L. Xie

π-SPECFormer: A Mass Spectrometry-based Foundation Model for Decoding the Dark Proteome

This paper introduces π-SPECFormer, a foundation model for mass spectrometry-based proteomics that decodes the dark proteome by pre-training on unannotated spectra and outperforms baselines in peptide sequencing and modification detection.

Virtual Growing Child (VGC): A general normative comparative system via quantitative dynamic MRI for quantifying pediatric regional respiratory anomalies with application in thoracic insufficiency syndrome (TIS)

The paper introduces VGC, a normative database for pediatric respiratory measurements using MRI, to quantify regional respiratory anomalies in thoracic insufficiency syndrome patients.

Beyond enumeration: Phenotype independent "labeling-capture-release" process enabling precise detection of circulating tumour cells and downstream applications

This paper introduces a labeling-capture-release method for isolating circulating tumor cells from blood samples with high efficiency and accuracy, enabling downstream applications.

Circular RNA HMGCS1 sponges miR4521 to aggravate type 2 diabetes-induced vascular endothelial dysfunction

This study identifies circHMGCS1 as a regulator of vascular endothelial dysfunction in diabetes by sponging miR4521, leading to impaired nitric oxide production and increased oxidative stress.

Targeting G9a translational mechanism of SARS-CoV-2 pathogenesis for multifaceted therapeutics of COVID-19 and its sequalae

This paper identifies G9a's role in SARS-CoV-2-induced pathogenesis by regulating translation of viral and host proteins, showing that G9a inhibitors can reverse disease-related proteomic changes.

A series of spontaneously blinking dyes for super-resolution microscopy

This paper introduces a series of spontaneously blinking dyes with adjustable duty cycles for improved single-molecule localization microscopy in cells and dense structures.

ATM-Mediated Translocation of RanBPM Regulates DNA Damage Response by Stabilizing p21 in Non-Small Cell Lung Cancer Cells

The paper identifies a novel mechanism where RanBPM stabilizes p21 via deubiquitination, regulating DNA damage response in NSCLC cells.

TDP-43 pathology links innate and adaptive immunity in amyotrophic lateral sclerosis

This study shows TDP-43 pathology activates immune cells in ALS, linking it to immune dysfunction and suggesting immune monitoring as a diagnostic tool.

Camel milk affects serum metabolites by modulating the intestinal microflora

This study shows that camel milk modulates gut microbiota and serum metabolites in rats, with beneficial bacteria and metabolites resembling those of healthy individuals.

A quantitative genetics framework for understanding the selection response of microbial communities

The paper develops a quantitative genetics framework to analyze selection response in microbial communities, showing heritability alone cannot predict success due to nonlinearities and evolutionary dynamics.

Monocytes reprogrammed by 4-PBA potently contribute to the resolution of inflammation and atherosclerosis

This study shows that 4-PBA reprograms monocytes to resolve inflammation and atherosclerosis by altering adhesion and increasing anti-inflammatory markers.

A muscle hypertrophy-derived myokine reprograms the stromal vascular fractions differentiation towards thermogenic adipocytes in subcutaneous adipose tissue

This study identifies Thbs4 as a muscle-derived myokine that promotes the conversion of white to beige adipocytes in subcutaneous adipose tissue, improving metabolic health and protecting against high-fat diet-induced disorders.

Brd4-Nutm1 fusion gene initiates NUT carcinoma in vivo

This study creates a genetically engineered mouse model of NUT carcinoma by inducing the Brd4::Nutm1 fusion gene, showing it can initiate aggressive tumors with features similar to human NC.

Seed size control via phloem end by callose deposition/degradation of β-1,3-glucanase

The paper identifies a mechanism for seed size regulation through callose deposition/degradation at the phloem end of the ovule, mediated by β-1,3-glucanase genes.

The TRIP6/LATS1 complex constitutes the tension sensor of α-catenin/vinculin at both bicellular and tricellular junctions

This study identifies TRIP6 and LATS1 as novel components of the tension sensor complex at bicellular and tricellular junctions, revealing their distinct distribution and dynamics compared to α-catenin/vinculin.

Engineering GliaTrap: a biodegradable non-swelling hydrogel with tuned release of CXCL12 to attract migrating glioblastoma cells

GliaTrap is a biodegradable non-swelling hydrogel with tuned release of a chemoattractant to attract invading glioma cells and serve as delivery platform for local therapeutics.

The Influence of Angiotensin II on the Gut Microbiome of Mice: Findings from a Retrospective Study

This study investigates how angiotensin II affects the gut microbiome in mice, finding its impact is smaller than factors like diet and facility.

GPR41/43 regulates blood pressure by improving gut epithelial barrier integrity to prevent TLR4 activation and renal inflammation

This study shows that GPR41/43 receptors regulate blood pressure by maintaining gut barrier integrity and preventing renal inflammation through TLR4 signaling.

A syntelog-based pan-genome provides insights into rice domestication and de-domestication

This paper constructs a syntelog-based pan-genome of rice using long-read sequencing to study domestication and de-domestication, identifying introgression events and domestication genes.

The Mechanism underlying B cell Developmental Dysfunction in Kawasaki Disease Based on Single-cell Transcriptomic Sequencing

This study uses single-cell transcriptomics to identify B cell developmental dysfunction in Kawasaki Disease, showing repression of immune processes and altered gene expression in HSPCs and B cells before treatment.

Excess PrPC inhibits muscle cell differentiation via miRNA-enhanced liquid-liquid phase separation implicated in myopathy

Preclinical Basis of the Efficacy and Pharmacodynamics of Finotonlimab, a Humanized Anti-PD-1 Monoclonal Antibody with Potent Implications for Clinical Benefit

This paper evaluates the preclinical efficacy and pharmacodynamics of Finotonlimab, a humanized anti-PD-1 antibody, showing high PD-1 binding affinity and sustained receptor occupancy in cynomolgus monkeys.

Machine learning prediction of cancer cell metabolism from autofluorescence lifetime images

This paper uses machine learning on autofluorescence lifetime images to predict metabolic pathway usage in cancer cells, achieving 95% accuracy in distinguishing glycolytic and oxidative metabolism.

A Peronophythora litchii RXLR effector PlAvh202 enhances plant susceptibility by destabilizing host SAMS

This study identifies PlAvh202, an RXLR effector from Peronophythora litchii, which enhances plant susceptibility by destabilizing SAMS and suppressing ethylene production.

Fatty acid binding protein 1 and fatty acid synthetase overexpression have differential effects on collagen III and cross-linking in Zongdihua pig tissues

This study investigates the effects of FABP1 and FAS overexpression on collagen III and cross-linking in Zongdihua pig tissues, identifying their roles in fat deposition.

Nonlytic cellular release of hepatitis A virus requires dual capsid recruitment of the ESCRT-associated Bro1 domain proteins HD-PTP and ALIX

This study identifies a viral export signal in hepatitis A virus that requires dual recruitment of HD-PTP and ALIX for nonlytic release in extracellular vesicles.

Microtubule-Connexin-43 regulation suppresses arrhythmias and fibrosis in Duchenne muscular dystrophy mice.

This study shows that Cx43 phosphorylation status affects microtubule organization in DMD mice, influencing arrhythmias and fibrosis.

Small molecule SWELL1-LRRC8 complex induction improves glycemic control and nonalcoholic fatty liver disease in murine Type 2 diabetes

This study identifies small molecule modulators of the SWELL1-LRRC8 complex that improve glycemic control and prevent NAFLD in murine T2D by restoring insulin signaling and secretion.

A snapshot of the root phenotyping landscape in 2021

This paper surveys the current state of root phenotyping, identifying key trends, challenges, and needs in the field.

FoQDE2-dependent milRNA promotes Fusarium oxysporum f. sp. cubense virulence by targeting a glycosyl hydrolase coding gene at transcriptional level