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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/.

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.

It is well known that excess iodide can lead to thyroid colloid retention, a classic characteristic of iodide-induced goiter. However, the mechanism has not been fully unrevealed. Iodide plays an important role in thyroid function at multiple steps of thyroid colloid synthesis and transport among which sodium/iodide symporter (NIS) and pendrin are essential. In our study, we fed female BALB/c mice with different concentrations of high-iodine water including group A (control group, 0 μg/L), group B (1500 μg/L), group C (3000 μg/L), group D (6000 μg/L), and group E (12,000 μg/L). After 7 months of feeding, we found that excess iodide could lead to different degrees of thyroid colloid retention. Besides, NIS and pendrin expression were downregulated in the highest dose group. The thyroid iodide intake function detected by urine iodine assay and thyroidal ¹²⁵I experiments showed that the urine level of iodine increased, while the iodine intake rate decreased when the concentration of iodide used in feeding water increased (all p 

The ultrafine electrolytic copper powders were coated by silver using a combination of displacement reaction and reduction method, and the bimetallic core-shell powders with a 10wt.% addition of silver were obtained. The effects of concentration of complexing-dispersing agent and reducing agent on the silver coating layer were studied. The morphology, composition and structure of bimetallic core-shell powders were characterized by scanning electron microscopy, X-ray diffraction and energy dispersive spectroscopy. The oxidation resistance and electric conductivity of the coated powders were also investigated. The experimental results showed that the powders have a better oxidation resistance and higher conductivity using the complexing-dispersing agent of 10g/L EDTA-2Na and the reducing agent n of 30 g/L formaldehyde.

IntroductionWhen 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.MethodThree-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.ResultsThe 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.ConclusionThe 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.

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 .

Single-crystalline hematite （α-Fe2O3） nanorings （short nanotubes） and nanotubes were synthesized by a hydrothermal method. High-resolution transmission electron microscopy and selected-area electron diffraction confirm that the axial directions of both the nanorings and nanotubes are parallel to the crystalline c-axis. Intriguingly, the Morin transition occurs at about 210 K in the short nanotubes with a mean tube length of about 115 nm and a mean outer diameter of about 169 nm. However, it does not occur in the nanotubes with a mean tube length of about 317 nm and a mean outer diameter of about 148 nm. Detailed analysis of magnetization data, X-ray diffraction patterns, and room-temperature M6ssbauer spectra demonstrates that this very strong shape-dependence of Morin transition is intrinsic to hematite. We explain this intriguing shape- dependence quantitatively, in terms of the opposite signs of the surface mag- netic anisotropy constants of the surface planes parallel and perpendicular to the c-axis.

With the increase of system scale, the inherent reliability of supercomputers becomes lower and lower. The cost of fault handling and task recovery increases so rapidly that the reliability issue will soon harm the usability of supercomputers. This issue is referred to as the ＂reliability wall＂, which is regarded as a critical problem for current and future supercomputers. To address this problem, we propose an autonomous fault-tolerant system, named Iaso, in MilkyWay- 2 system. Iaso introduces the concept of autonomous management in supercomputers. By autonomous management, the computer itself, rather than manpower, takes charge of the fault management work. Iaso automatically manage the whole lifecycle of faults, including fault detection, fault diagnosis, fault isolation, and task recovery. Iaso endows the autonomous features with MilkyWay-2 system, such as self-awareness, self-diagnosis, self-healing, and self-protection. With the help of Iaso, the cost of fault handling in supercomputers reduces from several hours to a few seconds. Iaso greatly improves the usability and reliability of MilkyWay-2 system.

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.

Chemisorbed atomic oxygen inducing Co segregation in CoNi (111) alloy is studied using periodic self-consistent density functional theory (DFT) calculations. In particular, the coverage dependence and possible adsorption-induced segregation phenomena are addressed by investigating segregation energies (the difference in calculated total free energy between surface sites and bulk-like sites) of isolated Co in CoNi (111) alloy. In agreement with previous experimental and theoretical investigations, segregation of Co is found to be oxygen-coverage dependent. While for ‘clean’ CoNi (111), Co prefers to be in the bulk. In the presence of more than 2/9 ML of oxygen, Co segregates to the surface. The analysis of oxygen adsorption trends and surface electronic structures explains the change in the local atomic arrangement which is expected to occur on the surface of alloys under reaction conditions. Our predictions for the high oxygen coverage cases are particularly relevant in underlining the importance of segregation phenomena to the hydrogen evolution performance of CoNi alloy hydrogen evolution electrode.