IsoTools 2.0: Software for Comprehensive Analysis of Long-read Transcriptome Sequencing Data.

Direct, single molecule measurement of RNA by long-read transcriptome sequencing (LRTS) enables the reliable detection of transcripts and alternative splicing events, thus contributing to the identification of splicing mechanisms, improvement of current gene models, as well as to the prediction of more reliable protein isoforms. LRTS data comes from either PacBio's single-molecule real time sequencing or from Oxford Nanopore's nanopore sequencing. Previously, we developed IsoTools, a software originally designed for processing and analyzing PacBio data.

Expression Atlas update: insights from sequencing data at both bulk and single cell level.

Expression Atlas (www.ebi.ac.

Molecular Subtypes and Prognostic Models for Predicting Prognosis of Lung Adenocarcinoma based on MiRNA-related Genes.

Background: MicroRNAs (miRNAs) are crucial in cancer development and progression, and therapies targeting miRNAs demonstrate great therapeutic promise.

Aim: We sought to predict the prognosis and therapeutic response of lung adenocarcinoma (LUAD) by classifying molecular subtypes and constructing a prognostic model based on miRNA-related genes.

Methods: This study was based on miRNA-mRNA action pairs and ceRNA networks in the Cancer Genome Atlas (TCGA) database.

Clinical and pathological evaluation of cladribine treatment response in a case series of patients with xanthoma disseminatum.

Background: Xanthoma disseminatum (XD) is a rare form of non-Langerhans histiocytosis with extensive cutaneous involvement. There is a paucity of evidence-based recommendations for treatment decision-making. Previous case reports have established purine analogues, especially cladribine, as a hopeful first-line treatment option, but characterization of the clinical and pathological responses is lacking.

Defects and asymmetries in the visual pathway of non-human primates with natural strabismus and amblyopia.

Strabismus and amblyopia are common ophthalmologic developmental diseases caused by abnormal visual experiences. However, the underlying pathogenesis and visual defects are still not fully understood. Most studies have used experimental interference to establish disease-associated animal models, while ignoring the natural pathophysiological mechanisms.

CD133, but Not CD44, May Serve as a Novel Biomarker for Differential Diagnosis Between Basal Cell Carcinoma and Trichoblastomas.

Purpose: To investigate the clinical value of CD133 and CD44 as putative cancer stem cell markers in distinguishing between basal cell carcinoma (BCC) and trichoblastomas (TB).

Patients And Methods: Tumor samples from 24 BCC and 23 TB patients were retrospectively retrieved for immunohistochemical staining of CD133 and CD44. The results were interpreted using a semiquantitative scoring system (H score).

Identification of TPBG-Expressing Amacrine Cells in DAT-tdTomato Mouse.

Purpose: Neurons are the bricks of the neuronal system and experimental access to certain neuron subtypes will be of great help to decipher neuronal circuits. Here, we identified trophoblast glycoprotein (TPBG)-expressing GABAergic amacrine cells (ACs) that were selectively labeled in DAT-tdTomato transgenic mice.

Methods: Retina and brain sections were prepared for immunostaining with antibodies against various biomarkers.

Single-Cell Analysis Reveals the Immune Characteristics of Myeloid Cells and Memory T Cells in Recovered COVID-19 Patients With Different Severities.

Despite many studies on the immune characteristics of Coronavirus disease 2019 (COVID-19) patients in the progression stage, a detailed understanding of pertinent immune cells in recovered patients is lacking. We performed single-cell RNA sequencing on samples from recovered COVID-19 patients and healthy controls. We created a comprehensive immune landscape with more than 260,000 peripheral blood mononuclear cells (PBMCs) from 41 samples by integrating our dataset with previously reported datasets, which included samples collected between 27 and 47 days after symptom onset.

Expression Atlas update: gene and protein expression in multiple species.

The EMBL-EBI Expression Atlas is an added value knowledge base that enables researchers to answer the question of where (tissue, organism part, developmental stage, cell type) and under which conditions (disease, treatment, gender, etc) a gene or protein of interest is expressed. Expression Atlas brings together data from >4500 expression studies from >65 different species, across different conditions and tissues. It makes these data freely available in an easy to visualise form, after expert curation to accurately represent the intended experimental design, re-analysed via standardised pipelines that rely on open-source community developed tools.

Genomic alterations caused by HPV integration in a cohort of Chinese endocervical adenocarcinomas.

The association between human papillomavirus (HPV) integration and relevant genomic changes in uterine cervical adenocarcinoma is poorly understood. This study is to depict the genomic mutational landscape in a cohort of 20 patients. HPV+ and HPV- groups were defined as patients with and without HPV integration in the host genome.

Oncologic and obstetric outcomes after conization for adenocarcinoma in situ or stage IA1 cervical cancer.

This study aims to reveal the risk factors associated with recurrence or new-onset high-grade squamous intraepithelial lesions (HSILs) or more severe lesions (HSILs +) and analyze obstetrical outcomes in patients with adenocarcinoma in situ (AIS) or stage IA1 cervical cancer patients after conization. A retrospective cohort study was developed from January 1, 2002, and July 1, 2018, in a single center, where all patients with AIS or stage IA1 cervical cancer who accepted conization for primary surgery were reviewed and followed up until July 1, 2019, for the pathological findings of HSILs + and obstetric outcomes. Two hundred and seventeen patients were identified, including 114 cases of AIS, 76 cases of stage IA1 squamous cell carcinoma (SCC) and 27 cases of stage IA1 adenocarcinoma (ADC).

The genomic profile of parathyroid carcinoma based on whole-genome sequencing.

Parathyroid carcinoma (PC) is a rare endocrine malignancy with poor outcomes. Although some mutations such as CDC73 have been found in patients, the molecular mechanism of PC still needs extensive data to clarify. Whole-genome sequencing (WGS) was performed with frozen samples from 23 PC patients.

Successful management of nongestational ovarian choriocarcinoma complicated with choriocarcinoma syndrome: A case report and a literature review.

Nongestational ovarian choriocarcinoma (NGOC) accounts for <1% of ovarian germ cell tumors and may develop into the rare and fatal complication of choriocarcinoma syndrome. We reported a case of a 12-year-old girl with NGOC that metastasized to the lungs, retroperitoneal lymph nodes and brain. On day 2 of chemotherapy with actinomycin D and etoposide, choriocarcinoma syndrome developed due to a massive pulmonary hemorrhage, presenting as acute respiratory distress syndrome.

The effects of different instruments and suture methods of conization for cervical lesions.

This study is to compare the surgical outcomes of patients undergoing cold knife conization (CKC) versus electrosurgical conization (ESC). Among 10,086 patients in a single center admitted between January 2000 and January 2019, CKS or ESC was used for grade 3 cervical intraepithelial neoplasia (CIN3) or more severe lesions. Modified Sturmdorf or Figure-of-eight sutures were applied after conization.

Pathologically confirmed brain metastases from primary uterine cervical tumors: two cases and a literature review.

Background: Pathologically confirmed brain metastasis from primary cervical cancer is extremely rare. Herein, we report two cases of intracranial metastasis from cervical cancer that were histopathologically confirmed after surgical excision. In addition, we conducted a literature review to characterize the clinical manifestation, pathogenesis, and treatment of these patients.

Identification and injury to the inferior hypogastric plexus in nerve-sparing radical hysterectomy.

Waterjet dissection of the inferior hypogastric plexus (IHP) resulted in a more rapid return of normal urodynamics than blunt dissection (control group) in patients who received laparoscopic nerve-sparing radical hysterectomy (NSRH) in a randomized controlled study. However, the definite reasons for these results were unknown. This subgroup analysis compared the neural areas and impairment in the IHP uterine branches harvested during NSRH as an alternative to the IHP vesical branches between the waterjet and control groups.

Malignant transformation of vaginal adenosis to clear cell carcinoma without prenatal diethylstilbestrol exposure: a case report and literature review.

Background: We report an extremely rare case of vaginal clear cell carcinoma, which originated from the malignant transformation of vaginal adenosis without prenatal diethylstilbestrol (DES) exposure.

Case Presentation: In this case, the patient was a Chinese woman with a history of two decades of intermittent vaginal pain, sexual intercourse pain and vaginal contact bleeding. On September 1, 2011, when the patient was 39 years old, a vaginal biopsy revealed vaginal adenosis.

The Prognosis of Stage IA Mixed Endometrial Carcinoma.

Objectives: To explore the survival and definition of stage IA mixed endometrial carcinoma.

Methods: From June 1, 2010, to June 1, 2017, cases with stage IA endometrial cancer were included in this study. The survival outcomes were compared among patients with endometrioid (group A), nonendometrioid (group B), and mixed subtypes (group C) and among patients with different proportions of nonendometrioid components (<5%, >50%, and others).

Comparison of screening strategies for Lynch syndrome in patients with newly diagnosed endometrial cancer: a prospective cohort study in China.

Background: The prevalence of Lynch syndrome and screening strategies for this disorder in Chinese patients with endometrial cancer have seldom been investigated. Such data would be essential for the screening, prevention, genetic counseling, and treatment of Lynch syndrome. The purpose of this prospective study was to determine the accuracy of the mismatch repair (MMR) protein immunohistochemistry (IHC), microsatellite instability (MSI) test, and clinical diagnostic criteria in screening for Lynch syndrome-associated endometrial cancer (LS-EC) in a prospective Chinese cohort.

Ovarian primary primitive neuroectodermal tumor: a review of cases at PUMCH and in the published literature.

Background: The pathological characteristics, treatment strategies and prognosis of ovarian primary primitive neuroectodermal tumor (PNET) were unclear due to the rarity of PNET. All cases treated at Peking Union Medical College Hospital (PUMCH) between 1975 and 2016 and published in the English literature between 1980 to 2017 were reviewed.

Results: Finally four cases from PUMCH and 15 cases in the literature were included.

Concurrent Driver Gene Mutations as Negative Predictive Factors in Epidermal Growth Factor Receptor-Positive Non-Small Cell Lung Cancer.

Background: Tyrosine kinase inhibitors (TKIs) are clinically effective in non-small cell lung cancer (NSCLC) patients harbouring epidermal growth factor receptor (EGFR) oncogene mutations. Genetic factors, other than EGFR sensitive mutations, that allow prognosis of TKI treatment remain undefined.

Methods: We retrospectively screened 423 consecutive patients with advanced NSCLC and EGFR 19del or 21L858R mutations.

THE INFLUENCE OF SURGICAL EXTENT AND PARAFIBROMIN STAINING ON THE OUTCOME OF PARATHYROID CARCINOMA: 20-YEAR EXPERIENCE FROM A SINGLE INSTITUTE.

Parathyroid carcinoma (PC) is a rare endocrine malignancy with a poor prognosis. The optimal surgical procedure and prognostic factors for PC remain controversial. Clinical information and parafibromin staining results from 53 patients with PC were reviewed retrospectively from 1997 to 2018.

Genome‑wide DNA methylation profile of thymomas and potential epigenetic regulation of thymoma subtypes.

The aim of the present study was to examine the whole‑genome DNA methylation status of thymomas and identify differences in thymoma DNA methylation profiles. DNA methylation profiles of tissues (n=12) were studied using the Infinium MethylationEPIC BeadChip microarray (850K) and analyzed in relation to gene expression data. Functional annotation analysis of DNA methylation between the different groups was performed using the online tool GeneCodis3.

Clinicopathologic features and outcomes of primary vaginal adenosis as a dermatologic and gynecologic burden: A retrospective study.

In the recent 20 years, primary vaginal adenosis is extremely rare and the data of clinical presentations, management, and outcome have not been studied systematically.In this retrospective study, women with vaginal adenosis between January 1997 and June 2017 were identified from the hospital's medical records. Data on patient age, history, symptoms, mass location, size, diagnosis, complications, treatment, and recurrence were analyzed by SPSS 20.