Treeio: An R Package for Phylogenetic Tree Input and Output with Richly Annotated and Associated Data.

Phylogenetic trees and data are often stored in incompatible and inconsistent formats. The outputs of software tools that contain trees with analysis findings are often not compatible with each other, making it hard to integrate the results of different analyses in a comparative study. The treeio package is designed to connect phylogenetic tree input and output.

Californium-252 neutron brachytherapy combined with external pelvic radiotherapy plus concurrent chemotherapy for cervical cancer: a retrospective clinical study.

Background: Cervical cancer is the sixth most common cancer in Chinese women. A standard treatment modality for cervical cancer is the combination of surgery, chemotherapy, external-beam radiotherapy and intracavitary brachytherapy. The aim of this study was to retrospectively assess the long-term treatment outcomes of patients with cervical cancer who were treated with californium-252 neutron brachytherapy combined with external-beam radiotherapy plus concurrent chemotherapy.

ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization.

Unlabelled: ChIPseeker is an R package for annotating ChIP-seq data analysis. It supports annotating ChIP peaks and provides functions to visualize ChIP peaks coverage over chromosomes and profiles of peaks binding to TSS regions. Comparison of ChIP peak profiles and annotation are also supported.

DOSE: an R/Bioconductor package for disease ontology semantic and enrichment analysis.

Summary: Disease ontology (DO) annotates human genes in the context of disease. DO is important annotation in translating molecular findings from high-throughput data to clinical relevance. DOSE is an R package providing semantic similarity computations among DO terms and genes which allows biologists to explore the similarities of diseases and of gene functions in disease perspective.

The complete recanalization of PICC-related venous thrombosis in cancer patients: A series of case reports.

In this study, cancer patients with venous thrombosis associated with the use of peripherally inserted central catheters (PICCs) underwent complete recanalization by the administration of saponins (PNS), which vary from heparin or urokinase in that they do not have the same risks associated with thrombolysis, including bleeding. To the best of our knowledge, this is the first study concerning the treatment of cancers with PNS to be reported in the literature. Three cancer patients aged 30-50 years old, two females and one male, were subjected to chemotherapy.

LXtoo: an integrated live Linux distribution for the bioinformatics community.

Background: Recent advances in high-throughput technologies dramatically increase biological data generation. However, many research groups lack computing facilities and specialists. This is an obstacle that remains to be addressed.

clusterProfiler: an R package for comparing biological themes among gene clusters.

Increasing quantitative data generated from transcriptomics and proteomics require integrative strategies for analysis. Here, we present an R package, clusterProfiler that automates the process of biological-term classification and the enrichment analysis of gene clusters. The analysis module and visualization module were combined into a reusable workflow.

Design and finite-element evaluation of a versatile assembled lumbar interbody fusion cage.

Introduction: When an interbody cage is inserted into a human being's lumbar spine, not only the design, but also the material used is considerably crucial, particularly when minimally invasive lumbar fusion (MILIF) approaches are considered. The purpose of this study was to design a multi-function cage (either for MILIF or open lumbar interbody fusion) and also to evaluate the strength of the design based on a finite-element model analysis.

Method: Three-dimensional finite-element models that were instrumental in the reproduction of post-operative conditions under which different cages, such as assembled lumbar interbody fusion cages (ALIFC) and the separated ones, could be examined and traced after implantation were developed.

[Analysis of the results of 143 cases of pituitary micro-adenoma treated by Linac X-Knife stereotactic radioneurosurgery].

Background & Objective: The trans-sphenoid surgery was one of the main methods for the treatment of functional pituitary micro-adenoma for many years, while the development of radiosurgical techniques in recent years has given neurosurgeons new ways to treat functional pituitary micro-adenoma. This report aimed to ascertain the effectiveness of X-Knife stereotactic radioneurosurgery on pituitary micro-adenoma.

Methods: From June 1996 to June 2001, 143 cases of functional pituitary micro-adenoma were treated by X-Knife radiosurgery, in which 73 cases of secreting prolactin (PRL),54 cases of secreting growth hormone(GH), 13 cases of secreting adrenal corticotrophin hormone (ACTH), and 3 cases of secreting both PRL and GH.

Brain metastasis: experience of the Xi-Jing hospital.

Background: The management of metastatic brain tumors is an important issue in patients with malignant tumors or cancer. The authors summarize the results of patients with brain metastases treated at the Xi-Jing Hospital during a 10-year period, in order to assess the best modality of treatment for patients with brain metastases.

Methods: Between 1990 and 2000, 463 patients with brain-metastatic tumors were treated at the Xi-Jing Hospital of the Fourth Military Medical University, Xian, China.