Phylogeny and divergence of the pinnipeds (Carnivora: Mammalia) assessed using a multigene dataset

Background  

Phylogenetic comparative methods are often improved by complete phylogenies with meaningful branch lengths (e.g., divergence dates). This study presents a dated molecular supertree for all 34 world pinniped species derived from a weighted matrix representation with parsimony (MRP) supertree analysis of 50 gene trees, each determined under a maximum likelihood (ML) framework. Divergence times were determined by mapping the same sequence data (plus two additional genes) on to the supertree topology and calibrating the ML branch lengths against a range of fossil calibrations. We assessed the sensitivity of our supertree topology in two ways: 1) a second supertree with all mtDNA genes combined into a single source tree, and 2) likelihood-based supermatrix analyses. Divergence dates were also calculated using a Bayesian relaxed molecular clock with rate autocorrelation to test the sensitivity of our supertree results further.     

Semantic associations between signs and numerical categories in the prefrontal cortex

The utilization of symbols such as words and numbers as mental tools endows humans with unrivalled cognitive flexibility. In the number domain, a fundamental first step for the acquisition of numerical symbols is the semantic association of signs with cardinalities. We explored the primitives of such a semantic mapping process by recording single-cell activity in the monkey prefrontal and parietal cortices, brain structures critically involved in numerical cognition. Monkeys were trained to associate visual shapes with varying numbers of items in a matching task. After this long-term learning process, we found that the responses of many prefrontal neurons to the visual shapes reflected the associated numerical value in a behaviorally relevant way. In contrast, such association neurons were rarely found in the parietal lobe. These findings suggest a cardinal role of the prefrontal cortex in establishing semantic associations between signs and abstract categories, a cognitive precursor that may ultimately give rise to symbolic thinking in linguistic humans.     

The LabBM score is an excellent survival prediction tool in patients undergoing palliative radiotherapy

Background and aimThe prognostic assessment of patients referred for palliative radiotherapy can be conducted by site-specific scores. A quick assessment that would cover the whole spectrum could simplify the working day of clinicians who are not specialists for a particular disease site. This study evaluated a promising score, the LabBM (validated for brain metastases), in patients treated for other indications.Materials and methodsThe LabBM score was calculated in 375 patients by assigning 1 point each for C-reactive protein and lactate dehydrogenase above the upper limit of normal, and 0.5 points each for hemoglobin, platelets and albumin below the lower limit of normal. Uni- and multivariate analyses were performed.ResultsMedian overall survival gradually decreased with increasing point sum (range 25.1–1.1 months). When grouped according to the original three-tiered model, excellent discrimination was found. Patients with 0–1 points had a median survival of 15.7 months. Those with 1.5–2 points had a median survival of 5.8 months. Finally, those with 2.5–3.5 points had a median survival of 3.2 months (all p-values ≤ 0.001).ConclusionThe LabBM score, which is derived from inexpensive blood tests and easy to use, stratified patients into three very distinct prognostic groups and deserves further validation.     

Effect of Host Tree Traits on Epiphyte Diversity in Natural and Anthropogenic Habitats in Ecuador

Vascular epiphytes represent a highly diverse element of tropical rain forests, but they depend strongly on the structure and taxonomic composition of their tree communities. For conservation planning, it is therefore critical to understand the effect of host tree characteristics on epiphyte species richness in natural and anthropogenically transformed vegetation. Our study compares the effect of human land‐use on epiphyte diversity based on 220 study plots in a lowland rain forest and an Andean cloud forest in western Ecuador. We evaluate the relevance of host tree size and taxonomic identity for epiphyte species richness in contiguous primary forests, forest fragments, isolated remnant trees (IRTs), and secondary forests. At both study sites, epiphyte diversity was highest in primary forests, and it was lowest on IRTs and in secondary forests. Epiphyte species numbers of forest fragments were significantly reduced compared with the contiguous primary forest at the lowland study site, but not in the cloud forest area. Host tree size was a core predictor among secondary forests, but it had less significance within other habitat types. Taxonomic identity of the host trees also explained up to 61 percent of the variation in epiphyte diversity, especially for IRTs. The structural and taxonomic composition of the tree community in anthropogenically transformed habitat types proved to be fundamental to epiphyte diversity. This highlights the importance of deliberate selection of tree species for reforestation in conservation programs and the possible negative effects of selective logging in primary forests. Abstract in Spanish is available at http://www.blackwell‐synergy.com/loi/btp .     

In vivo and in vitro escape from neutralizing antibodies 2G12, 2F5, and 4E10

Recently, passive immunization of human immunodeficiency virus (HIV)-infected individuals with monoclonal antibodies (MAbs) 2G12, 2F5, and 4E10 provided evidence of the in vivo activity of 2G12 but raised concerns about the function of the two membrane-proximal external region (MPER)-specific MAbs (A. Trkola, H. Kuster, P. Rusert, B. Joos, M. Fischer, C. Leemann, A. Manrique, M. Huber, M. Rehr, A. Oxenius, R. Weber, G. Stiegler, B. Vcelar, H. Katinger, L. Aceto, and H. F. Gunthard, Nat. Med. 11:615-622, 2005). In the light of MPER-targeting vaccines under development, we performed an in-depth analysis of the emergence of mutations conferring resistance to these three MAbs to further elucidate their activity. Clonal analysis of the MPER of plasma virus samples derived during antibody treatment confirmed that no changes in this region had occurred in vivo. Sequence analysis of the 2G12 epitope relevant N-glycosylation sites of viruses derived from 13 patients during the trial supported the phenotypic evaluation, demonstrating that mutations in these sites are associated with resistance. In vitro selection experiments with isolates of four of these individuals corroborated the in vivo finding that virus strains rapidly escape 2G12 pressure. Notably, in vitro resistance mutations differed, in most cases, from those found in vivo. Importantly, in vitro selection with 2F5 and 4E10 demonstrated that resistance to these MAbs can be difficult to achieve and can lead to selection of variants with impaired infectivity. This remarkable vulnerability of the virus to interference within the MPER calls for a further evaluation of the safety and efficacy of MPER-targeting therapeutic and vaccination strategies.     

Definitive,intensity modulated tomotherapy with a simultaneous integrated boost for prostate cancer patients – Long term data on toxicity and biochemical control

AimTo report long-term data regarding biochemical control and late toxicity of simultaneous integrated boost intensity modulated radiotherapy (SIB-IMRT) with tomotherapy in patients with localized prostate cancer.BackgroundDose escalation improves cancer control after curative intended radiation therapy (RT) to patients with localized prostate cancer, without increasing toxicity, if IMRT is used.Materials and methodsIn this retrospective analysis, we evaluated long-term toxicity and biochemical control of the first 40 patients with intermediate risk prostate cancer receiving SIB-IMRT. Primary target volume (PTV) 1 including the prostate and proximal third of the seminal vesicles with safety margins was treated with 70 Gy in 35 fractions. PTV 2 containing the prostate with smaller safety margins was treated as SIB to a total dose of 76 Gy with 2.17 Gy per fraction. Toxicity was evaluated using an adapted CTCAE-Score (Version 3).ResultsMedian follow-up of living patients was 66 (20–78) months. No late genitourinary toxicity higher than grade 2 has been reported. Grade 2 genitourinary toxicity rates decreased from 58% at the end of the treatment to 10% at 60 months. Late gastrointestinal (GI) toxicity was also moderate, though the prescribed PTV Dose of 76 Gy was accepted at the anterior rectal wall. 74% of patients reported any GI toxicity during follow up and no toxicity rates higher than grade 2 were observed. Grade 2 side effects were reported by 13% of the patients at 60 months. 5-year freedom from biochemical failure was 95% at our last follow up.ConclusionSIB-IMRT using daily MV-CT guidance showed excellent long-term biochemical control and low toxicity rates.     

Burrowing and feeding behaviour in the rat

Little information is available on the burrowing activity of the brown rat, Rattus norvegicus (Berk.), in the field or laboratory. Three groups of rats (laboratory, hybrid and wild) were studied in a semi-natural environment. The observational area was entirely enclosed by a steel net and comprised a channel (22 m long) fed by Po river water and a terrestrial area of 50 m². The development of the burrow systems and their structure was not significantly different in the three groups of rats, and was comparable to those reported by other authors. The results suggest that the complexity of the burrow systems and pathways is connected to the population density of the rat group under study. An intense predation on freshwater molluscs was observed. A relationship was found between prey size and the probability of their being carried into the food-sites and burrows for consumption.     

Interrelation of kinetic and stereoscopic depth: behavior and physiology in vertebrates

The target article gathers compelling behavioral evidence that motion parallax provides depth information in a variety of animal species. A more general evaluation of kinetic depth cues subserving depth perception would call attention to recent studies in monkeys, demonstrating the interrelation of kinetic and stereoscopic depth cues both on a behavioral and physiological level. Furthermore, it is argued that binocularity in birds has a clear function in stereopsis.