significantly boosted in recent years, necessitating treatment optimization. Serum amyloid A (SAA) is a class of 104 amino acid conservative acute-phase proteins, which is...

Background Treatment failures (TFs) generally exist in the course of ulcerative colitis (UC), while early reliable predictors of TFs are still lacking. We aimed to generate nomograms for the prediction of TFs. Methods In this retrospective case–control study, the endpoint was the occurrence of TFs, which included medically associated treatment fai...

Increasing seawater temperatures pose a great threat to marine organisms, especially those settled in fluctuating intertidal areas. DNA methylation, which can be induced by environmental variation, can influence gene expression and mediate phenotypic plasticity. However, the regulatory mechanisms of DNA methylation in gene expression-mediated adapt...

Background Patients with isolated anastomotic lesions (iAL) are common in postoperative Crohn’s disease (CD) and have heterogeneous prognosis. Objectives To investigate the prognostic value of neutrophil-to-lymphocyte ratio (NLR) in CD patients with iAL. Design A bicenter retrospective cohort study. Methods CD patients who received ileocolonic r...

Background Fibroblast growth factors (FGFs) and their receptors (FGFRs) play a crucial role in cell fate and angiogenesis, with dysregulation of the signaling axis driving tumorigenesis. Therefore, many studies have targeted FGF/FGFR signaling for cancer therapy and several FGFR inhibitors have promising results in different tumors but treatment ef...

Breast carcinoma is the second largest cancer in the world among women. Early detection of breast cancer has been shown to increase the survival rate, thereby significantly increasing patients’ lifespan. Mammography, a noninvasive imaging tool with low cost, is widely used to diagnose breast disease at an early stage due to its high sensitivity. Al...

Background Despite great success, immunotherapy still faces many challenges in practical applications. It was previously found that family with sequence similarity 110 member A (FAM110A) participate in the regulation of the cell cycle and plays an oncogenic role in pancreatic cancer. However, the prognostic value of FAM110A in pan-cancer and its in...

Climate change and intensifying human activity are posing serious threats to marine organisms. The fluctuating intertidal zone forms a miniature ecosystem of a rapidly changing environment for studying biological adaptation. Transgenerational plasticity (TGP), an evolutionary phenomenon in which parental experience influences offspring phenotypes,...

Rat sarcoma virus homolog (Rho) guanosine triphosphatases (GTPases) function as “molecular switch” in cellular signaling regulation processes and are associated with the pathogenesis of inflammatory bowel disease (IBD). This chronic intestinal tract inflammation primarily encompasses two diseases: Crohn’s disease and ulcerative colitis. The pathoge...

The evolution of phenotypic plasticity plays an essential role in adaptive responses to climate change; however, its regulatory mechanisms in marine organisms which exhibit high phenotypic plasticity still remain poorly understood. The temperature-responsive trait oleic acid content and its major gene stearoyl-CoA desaturase (Scd) expression have d...

Climate change, represented by rising and fluctuating temperature, induces systematic changes in marine organisms and in their bacterial symbionts. However, the role of host-microbiota interactions in the host's response to rising temperature and the underlying mechanisms are incompletely understood in marine organisms. Here, the symbiotic intestin...

We propose a general methodology and reconfigurable architecture for computing $\boldsymbol {A^{B}}$ -like functions in the complex field. CORDIC and the parabolic synthesis approximation method help the proposed method to be flexible to adjust the precision and complexity of computation. The proposed architecture is reconfigurable to adapt to di...

To avoid overheating of three-dimensional Network-on-Chip (NoC)-based multicore systems, many researchers have used Dynamic Thermal Management (DTM) techniques, which need embedded thermal sensors to provide accurate temperature information. However, only a few sensors can be embedded due to the limited hardware cost. So, it is crucial to find an a...

F-box and WD repeat domain-containing 5 (FBXW5), with WD40 repeats, can bind to the PPxY sequence of the large tumor suppressor kinases 1/2 (LATS1/2) kinase domain, resulting in ubiquitination. Ubiquitination and the subsequent degradation of LATS1/2 abrogate the Hippo pathway and worsen gastric cancer (GC). However, the effects and molecular mecha...

In this paper, we propose a spike-time based unsupervised learning method using spiking-timing dependent plasticity (STDP). A simplified linear STDP learning rule is proposed for the energy efficient weight updates. To reduce unnecessary computations for the input spike values, a stop mechanism of the forward pass is introduced in the forward pass....

In locally advanced rectal cancer (LARC), an improved ability to predict prognosis before and after treatment is needed for individualized treatment. We aimed to utilize pre- and post-treatment clinical predictors and baseline magnetic resonance imaging (MRI) radiomic features for establishing prognostic models to predict progression-free survival...

Glycogen, amino acids, fatty acids, and other nutrient components affect the flavor and nutritional quality of oysters. Methods based on near-infrared reflectance spectroscopy (NIRS) were developed to rapidly and proximately determine the nutrient content of the Pacific oyster Crassostrea gigas. Samples of C. gigas from 19 costal sites were freeze-...

The strongly supervised deep convolutional neural network (DCNN) has better performance in assessing breast cancer (BC) because of the more accurate features from the slice-level precise labeling compared with the image-level labeling weakly supervised DCNN. However, manual slice-level precise labeling is time consuming and expensive. In addition,...