Abstract
US has become an important diagnostic tool for musculoskeletal diseases. Because of its wide availability in rheumatology practice, US has also been applied in other rheumatic diseases such ...as GCA. In acute GCA, US displays a non-compressible, hypoechoic, most commonly concentric arterial wall thickening. Temporal and axillary arteries should be examined in patients with suspected GCA and PMR. Additionally, almost all other large arteries, with the exception of the thoracic aorta, can be easily delineated by US. Many studies and several meta-analyses have been conducted to evaluate the diagnostic performance of US. US is more sensitive than temporal artery biopsy (TAB) because TAB evaluates only a limited anatomical region in a systemic disease. Most US studies arrive at specificities between 90 and 100% compared with the final clinical diagnosis. Reliability for reading US images and videos is excellent and comparable to reliability for reading TAB specimens. The advantage of US over other imaging techniques in GCA is its availability, safety and tolerability and its high resolution of 0.1 mm. Rheumatology departments are increasingly establishing fast-track clinics. Physicians can refer patients with suspected GCA within 24 h. Patients receive clinical and US examination by experienced specialists, establishing a clear diagnosis either before TAB or without the need for TAB. The introduction of fast-track clinics has led to a significant reduction of permanent vision loss. Furthermore, a process that primarily includes US is significantly more cost-effective than TAB.
The EU has become increasingly politicized not only at the bottom, due to polarized debates, divided electorates, declining mainstream parties, and rising Euroskeptic populism; or from the bottom up, ...as national politics permeates member-state leaders' positions in the Council. It has also emerged purely at the top, in the increasingly politically charged dynamics of interaction within and among EU actors. Such politicization involves struggles for power and influence that are ideational as much as institutional and coercive. Current theorists of EU integration, because of their tendency to focus on only one or another EU actor have overlooked the EU's politicized dynamics, even though their accounts, taken together, provide ample evidence of it. The article shows that the EU has gone from what was once metaphorically described with the catchphrase of 'politics without policy' at the national level to 'politics against policy' in more contentious areas, whereas at the EU level it has moved from 'policy without politics' to 'politics with policy'. The paper illustrates with the cases of the Council and the Commission in the Eurozone crisis.
Recent developments in third-gen long read sequencing and diploid-aware assemblers have resulted in the rapid release of numerous reference-quality assemblies for diploid genomes. However, assembly ...of highly heterozygous genomes is still problematic when regional heterogeneity is so high that haplotype homology is not recognised during assembly. This results in regional duplication rather than consolidation into allelic variants and can cause issues with downstream analysis, for example variant discovery, or haplotype reconstruction using the diploid assembly with unpaired allelic contigs.
A new pipeline-Purge Haplotigs-was developed specifically for third-gen sequencing-based assemblies to automate the reassignment of allelic contigs, and to assist in the manual curation of genome assemblies. The pipeline uses a draft haplotype-fused assembly or a diploid assembly, read alignments, and repeat annotations to identify allelic variants in the primary assembly. The pipeline was tested on a simulated dataset and on four recent diploid (phased) de novo assemblies from third-generation long-read sequencing, and compared with a similar tool. After processing with Purge Haplotigs, haploid assemblies were less duplicated with minimal impact on genome completeness, and diploid assemblies had more pairings of allelic contigs.
Purge Haplotigs improves the haploid and diploid representations of third-gen sequencing based genome assemblies by identifying and reassigning allelic contigs. The implementation is fast and scales well with large genomes, and it is less likely to over-purge repetitive or paralogous elements compared to alignment-only based methods. The software is available at https://bitbucket.org/mroachawri/purge_haplotigs under a permissive MIT licence.
To examine the validity of popular smartphone accelerometer applications and a consumer activity wristband compared to a widely used research accelerometer while assessing the impact of the phone's ...position on the accuracy of step detection. Twenty volunteers from 2 different age groups (Group A: 18‐25 years, n = 10; Group B 45‐70 years, n = 10) were equipped with 3 iPhone SE smartphones (placed in pants pocket, shoulder bag, and backpack), 1 Samsung Galaxy S6 Edge (pants pocket), 1 Garmin Vivofit 2 wristband, and 2 ActiGraph wGTX+ devices (worn at wrist and hip) while walking on a treadmill (1.6, 3.2, 4.8, and 6.0 km/h) and completing a walking course. All smartphones included 6 accelerometer applications. Video observation was used as gold standard. Validity was evaluated by comparing each device with the gold standard using mean absolute percentage errors (MAPE). The MAPE of the iPhone SE (all positions) and the Garmin Vivofit was small (<3) for treadmill walking ≥3.2 km/h and for free walking. The Samsung Galaxy and hip‐worn ActiGraph showed small MAPE only for treadmill walking at 4.8 and 6.0 km/h and for free walking. The wrist‐worn ActiGraph showed high MAPE (17‐47) for all walking conditions. The iPhone SE and the Garmin Vivofit 2 are accurate tools for step counting in different age groups and during various walking conditions, even during slow walking. The phone's position does not impact the accuracy of step detection, which substantially improves the versatility for physical activity assessment in clinical and research settings.
Abstract
IQ-TREE (http://www.iqtree.org, last accessed February 6, 2020) is a user-friendly and widely used software package for phylogenetic inference using maximum likelihood. Since the release of ...version 1 in 2014, we have continuously expanded IQ-TREE to integrate a plethora of new models of sequence evolution and efficient computational approaches of phylogenetic inference to deal with genomic data. Here, we describe notable features of IQ-TREE version 2 and highlight the key advantages over other software.
Acute wound healing in the skin involves the communication of multiple cell types to coordinate keratinocyte and fibroblast proliferation and migration for epidermal and dermal repair. Many studies ...have focused on the interplay between hematopoietic cells, keratinocytes and fibroblasts during skin wound healing, yet the possible roles for other cell types within the skin, such as intradermal adipocytes, have not been investigated during this process. Here, we identify that adipocyte lineage cells are activated and function during acute skin wound healing. We find that adipocyte precursor cells proliferate and mature adipocytes repopulate skin wounds following inflammation and in parallel with fibroblast migration. Functional analysis of mice with defects in adipogenesis demonstrates that adipocytes are necessary for fibroblast recruitment and dermal reconstruction. These data implicate adipocytes as a key component of the intercellular communication that mediates fibroblast function during skin wound healing.
Large phylogenomics data sets require fast tree inference methods, especially for maximum-likelihood (ML) phylogenies. Fast programs exist, but due to inherent heuristics to find optimal trees, it is ...not clear whether the best tree is found. Thus, there is need for additional approaches that employ different search strategies to find ML trees and that are at the same time as fast as currently available ML programs. We show that a combination of hill-climbing approaches and a stochastic perturbation method can be time-efficiently implemented. If we allow the same CPU time as RAxML and PhyML, then our software IQ-TREE found higher likelihoods between 62.2% and 87.1% of the studied alignments, thus efficiently exploring the tree-space. If we use the IQ-TREE stopping rule, RAxML and PhyML are faster in 75.7% and 47.1% of the DNA alignments and 42.2% and 100% of the protein alignments, respectively. However, the range of obtaining higher likelihoods with IQ-TREE improves to 73.3-97.1%. IQ-TREE is freely available at http://www.cibiv.at/software/iqtree.
Abstract Objective The aim of this study was to summarize the clinical experience at our clinic with pelvic exenteration as a treatment for cervical cancer with special regard to the indications and ...outcomes of specific patient groups. Methods Medical records of 282 women who underwent pelvic exenteration to treat cervical cancer were analyzed. Results In total, 70 patients (25%) underwent primary exenteration, and 212 (75%) underwent secondary exenteration. Exenteration was anterior for 14 (5%) patients, posterior for 6 (2%) and total for 262 (93%). The overall survival (OS) of the 282 patients was 41% at 5 years and 37% at 10 years. The disease-free survival at 5 years was 61%. For 133 patients for whom pelvic exenteration was a curative procedure, the OS was 64% at 5 years and 57% at 10 years. For cases of pelvic exenteration as a palliative intervention, the OS was 19% at 5 years and 18% at 10 years. No difference was seen in the OS at 5 years between patients who received primary and secondary operations. No significant difference in the OS was found regardless of whether the patients had positive pelvic lymph nodes, whereas in cases of paraaortic lymph node metastasis, the OS was significantly lower. Out of all of the procedures, 139 (49%) involved no perioperative or postoperative complications. One major complication was reported for 72 (26%) patients, two complications occurred for 42 patients (15%) and more than three complications were noted for 29 (10%) patients. Conclusion Pelvic exenteration is an effective technique with a high percentage of long-term survivors. To the best of our knowledge, our study involves the largest published number of patients treated with pelvic exenteration for a single gynecological cancer and shows that previous contraindications for pelvic exenteration, such as lymph node metastasis (especially when confined to the pelvic lymph nodes), older age or palliative intent, should be reconsidered.
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