Problems with supertrees based on the subtree prune‐and‐regraft distance,with comments on majority rule supertrees

This paper examines a recent proposal to calculate supertrees by minimizing the sum of subtree prune‐and‐regraft distances to the input trees. The supertrees thus calculated may display groups present in a minority of the input trees but contradicted by the majority, or groups that are not supported by any input tree or combination of input trees. The proponents of the method themselves stated that these are serious problems of “matrix representation with parsimony”, but they can in fact occur in their own method. The majority rule supertrees, being explicitly clade‐based, cannot have these problems, and seem much more suited to retrieving common clades from a set of trees with different taxon sets. However, it is dubious that so‐called majority rule supertrees can always be interpreted as displaying those clades present (or compatible with) with a majority of the trees. The majority rule consensus is always a median tree, in terms of the Robinson–Foulds distances (i.e. it minimizes the sum of Robinson–Foulds distances to the input trees). In contrast, majority rule supertrees may not be median—different, contradictory trees may minimize Robinson–Foulds distances, while their strict consensus does not. If being “majority” results from being median in Robinson–Foulds distances, this means that in the supertree setting a “majority” is ambiguously defined, sometimes achievable only by mutually contradictory trees.     

Enhancement of the Amazonian Açaí Waste Fibers through Variations of Alkali Pretreatment Parameters

The açaí fruit depulping produces large amounts of long lignocellulosic fiber bundles that are disposed in the environment. Chemical pretreatments may improve açaí fibers favoring their usage in advanced materials. This work aimed to define optimal alkali reaction parameters to improve the properties of açaí fibers. Two NaOH concentrations (5 % and 10 %) and two reaction temperatures (80 °C and 100 °C) were tested. The raw and treated fibers were analyzed by scanning electron microscopy, Fourier transformed infrared spectroscopy, X‐ray diffraction, and thermal analyses. All the alkali pretreatments separated fibers from the bundles, unblocked pit channels by removing silicon structures, exposed the inner lignin, partially removed non‐cellulosic compounds, and raised the cellulose crystalline index. The highest temperature and NaOH content resulted in better cleaning and isolation of the fibers, while milder conditions better preserved the cellulose crystalline structure and thermal stability.     

Biosynthesis and bioactivity of Cynara cardunculus L. guaianolides and hydroxycinnamic acids: a genomic,biochemical and health-promoting perspective

Phytochemistry Reviews - Cynara cardunculus health benefits have aroused much interest, leading to the discovery of valuable bioactive compounds with a crucial role in plant defence. Guaianolides...     

Impact of genetic variations in ADORA2A gene on depression and symptoms: a cross-sectional population-based study

Purinergic Signalling - Genetic variants involved in adenosine metabolism and its receptors were associated with increased risk for psychiatric disorders, including anxiety, depression, and...     

A bootstrap-aggregated hybrid semi-parametric modeling framework for bioprocess development

Bioprocess and Biosystems Engineering - Hybrid semi-parametric modeling, combining mechanistic and machine-learning methods, has proven to be a powerful method for process development. This paper...     

Benzyl propionate synthesis by fed-batch esterification using commercial immobilized and lyophilized Cal B lipase

Bioprocess and Biosystems Engineering - In this work, a fed-batch approach was adopted to overcome propionic acid lipase inactivation effects in the benzyl propionate direct esterification mediated...     

Synthesis of a green polyurethane foam from a biopolyol obtained by enzymatic glycerolysis and its use for immobilization of lipase NS-40116

The use of green sources for materials synthesis has gained popularity in recent years. This work investigated the immobilization of lipase NS-40116 (Thermomyces lanuginosus lipase) in polyurethane foam (PUF) using a biopolyol obtained through the enzymatic glycerolysis between castor oil and glycerol, catalyzed by the commercial lipase Novozym 435 for the PUF formation. The reaction was performed to obtain biopolyol resulting in the conversion of 64% in mono- and diacylglycerol, promoting the efficient use of the reaction product as biopolyol to obtain polyurethane foam. The enzymatic derivative with immobilized lipase NS-40116 presented apparent density of 0.19 ± 0.03 g/cm³ and an immobilization yield was 94 ± 4%. Free and immobilized lipase NS-40116 were characterized in different solvents (methanol, ethanol, and propanol), temperatures (20, 40, 60 and 80 °C), pH (3, 5, 7, 9 and 11) and presence of ions Na⁺, Mg⁺⁺, and Ca⁺⁺. The support provided higher stability to the enzyme, mainly when subjected to acid pH (free lipase lost 80% of relative activity after 360 h of contact, when the enzymatic derivative lost around 22%) and high-temperature free lipase lost 50% of relative activity, while the immobilized remained 95%. The enzymatic derivative was also used for esterification reactions and conversions around 66% in fatty acid methyl esters, using abdominal chicken fat as feedstock, were obtained in the first use, maintaining this high conversion until the fourth reuse, proving that the support obtained using environmentally friendly techniques is applicable.

     

Ethical issues associated with HIV phylogenetics in HIV transmission dynamics research: A review of the literature using the Emanuel Framework

The reduced costs of DNA sequencing and the use of such data for HIV‐1 clinical management and phylogenetic analysis have led to a massive increase of HIV‐1 sequences in the last few years. Phylogenetic analysis has shed light on the origin, spread and characteristics of HIV‐1 epidemics and outbreaks. Phylogenetic analysis is now also being used to advance our knowledge of the drivers of HIV‐1 transmission in order to design effective interventions. However, HIV phylogenetic analysis presents unique ethical challenges, which have not been fully explored. This review presents an analysis of what appear to be key ethical issues in HIV phylogenetics in the hope of stimulating further conceptual and empirical work in this rapidly emerging area. We structure the review using the Emanuel Framework, a systematic, holistic framework, which has been adapted for use in developing countries, which bear the brunt of the HIV‐1 pandemic.     

Diet composition of expanding breeding populations of the Magellanic Penguin

The Magellanic Penguin (Spheniscus magellanicus) is the most abundant and widely distributed seabird breeding on the Patagonian Coast of Argentina. We combined conventional stomach content and stable isotope analysis to assess Magellanic Penguin diet during the chick rearing stage at the two northernmost colonies in an area subject to fisheries. In 2011 and 2013, Thornfish (Bovichtus argentinus) was the main prey by mass at Complejo Islote Lobos (63.0% and 32.3%, respectively) and Argentine Anchovy (Engraulis anchoita) at Estancia San Lorenzo (85.2 and 63.3%, respectively). Magellanic Penguins from both colonies showed low isotopic niche overlap in 2011 (36%) and no overlap in 2013, suggesting a different use of prey species and/or foraging areas. Stable isotope mixing models showed that Argentine Anchovy (52.8%) and Thornfish (65.9%) were the main prey at Complejo Islote Lobos in 2011 and 2013, respectively, while Patagonian Redfish (Sebastes oculatus) (46.4%) and Squat Lobster (Munida gregaria) (50%) were the main prey at Estancia San Lorenzo in 2011 and 2013, respectively. Results show that in addition to Argentine Anchovy, previously recognized as main prey for breeding Magellanic Penguins in northern Patagonia, other juvenile or small sized fish are important diet items. Diet results suggest different scenarios of food conditions for each colony, despite the relative short distance between breeding locations. The low contribution of Argentine Hake (Merluccius hubbsi) and Argentine Shortfin Squid (Illex argentinus) suggests a low trophic overlap with commercial fisheries. The information provided is key to understand changes in the marine ecosystem and potential penguin-fishery interactions.