Long-Term Follow-up and Mortality Rate of Patients of the Randomized Freeway Stent Study.

PURPOSE: This follow-up study was designed as a reopen of the completed Freeway Stent Study and collected mortality and clinical outcome data for at least 5 years after enrollment to evaluate long-term patient safety and treatment efficacy. The primary study enrolled 204 patients with stenosis or occlusion in the superficial femoral artery and proximal popliteal artery. Patients were randomized to primary nitinol stenting followed by standard PTA or primary nitinol stenting followed by FREEWAY™ paclitaxel-eluting balloon PTA. METHODS: Previous patients were recontacted by phone or during a routine hospital visit, and medical records were reviewed. Vital and clinical status information was collected. RESULTS: No increased late mortality was observed at 5 years, with an all-cause mortality rate of 12.0% in the FREEWAY drug-eluting balloon group versus 15.0% in the non-paclitaxel PTA group. No accumulation of any cause of death was observed in either group, nor was there any correlation with the dose of paclitaxel used. Freedom from clinically driven target lesion revascularization at 5 years was significantly higher in the FREEWAY drug eluting balloon group (85.3%) compared to standard PTA group (72.7%) Log-rank p = 0.032. CONCLUSION: The safety results presented support the recent conclusions that the use of paclitaxel technology does not lead to an increase in mortality. At the same time, the efficacy results clearly demonstrate that the potential benefits of drug-eluting balloon treatment are maintained over a 5-year period.

The Randomized Freeway Stent Study: Drug-Eluting Balloons Outperform Standard Balloon Angioplasty for Postdilatation of Nitinol Stents in the SFA and PI Segment.

PURPOSE: The prospective randomized multicenter Freeway study evaluated the possible hemodynamic and clinical benefits of primary stent insertion followed by percutaneous transluminal angioplasty (PTA) with drug-eluting balloons (DEB) over post-stent insertion PTA with standard balloons in the treatment of symptomatic femoropopliteal arteriosclerotic lesions. METHODS: In total, 204 patients in 13 centers in Germany and Austria were enrolled and randomized to primary stenting followed by either FREEWAY™ drug-eluting balloon or standard PTA balloon angioplasty. The primary endpoint was the rate of clinically driven target lesion revascularization (TLR) at 6 months; the secondary endpoints include TLR rate at 12 months and primary patency, shift in Rutherford classification, ankle-brachial index (ABI) and major adverse events (MAE) at 6 and 12 months. Lesion characteristics and vessel patency were analyzed by an independent and blinded corelab. RESULTS: At 6-month and 12-month follow-up, TLR rate was lower in the DEB arm compared to standard PTA but did not reach statistical significance (4.1% vs. 9.0% p = 0.234 and 7.9% vs. 17.7% p = 0.064, respectively). Primary patency was significantly better for patients treated with the DEB at 6 months (90.3% vs. 69.8% p = 0.001) and 12 months (77.4% vs. 61.0% p = 0.027). Improvement in Rutherford classifications was likewise significantly better for patients in the DEB group at 6 (94.9% vs. 84.3% p = 0.027) and 12 months (95.5% vs. 79.9% p = 0.003). The percentage of patients with an improved ABI of 1.0-1.2 was significantly higher in the DEB group compared to the PTA group at 6 months (55.3% vs. 35.3%; p = 0.015) but without significant difference at 12 months (48.2% vs. 32.9%; p = 0.055). At 6 months, rate of major adverse events (MAE) was 1% in both arms, and at 12 months 2.2% for the DEB and 3.8% for the PTA group. CONCLUSION: The Freeway Stent Study shows that the usage of DEB as a restenosis prophylaxis seems to be safe and feasible. The 12-month follow-up results give a clear sign in favor of the DEB group.

Nightly Biting Cycles of Anopheles Species in Rural Northwestern Burkina Faso.

The biting behavior of anophelines is an important determinant of malaria transmission. Understanding the local vector host-seeking behavior, its outdoor/ indoor biting preference, and nocturnal biting periods is essential for effectively applying and improving vector control methods, such as Long Lasting Insecticidal Nets (LLINs) and personal protective measures. To better understand the biting and host-seeking patterns of Anopheles mosquitoes in Northwestern Burkina Faso, we performed biweekly Human Landing Catches (HLC) in six villages during the period of highest mosquito abundance and malaria transmission. We applied a negative binomial regression framework to statistically analyze the host-seeking activities of Anopheles species and test for differences across hours, months, and villages, as well as for differences between indoor and outdoor capture points. Anopheles gambiae s.l. was identified as the main malaria vector in this region, representing about 90% of the total anopheline population. Biting activity was significantly different across hours and showed a peaked plateau between 2000 and 0200 hours. Differences in the pattern of biting cycles were observed between the early and late rainy season. This study shows that anopheline biting activity in Northwest Burkina Faso is high throughout the night, at indoor and outdoor posts alike. Consequently, bed nets alone may not provide sufficient protection against early biting anophelines and should be complemented with additional strategies such as indoor residual spraying (IRS) and larval source management (LSM) to meet the WHO's ambitious goals that are reflected in the global technical malaria strategy for 2030.

Evaluating the significance of paleophylogeographic species distribution models in reconstructing quaternary range-shifts of nearctic chelonians.

The climatic cycles of the Quaternary, during which global mean annual temperatures have regularly changed by 5-10°C, provide a special opportunity for studying the rate, magnitude, and effects of geographic responses to changing climates. During the Quaternary, high- and mid-latitude species were extirpated from regions that were covered by ice or otherwise became unsuitable, persisting in refugial retreats where the environment was compatible with their tolerances. In this study we combine modern geographic range data, phylogeny, Pleistocene paleoclimatic models, and isotopic records of changes in global mean annual temperature, to produce a temporally continuous model of geographic changes in potential habitat for 59 species of North American turtles over the past 320 Ka (three full glacial-interglacial cycles). These paleophylogeographic models indicate the areas where past climates were compatible with the modern ranges of the species and serve as hypotheses for how their geographic ranges would have changed in response to Quaternary climate cycles. We test these hypotheses against physiological, genetic, taxonomic and fossil evidence, and we then use them to measure the effects of Quaternary climate cycles on species distributions. Patterns of range expansion, contraction, and fragmentation in the models are strongly congruent with (i) phylogeographic differentiation; (ii) morphological variation; (iii) physiological tolerances; and (iv) intraspecific genetic variability. Modern species with significant interspecific differentiation have geographic ranges that strongly fluctuated and repeatedly fragmented throughout the Quaternary. Modern species with low genetic diversity have geographic distributions that were highly variable and at times exceedingly small in the past. Our results reveal the potential for paleophylogeographic models to (i) reconstruct past geographic range modifications, (ii) identify geographic processes that result in genetic bottlenecks; and (iii) predict threats due to anthropogenic climate change in the future.

A comprehensive analysis of bilaterian mitochondrial genomes and phylogeny.

About 2800 mitochondrial genomes of Metazoa are present in NCBI RefSeq today, two thirds belonging to vertebrates. Metazoan phylogeny was recently challenged by large scale EST approaches (phylogenomics), stabilizing classical nodes while simultaneously supporting new sister group hypotheses. The use of mitochondrial data in deep phylogeny analyses was often criticized because of high substitution rates on nucleotides, large differences in amino acid substitution rate between taxa, and biases in nucleotide frequencies. Nevertheless, mitochondrial genome data might still be promising as it allows for a larger taxon sampling, while presenting a smaller amount of sequence information. We present the most comprehensive analysis of bilaterian relationships based on mitochondrial genome data. The analyzed data set comprises more than 650 mitochondrial genomes that have been chosen to represent a profound sample of the phylogenetic as well as sequence diversity. The results are based on high quality amino acid alignments obtained from a complete reannotation of the mitogenomic sequences from NCBI RefSeq database. However, the results failed to give support for many otherwise undisputed high-ranking taxa, like Mollusca, Hexapoda, Arthropoda, and suffer from extreme long branches of Nematoda, Platyhelminthes, and some other taxa. In order to identify the sources of misleading phylogenetic signals, we discuss several problems associated with mitochondrial genome data sets, e.g. the nucleotide and amino acid landscapes and a strong correlation of gene rearrangements with long branches.

Isolation and characterization of nine polymorphic microsatellite markers for the deep-sea shrimp Nematocarcinus lanceopes (Crustacea: Decapoda: Caridea).

BACKGROUND: The shrimp Nematocarcinus lanceopes Bate, 1888 is found in the deep sea around Antarctica and sub-Antarctic islands. Previous studies on mitochondrial data and species distribution models provided evidence for a homogenous circum-Antarctic population of N. lanceopes. However, to analyze the fine-scale population genetic structure and to examine influences of abiotic environmental conditions on population composition and genetic diversity, a set of fast evolving nuclear microsatellite markers is required. FINDINGS: We report the isolation and characterization of nine polymorphic microsatellite markers from the Antarctic deep-sea shrimp species Nematocarcinus lanceopes (Crustacea: Decapoda: Caridea). Microsatellite markers were screened in 55 individuals from different locations around the Antarctic continent. All markers were polymorphic with 9 to 25 alleles per locus. The observed heterozygosity ranged from 0.545 to 0.927 and the expected heterozygosity from 0.549 to 0.934. CONCLUSIONS: The reported markers provide a novel tool to study genetic structure and diversity in Nematocarcinus lanceopes populations in the Southern Ocean and monitor effects of ongoing climate change in the region on the populations inhabiting these.

Correction: Effects of Late-Cenozoic Glaciation on Habitat Availability in Antarctic Benthic Shrimps (Crustacea: Decapoda: Caridea).

[This corrects the article DOI: 10.1371/journal.pone.0046283.].

Exploring Pandora's box: potential and pitfalls of low coverage genome surveys for evolutionary biology.

High throughput sequencing technologies are revolutionizing genetic research. With this "rise of the machines", genomic sequences can be obtained even for unknown genomes within a short time and for reasonable costs. This has enabled evolutionary biologists studying genetically unexplored species to identify molecular markers or genomic regions of interest (e.g. micro- and minisatellites, mitochondrial and nuclear genes) by sequencing only a fraction of the genome. However, when using such datasets from non-model species, it is possible that DNA from non-target contaminant species such as bacteria, viruses, fungi, or other eukaryotic organisms may complicate the interpretation of the results. In this study we analysed 14 genomic pyrosequencing libraries of aquatic non-model taxa from four major evolutionary lineages. We quantified the amount of suitable micro- and minisatellites, mitochondrial genomes, known nuclear genes and transposable elements and searched for contamination from various sources using bioinformatic approaches. Our results show that in all sequence libraries with estimated coverage of about 0.02-25%, many appropriate micro- and minisatellites, mitochondrial gene sequences and nuclear genes from different KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways could be identified and characterized. These can serve as markers for phylogenetic and population genetic analyses. A central finding of our study is that several genomic libraries suffered from different biases owing to non-target DNA or mobile elements. In particular, viruses, bacteria or eukaryote endosymbionts contributed significantly (up to 10%) to some of the libraries analysed. If not identified as such, genetic markers developed from high-throughput sequencing data for non-model organisms may bias evolutionary studies or fail completely in experimental tests. In conclusion, our study demonstrates the enormous potential of low-coverage genome survey sequences and suggests bioinformatic analysis workflows. The results also advise a more sophisticated filtering for problematic sequences and non-target genome sequences prior to developing markers.

Effects of late-cenozoic glaciation on habitat availability in Antarctic benthic shrimps (Crustacea: Decapoda: Caridea).

Marine invertebrates inhabiting the high Antarctic continental shelves are challenged by disturbance of the seafloor by grounded ice, low but stable water temperatures and variable food availability in response to seasonal sea-ice cover. Though a high diversity of life has successfully adapted to such conditions, it is generally agreed that during the Last Glacial Maximum (LGM) the large-scale cover of the Southern Ocean by multi-annual sea ice and the advance of the continental ice sheets across the shelf faced life with conditions, exceeding those seen today by an order of magnitude. Conditions prevailing at the LGM may have therefore acted as a bottleneck event to both the ecology as well as genetic diversity of today's fauna. Here, we use for the first time specific Species Distribution Models (SDMs) for marine arthropods of the Southern Ocean to assess effects of habitat contraction during the LGM on the three most common benthic caridean shrimp species that exhibit a strong depth zonation on the Antarctic continental shelf. While the shallow-water species Chorismus antarcticus and Notocrangon antarcticus were limited to a drastically reduced habitat during the LGM, the deep-water shrimp Nematocarcinus lanceopes found refuge in the Southern Ocean deep sea. The modeling results are in accordance with genetic diversity patterns available for C. antarcticus and N. lanceopes and support the hypothesis that habitat contraction at the LGM resulted in a loss of genetic diversity in shallow water benthos.

Parametric and non-parametric masking of randomness in sequence alignments can be improved and leads to better resolved trees.

BACKGROUND: Methods of alignment masking, which refers to the technique of excluding alignment blocks prior to tree reconstructions, have been successful in improving the signal-to-noise ratio in sequence alignments. However, the lack of formally well defined methods to identify randomness in sequence alignments has prevented a routine application of alignment masking. In this study, we compared the effects on tree reconstructions of the most commonly used profiling method (GBLOCKS) which uses a predefined set of rules in combination with alignment masking, with a new profiling approach (ALISCORE) based on Monte Carlo resampling within a sliding window, using different data sets and alignment methods. While the GBLOCKS approach excludes variable sections above a certain threshold which choice is left arbitrary, the ALISCORE algorithm is free of a priori rating of parameter space and therefore more objective. RESULTS: ALISCORE was successfully extended to amino acids using a proportional model and empirical substitution matrices to score randomness in multiple sequence alignments. A complex bootstrap resampling leads to an even distribution of scores of randomly similar sequences to assess randomness of the observed sequence similarity. Testing performance on real data, both masking methods, GBLOCKS and ALISCORE, helped to improve tree resolution. The sliding window approach was less sensitive to different alignments of identical data sets and performed equally well on all data sets. Concurrently, ALISCORE is capable of dealing with different substitution patterns and heterogeneous base composition. ALISCORE and the most relaxed GBLOCKS gap parameter setting performed best on all data sets. Correspondingly, Neighbor-Net analyses showed the most decrease in conflict. CONCLUSIONS: Alignment masking improves signal-to-noise ratio in multiple sequence alignments prior to phylogenetic reconstruction. Given the robust performance of alignment profiling, alignment masking should routinely be used to improve tree reconstructions. Parametric methods of alignment profiling can be easily extended to more complex likelihood based models of sequence evolution which opens the possibility of further improvements.