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. It supports extracting phylogenetic trees as well as the outputs of commonly used analytical software. It can link external data to phylogenies and merge tree data obtained from different sources, enabling analyses of phylogeny-associated data from different disciplines in an evolutionary context. Treeio also supports export of a phylogenetic tree with heterogeneous-associated data to a single tree file, including BEAST compatible NEXUS and jtree formats; these facilitate data sharing as well as file format conversion for downstream analysis. The treeio package is designed to work with the tidytree and ggtree packages. Tree data can be processed using the tidy interface with tidytree and visualized by ggtree. The treeio package is released within the Bioconductor and rOpenSci projects. It is available at https://www.bioconductor.org/packages/treeio/.

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. Moreover, it supports evaluating significant overlap among ChIP-seq datasets. Currently, ChIPseeker contains 15 000 bed file information from GEO database. These datasets can be downloaded and compare with user's own data to explore significant overlap datasets for inferring co-regulation or transcription factor complex for further investigation. AVAILABILITY AND IMPLEMENTATION: ChIPseeker is released under Artistic-2.0 License. The source code and documents are freely available through Bioconductor (http://www.bioconductor.org/packages/release/bioc/html/ChIPseeker.html).

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. Enrichment analyses including hypergeometric model and gene set enrichment analysis are also implemented to support discovering disease associations of high-throughput biological data. This allows biologists to verify disease relevance in a biological experiment and identify unexpected disease associations. Comparison among gene clusters is also supported. AVAILABILITY AND IMPLEMENTATION: DOSE is released under Artistic-2.0 License. The source code and documents are freely available through Bioconductor (http://www.bioconductor.org/packages/release/bioc/html/DOSE.html). SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. CONTACT: gcyu@connect.hku.hk or tqyhe@jnu.edu.cn.

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. Simulations were run to realize various loading conditions including axial compression, flexion, extension, lateral bending and rotation under a constant compressive preload. Meanwhile, the evaluation results derived from FEMs data focused on endplate stress distribution, peak stress of von Mises and stress of cage. Stress distributions on the bone surface were evaluated and discussed as well. RESULTS: The consequences of cage insertion, high strains and stresses, were concentrated in the areas where the cage and endplate were in contact with each other. Simultaneously, contact stresses around the implants seemed to be concentrated around the periphery of the device. After implantation of ALIFC, the stiffness of the new cages was similar to that of traditional cages in an assemble condition, according to the biomechanical data dealing with FEM. Once a separated cage was in the place of an assembled cage, the stresses would get symmetrically distributed in the lateral areas of the endplate and decrease significantly at the center where the separated cage was not in contact with the endplate. The stress of the cage was going to be high once being rotating; most significant difference of stresses distribution due to the alternative choice has been found in the state of rotation. On comparison of peak von Mises stresses on the endplates in the new cage, the stresses were symmetrically distributed in the lateral areas of the endplate when a separated cage was used in place of an assembled cage. CONCLUSION: The new cage was more advantages with regard to endplate stress distribution, peak stress of von Mises and stress of cage than the assembled state. ALIFC can provide sufficient primary stability for lumbar intervertebral fusion and the new cage may be regarded as a suitable device for load-bearing implantation.

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. METHODS: We retrospectively analyzed the medical records of 150 patients with primary stages IB-IVB cervical cancer who received neutron brachytherapy combined with external-beam radiotherapy concurrently with cisplatin chemotherapy. All patients were followed up. Using an actuarial analysis, patient outcomes and treatment-related adverse effects were evaluated and compared. RESULTS: The median overall survival (OS) was 33.2 months. The 3-year progression-free survival rates for patients with stages I-II, III, and IV diseases were 81.0% (68/84), 65.0% (39/60), and 0% (0/6), respectively; the 3-year OS rates were 90.5% (76/84), 85.0% (51/60), and 16.7% (1/6), respectively. Vaginal bleeding was controlled within the median time of 4.0 days. One month after treatment, 97.3% of patients achieved short-term local control. The local recurrence rates for patients with stages I-II, III, and IV disease were 4.8% (4/84), 11.7% (7/60), and 33.3% (2/6), respectively, and the occurrence rates of distant metastasis were 16.7% (14/84), 25.0% (15/60), and 100.0% (6/6), respectively. Cancer stage, tumor size, and lymph node metastasis were identified as prognostic risk factors, but only lymph node metastasis was found to be an independent prognostic factor. The most common adverse effects during treatment were grades 1 and 2 irradiation-related proctitis and radiocystitis. CONCLUSION: For patients with cervical cancer, neutron brachytherapy combined with external-beam radiotherapy plus concurrent chemotherapy produces a rapid response and greatly improves local control and long-term survival rates with tolerable adverse effects.

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 Panax notoginseng 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. On the first day of chemotherapy, a PICC was inserted into the right basilic vein with its tip in the superior vena cava. On the third day of chemotherapy, pain, swelling and skin flushing started. In the following days, particularly days 10-13, a Doppler ultrasound examination confirmed a long thrombus along the PICC line in the axillary vein and brachial veins in each patient. The patients rejected the insertion of an inferior vena cava filter, and neither heparin nor urokinase were administered due to contra-indications. An injection of PNS (200 mg) was administered every day. On days 20-28 of chemotherapy, the thrombus in the axillary and brachial veins disappeared in the three patients. It was concluded that PNS promote blood circulation, which prevents blood stasis and reduces the toxicity of cisplatin. The results suggest that PNS are a feasible and effective treatment option for many types of cancer, but have a broader clinical impact on cancer patients with PICC-related venous thrombosis. Therefore, this study is an original case report of particular interest to cancer patients with PICC-related venous thrombosis.

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. Currently, clusterProfiler supports three species, including humans, mice, and yeast. Methods provided in this package can be easily extended to other species and ontologies. The clusterProfiler package is released under Artistic-2.0 License within Bioconductor project. The source code and vignette are freely available at http://bioconductor.org/packages/release/bioc/html/clusterProfiler.html.

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. Here, we present a Linux distribution, LXtoo, to provide a flexible computing platform for bioinformatics analysis. FINDINGS: Unlike most of the existing live Linux distributions for bioinformatics limiting their usage to sequence analysis and protein structure prediction, LXtoo incorporates a comprehensive collection of bioinformatics software, including data mining tools for microarray and proteomics, protein-protein interaction analysis, and computationally complex tasks like molecular dynamics. Moreover, most of the programs have been configured and optimized for high performance computing. CONCLUSIONS: LXtoo aims to provide well-supported computing environment tailored for bioinformatics research, reducing duplication of efforts in building computing infrastructure. LXtoo is distributed as a Live DVD and freely available at http://bioinformatics.jnu.edu.cn/LXtoo.

[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. The radiosurgical procedure included local anesthesia administration, head-ring mounting, serial thin slice CT scanning with contrast enhancement, CT image transfer, treatment planning on the computer workstation, stereotactic localization of the target onto the Linac isocenter, and then the Linac was used to perform multiple non-coplannar arc radiation. All cases received single fraction radiosurgery. RESULTS: After X-Knife radiosurgery, follow-up ranged 3-60 months (median 38.4 month). Among those 112 cases that acquired follow-up, 78(69.7%) cases showed good clinical improvements, 10(8.9%) cases showed relatively good clinical improvements, 19(16.8%) cases showed no clinical improvement, and 5(4.6%) cases had progression of disease and enlargement of the adenoma. CONCLUSION: X-Knife radiosurgery is a safe and effective technique for the treatment of functional pituitary micro-adenoma. While for young patients, the diagnosis of pituitary micro-adenoma and use of X-Knife radiosurgery should be very cautious, otherwise hypopituitarism might be resulted.

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. In most patients, the pathologic diagnosis of primary cancer was obtained before they were referred for their brain metastasis. There were 34 (8.42%) cases with an unknown primary cancer site at the time of initial presentation. Patients were grouped according to treatment methods, which included neurosurgical craniotomy (NS; 130 patients), whole-brain radiotherapy (WBRT; 120 patients). Linac XKnife radiosurgery (RS; 130 patients) and Linac XKnife radiosurgery plus WBRT (RT; 83 cases). Survival was measured from the time of treatment and was analyzed by the Kaplan-Meier product-limit method and then plotted. Differences between curves were evaluated using the log-rank test. Multivariate factors associated with survival were analyzed using the Cox proportional hazards model. RESULTS: The survival time was 68.4 +/- 7.20 weeks after NS, 51.3 +/- 5.04 weeks after WBRT, 67.9 +/- 3.68 weeks after RS and 89.7 +/- 4.50 weeks after RT. The presence of active systemic cancer in a larger number of metastatic tumors was associated with a poor survival (p = 0.0003 and 0.0000). The female patients showed better survival rates over the male ones (p = 0.0000). Patients treated with RT had a better survival than those treated with NS, WBRT and RS (p = 0.0048, 0.0000 and 0.1222, respectively), although the latter did not show statistical significance. CONCLUSIONS: RS was an effective modality for patients with brain metastases, and if combined with WBRT, survival was better. Progression of systemic cancer and the number of metastatic tumors were the most significant factors for a poor survival after treatment of the brain metastases.