Machine learning combined with single-cell analysis reveals predictive capacity and immunotherapy response of T cell exhaustion-associated lncRNAs in uterine corpus endometrial carcinoma.

Background: The exhaustion of T-cells is a primary factor contributing to immune dysfunction in cancer. Long non-coding RNAs (lncRNAs) play a significant role in the advancement, survival, and treatment of Uterine Corpus Endometrial Carcinoma (UCEC). Nevertheless, there has been no investigation into the involvement of lncRNAs associated with T-cell exhaustion (TEXLs) in UCEC.

Demonstrating Path-Independent Anyonic Braiding on a Modular Superconducting Quantum Processor.

Anyons, exotic quasiparticles in two-dimensional space exhibiting nontrivial exchange statistics, play a crucial role in universal topological quantum computing. One notable proposal to manifest the fractional statistics of anyons is the toric code model; however, scaling up its size through quantum simulation poses a serious challenge because of its highly entangled ground state. In this Letter, we demonstrate that a modular superconducting quantum processor enables hardware-pragmatic implementation of the toric code model.

Genetic analysis of potential biomarkers and therapeutic targets associated with ferroptosis from bronchopulmonary dysplasia.

Ferroptosis is a recently identified form of cell death that is distinct from the conventional modes such as necrosis, apoptosis, and autophagy. Its role in bronchopulmonary dysplasia (BPD) remains inadequately understood. To address this gap, we obtained BPD-related RNA-seq data and ferroptosis-related genes (FRGs) from the GEO database and FerrDb, respectively.

Copy number alteration features in pan-cancer homologous recombination deficiency prediction and biology.

Homologous recombination deficiency (HRD) renders cancer cells vulnerable to unrepaired double-strand breaks and is an important therapeutic target as exemplified by the clinical efficacy of poly ADP-ribose polymerase (PARP) inhibitors as well as the platinum chemotherapy drugs applied to HRD patients. However, it remains a challenge to predict HRD status precisely and economically. Copy number alteration (CNA), as a pervasive trait of human cancers, can be extracted from a variety of data sources, including whole genome sequencing (WGS), SNP array, and panel sequencing, and thus can be easily applied clinically.

Accurate prediction of pan-cancer types using machine learning with minimal number of DNA methylation sites.

DNA methylation analysis has been applied to determine the primary site of cancer; however, robust and accurate prediction of cancer types with a minimum number of sites is still a significant scientific challenge. To build an accurate and robust cancer type prediction tool with a minimum number of DNA methylation sites, we internally benchmarked different DNA methylation site selection and ranking procedures, as well as different classification models. We used The Cancer Genome Atlas dataset (26 cancer types with 8296 samples) to train and test models and used an independent dataset (17 cancer types with 2738 samples) for model validation.

Identification of line-source transfer mobility and force density by ground acceleration measurements.

Ground-borne vibration caused by railway traffic has been a research concern due to its possible side effects on nearby residences. The force density and line-source mobility can effectively characterize the generation and transmission of train-induced vibrations, respectively. This research proposed a frequency-domain method for identifying the line-source transfer mobility and force density using measured vibrations at the ground surface, which was on the basis of the least-square method.

The repertoire of copy number alteration signatures in human cancer.

Copy number alterations (CNAs) are a predominant source of genetic alterations in human cancer and play an important role in cancer progression. However comprehensive understanding of the mutational processes and signatures of CNA is still lacking. Here we developed a mechanism-agnostic method to categorize CNA based on various fragment properties, which reflect the consequences of mutagenic processes and can be extracted from different types of data, including whole genome sequencing (WGS) and single nucleotide polymorphism (SNP) array.

Experimental Realization of Two Qutrits Gate with Tunable Coupling in Superconducting Circuits.

Gate-based quantum computation has been extensively investigated using quantum circuits based on qubits. In many cases, such qubits are actually made out of multilevel systems but with only two states being used for computational purpose. While such a strategy has the advantage of being in line with the common binary logic, it in some sense wastes the ready-for-use resources in the large Hilbert space of these intrinsic multidimensional systems.

Identification and immunological characterization of endoplasmic reticulum stress-related molecular subtypes in bronchopulmonary dysplasia based on machine learning.

Bronchopulmonary dysplasia (BPD) is a life-threatening lung illness that affects premature infants and has a high incidence and mortality. Using interpretable machine learning, we aimed to investigate the involvement of endoplasmic reticulum (ER) stress-related genes (ERSGs) in BPD patients. We evaluated the expression profiles of endoplasmic reticulum stress-related genes and immune features in bronchopulmonary dysplasia using the GSE32472 dataset.

Assessment of left ventricular function by spatio-temporal image correlation in fetuses with fetal growth restriction.

Aim: To compare the evaluation of left ventricular function by spatio-temporal image correlation (STIC) between fetal growth restriction (FGR) fetuses and normal fetuses.

Methods: Forty-two FGR fetuses and 50 normal fetuses with gestational age ranging from 28 to 35 weeks, were chosen for the study group and control group, respectively. The fetal heart was acquired using the STIC modality, beginning with a four-chamber view.

Quantification of Neoantigen-Mediated Immunoediting in Cancer Evolution.

Unlabelled: Immunoediting includes three temporally distinct stages, termed elimination, equilibrium, and escape, and has been proposed to explain the interactions between cancer cells and the immune system during the evolution of cancer. However, the status of immunoediting in cancer remains unclear, and the existence of neoantigen depletion in untreated cancer has been debated. Here we developed a distribution pattern-based method for quantifying neoantigen-mediated negative selection in cancer evolution.

Extrachromosomal DNA formation enables tumor immune escape potentially through regulating antigen presentation gene expression.

Extrachromosomal DNA (ecDNA) is a type of circular and tumor specific genetic element. EcDNA has been reported to display open chromatin structure, facilitate oncogene amplification and genetic material unequal segregation, and is associated with poor cancer patients' prognosis. The ability of immune evasion is a typical feature for cancer progression, however the tumor intrinsic factors that determine immune evasion remain poorly understood.

UCSCXenaShiny: an R/CRAN package for interactive analysis of UCSC Xena data.

Summary: UCSC Xena platform provides huge amounts of processed cancer omics data from large cancer research projects (e.g. TCGA, CCLE and PCAWG) or individual research groups and enables unprecedented research opportunities.

Simulation of higher-order topological phases and related topological phase transitions in a superconducting qubit.

Higher-order topological phases give rise to new bulk and boundary physics, as well as new classes of topological phase transitions. While the realization of higher-order topological phases has been confirmed in many platforms by detecting the existence of gapless boundary modes, a direct determination of the higher-order topology and related topological phase transitions through the bulk in experiments has still been lacking. To bridge the gap, in this work we carry out the simulation of a two-dimensional second-order topological phase in a superconducting qubit.

Copy number signature analysis tool and its application in prostate cancer reveals distinct mutational processes and clinical outcomes.

Genome alteration signatures reflect recurring patterns caused by distinct endogenous or exogenous mutational events during the evolution of cancer. Signatures of single base substitution (SBS) have been extensively studied in different types of cancer. Copy number alterations are important drivers for the progression of multiple cancer.

Pan-cancer noncoding genomic analysis identifies functional promoter mutation hotspots.

Noncoding DNA sequences occupy more than 98% of the human genome; however, few cancer noncoding drivers have been identified compared with cancer coding drivers, probably because cancer noncoding drivers have a distinct mutation pattern due to the distinct function of noncoding DNA. Here we performed pan-cancer whole genome mutation analysis to screen for functional noncoding mutations that influence protein factor binding. Recurrent mutations were identified in the promoter of gene.

Sigflow: an automated and comprehensive pipeline for cancer genome mutational signature analysis.

Summary: Mutational signatures are recurring DNA alteration patterns caused by distinct mutational events during the evolution of cancer. In recent years, several bioinformatics tools are available for mutational signature analysis. However, most of them focus on specific type of mutation or have limited scope of application.

Assessment of ventilation noise impact from metro depot with over-track platform structure on workers and nearby inhabitants.

In order to alleviate the shortage of land use accompanied with urbanization, over-track building complexes above metro depots are developed rapidly in China, resulting in the larger mechanical ventilation needs in the metro depot. Excessive noise exposure caused by the huge ventilation system will bring serious impacts on the health of workers in the metro depot. This research intends to evaluate the noise annoyance in the metro depot and the noise influences on adjacent residential buildings by the ventilation system.

The impacts of transcatheter occlusion for congenital atrial septal defect on atrial volume, function, and synchronicity in children: a three-dimensional echocardiography study.

Objective: To evaluate the impacts of transcatheter closure for atrial septal defect (ASD) on the atria.

Methods: Thirty-four patients with ASD undergoing transcatheter occlusion were recruited in the study, and 34 patients undergoing surgical operation and 34 healthy children were age-matched as controls. A real time three-dimensional (RT3DE) echocardiography was used to measure the volume, function, and synchronicity of the atria.

[The study of vascular lesion using ultrasound in children with a history of Kawasaki disease].

Objective: To explore the endothelial function, carotid artery stiffness index and carotid intima-media thickness in children with a history of Kawasaki disease (KD).

Methods: A cohort of 204 children was studied, which comprised 51 patients with Kawasaki disease with coronary artery lesion (CAL group), 50 patients with Kawasaki disease with normal coronary arteries (normal coronary arteries group), and 103 healthy age matched children (control group). Their systemic blood pressure, fasting cholesterol concentrations, flow-mediated dilation (FMD) of the brachial artery, carotid artery stiffness index and carotid intima-media thickness (IMT) were compared.

Value of real-time 3-dimensional echocardiography sectional diagnosis in complex congenital heart disease evaluated by receiver operating characteristic analysis.

Objective: We sought to evaluate the value of real-time 3-dimensional (3D) echocardiography (RT-3DE) in the pathologic morphology of complex congenital heart disease (CHD) using receiver operating characteristic (ROC) analysis.

Methods: Thirty patients with complex CHD were examined by 2-dimensional echocardiography (2DE) and RT-3DE. Their diagnoses of pathologic morphology were made by 3 echocardiographers blinded to clinical data.

Methodological study on real-time three-dimensional echo-cardiography and its application in the diagnosis of complex congenital heart disease.

Background: Real-time three-dimensional echocardiography (RT-3DE) has made revolutionized improvements of cardiac imaging during the past few years. However, there is no standard examination method for RT-3DE so far. This study aimed to establish the diagnostic method of RT-3DE and evaluate its application in the diagnosis of complex congenital heart diseases (CHD).