Unrecognized diversity and distribution of soil algae from Maritime Antarctica (Fildes Peninsula, King George Island).

Introduction: Eukaryotic algae in the top few centimeters of fellfield soils of ice-free Maritime Antarctica have many important effects on their habitat, such as being significant drivers of organic matter input into the soils and reducing the impact of wind erosion by soil aggregate formation. To better understand the diversity and distribution of Antarctic terrestrial algae, we performed a pilot study on the surface soils of Meseta, an ice-free plateau mountain crest of Fildes Peninsula, King George Island, being hardly influenced by the marine realm and anthropogenic disturbances. It is openly exposed to microbial colonization from outside Antarctica and connected to the much harsher and dryer ice-free zones of the continental Antarctic. A temperate reference site under mild land use, SchF, was included to further test for the Meseta algae distribution in a contrasting environment. Methods: We employed a paired-end metabarcoding analysis based on amplicons of the highly variable nuclear-encoded ITS2 rDNA region, complemented by a clone library approach. It targeted the four algal classes, Chlorophyceae, Trebouxiophyceae, Ulvophyceae, and Xanthophyceae, representing key groups of cold-adapted soil algae. Results: A surprisingly high diversity of 830 algal OTUs was revealed, assigned to 58 genera in the four targeted algal classes. Members of the green algal class Trebouxiophyceae predominated in the soil algae communities. The major part of the algal biodiversity, 86.1% of all algal OTUs, could not be identified at the species level due to insufficient representation in reference sequence databases. The classes Ulvophyceae and Xanthophyceae exhibited the most unknown species diversity. About 9% of the Meseta algae species diversity was shared with that of the temperate reference site in Germany. Discussion: In the small portion of algal OTUs for which their distribution could be assessed, the entire ITS2 sequence identity with references shows that the soil algae likely have a wide distribution beyond the Polar regions. They probably originated from soil algae propagule banks in far southern regions, transported by aeolian transport over long distances. The dynamics and severity of environmental conditions at the soil surface, determined by high wind currents, and the soil algae's high adaptability to harsh environmental conditions may account for the high similarity of soil algal communities between the northern and southern parts of the Meseta.

App-SpaM: phylogenetic placement of short reads without sequence alignment.

Motivation: Phylogenetic placement is the task of placing a query sequence of unknown taxonomic origin into a given phylogenetic tree of a set of reference sequences. A major field of application of such methods is, for example, the taxonomic identification of reads in metabarcoding or metagenomic studies. Several approaches to phylogenetic placement have been proposed in recent years. The most accurate of them requires a multiple sequence alignment of the references as input. However, calculating multiple alignments is not only time-consuming but also limits the applicability of these approaches. Results: Herein, we propose Alignment-free phylogenetic placement algorithm based on Spaced-word Matches (App-SpaM), an efficient algorithm for the phylogenetic placement of short sequencing reads on a tree of a set of reference sequences. App-SpaM produces results of high quality that are on a par with the best available approaches to phylogenetic placement, while our software is two orders of magnitude faster than these existing methods. Our approach neither requires a multiple alignment of the reference sequences nor alignments of the queries to the references. This enables App-SpaM to perform phylogenetic placement on a broad variety of datasets. Availability and implementation: The source code of App-SpaM is freely available on Github at https://github.com/matthiasblanke/App-SpaM together with detailed instructions for installation and settings. App-SpaM is furthermore available as a Conda-package on the Bioconda channel. Contact: matthias.blanke@biologie.uni-goettingen.de. Supplementary information: Supplementary data are available at Bioinformatics Advances online.

Elastic Stable Chest Repair as a Means of Stabilizing the Anterior Chest Wall in Recurrent Pectus Excavatum with Sternocostal Pseudarthrosis: An Innovative Fixation Device.

INTRODUCTION: Open surgical procedures in the treatment of pectus excavatum (PE) involve predetermined incisions in the parasternal cartilage and the bony ribs. For some procedures, the ribs are even dissected from the sternum for better sternal mobilization and thus better elevation of the funnel. Secure restoration of the sternocostal junction is then required, with the consequence that healing may be quite impaired. Patients may also subsequently suffer from sternocostal nonunion, for example, pseudarthrosis, and dislocated ribs, as well as pain and a recurrence of PE. MATERIALS AND METHODS: Patients underwent another open surgery with revision of the pseudarthrotic sternocostal junctions and sufficient mobilization of the anterior chest wall, followed by an open reduction and internal fixation using Matrix Rib titanium plates (Synthes, Oberdorf, Switzerland). This procedure consisted of elevating the anterior chest wall and fixing the ribs to the sternum. In 2011 and 2012, we studied this procedure, known as elastic stable chest repair (ESCR), in a series of 20 patients. The patients underwent clinical and ultrasound examinations and X-ray radiographs after the operation, after 6 weeks, and at 3- and 12-month intervals. RESULTS: Follow-up showed high patient tolerance, although a loose plate was observed in one patient and a broken plate in three patients. A stable union was achieved for all sternocostal pseudarthroses. PE improved highly significantly (p < 0.001), as the Haller index decreased from 3.6 (range: 2.7-6.6, standard deviation [SD]: 0.92) to 2.7 (range: 2.0-3.7, SD: 0.42). Pain in the anterior chest wall was significantly reduced after the operation in the majority of cases. All but one patient was mobilized already the day after the operation. CONCLUSIONS: ESCR in recurrent PE achieved functional stabilization of the anterior chest wall combined with satisfactory results.

Surgical fixation of sternal fractures: locked plate fixation by low-profile titanium plates--surgical safety through depth limited drilling.

PURPOSE: Operative treatment of sternal fractures has become a matter of increasing interest. Anterior plating seems to be the most appropriate method for fixing sternal fractures. However, there are several concerns in relation to the operative procedure such as severe injuries to mediastinal organs, patient comfort and proper stabilisation, for example. This paper describes a safe method of anterior sternal plating using locked plate fixation with limited depth drilling. METHODS: Ten patients with sternal fractures were included in this cohort study and were treated by anterior plating using one or two plates in parallel through a median approach to the sternum. Follow up was performed after six weeks, 12 weeks and six months. RESULTS: Follow up revealed no serious complications. One patient suffered from postoperative wound seroma. No problems were caused by the plates. CONCLUSIONS: Sternal plating using low profile locked titanium plates seems to be a safe and stable method with a high level of patient comfort.

Magnetic resonance imaging of the knee at 3 and 7 tesla: a comparison using dedicated multi-channel coils and optimised 2D and 3D protocols.

OBJECTIVES: To show the feasibility and possible superiority of two 7 Tesla knee protocols ("7 T high resolution" and "7 T quick") using a new 28-channel knee coil compared to an optimised 3 T knee protocol using an 8-channel knee coil. METHODS: The study was approved by the ethics committee. Both 3 T and 7 T MRI of the knee were performed in 10 healthy volunteers (29.6 ± 7.9 years), with two 2D sequences (PD-TSE and T1-SE) and three isotropic 3D sequences (TRUFI, FLASH and PD-TSE SPACE). Quantitative contrast-to-noise ratio (CNR) and qualitative evaluations were performed by different readers, and intra- and inter-rater agreement was assessed. RESULTS: The signal-to-noise ratio (SNR) as well as the CNR values for cartilage-bone, cartilage-fluid, cartilage-menisci and menisci-fluid were, in most cases, higher at 7 T compared to 3 T, and the 7 T quick measurement was slightly superior compared to the 7 T high-resolution measurement. The results of the subjective qualitative analysis were higher for the 7 T measurements compared to the 3 T measurements. Inter- and intra-observer reliability was high (0.884-0.999). CONCLUSIONS: Through higher field strength and an optimal coil, resolution at 7 T can be increased and acquisition time can be reduced, with superior quantitative and comparable qualitative results compared to 3 T.

Evaluation of cartilage repair tissue after matrix-associated autologous chondrocyte transplantation using a hyaluronic-based or a collagen-based scaffold with morphological MOCART scoring and biochemical T2 mapping: preliminary results.

BACKGROUND: In cartilage repair, bioregenerative approaches using tissue engineering techniques have tried to achieve a close resemblance to hyaline cartilage, which might be visualized using advanced magnetic resonance imaging. PURPOSE: To compare cartilage repair tissue at the femoral condyle noninvasively after matrix-associated autologous chondrocyte transplantation using Hyalograft C, a hyaluronic-based scaffold, to cartilage repair tissue after transplantation using CaReS, a collagen-based scaffold, with magnetic resonance imaging using morphologic scoring and T2 mapping. STUDY DESIGN: Cohort study; Level of evidence, 3. METHODS: Twenty patients after matrix-associated autologous chondrocyte transplantation (Hyalograft C, n = 10; CaReS, n = 10) underwent 3-T magnetic resonance imaging 24 months after surgery. Groups were matched by age and defect size/localization. For clinical outcome, the Brittberg score was assessed. Morphologic analysis was applied using the magnetic resonance observation of cartilage repair tissue score, and global and zonal biochemical T2 mapping was performed to reflect biomechanical properties with regard to collagen matrix/content and hydration. RESULTS: The clinical outcome was comparable in each group. The magnetic resonance observation of cartilage repair tissue score showed slightly but not significantly (P= .210) better results in the CaReS group (76.5) compared to the Hyalograft C group (70.0), with significantly better (P= .004) constitution of the surface of the repair tissue in the CaReS group. Global T2 relaxation times (milliseconds) for healthy surrounding cartilage were comparable in both groups (Hyalograft C, 49.9; CaReS, 51.9; P= .398), whereas cartilage repair tissue showed significantly higher results in the CaReS group (Hyalograft C, 48.2; CaReS, 55.5; P= .011). Zonal evaluation showed no significant differences (P > or = .05). CONCLUSION: Most morphologic parameters provided comparable results for both repair tissues. However, differences in the surface and higher T2 values for the cartilage repair tissue that was based on a collagen scaffold (CaReS), compared to the hyaluronic-based scaffold, indicated differences in the composition of the repair tissue even 2 years postimplantation. CLINICAL RELEVANCE: In the follow-up of cartilage repair procedures using matrix-associated autologous chondrocyte transplantation, differences due to scaffolds have to be taken into account.

T2 and T2* mapping in patients after matrix-associated autologous chondrocyte transplantation: initial results on clinical use with 3.0-Tesla MRI.

OBJECTIVES: To use T2 and T2* mapping in patients after matrix-associated autologous chondrocyte transplantation (MACT) of the knee, and to compare and correlate both methodologies. METHODS: 3.0-Tesla MRI was performed on 30 patients (34.6 +/- 9.9 years) with a follow-up period of 28.1 +/- 18.8 months after MACT. Multi-echo, spin-echo-based T2 mapping using six echoes and gradient-echo-based T2* mapping using six echoes were prepared. T2 and T2* maps were obtained using a pixel-wise, mono-exponential, non-negative least-squares fit analysis. Region-of-interest analysis was performed for mean (full-thickness) as well as deep and superficial aspects of the cartilage repair tissue and control cartilage sites. RESULTS: Mean T2 values (ms) were comparable for the control cartilage (53.4 +/- 11.7) and the repair tissue (55.5 +/- 11.6) (p > 0.05). Mean T2* values (ms) for control cartilage (30.9 +/- 6.6) were significantly higher than those of the repair tissue (24.5 +/- 8.1) (p < 0.001). Zonal stratification was more pronounced for T2* than for T2. The correlation between T2 and T2* was highly significant (p < 0.001), with a Pearson coefficient between 0.276 and 0.433. CONCLUSION: T2 and T2* relaxation time measurements in the evaluation of cartilage repair tissue and its zonal variation show promising results, although the properties visualised by T2 and T2* may differ.