Estimating the relative order of speciation or coalescence events on a given phylogeny

The reconstruction of large phylogenetic trees from data that violates clocklike evolution (or as a supertree constructed from any m input trees) raises a difficult question for biologists - how can one assign relative dates to the vertices of the tree? In this paper we investigate this problem, assuming a uniform distribution on the order of the inner vertices of the tree (which includes, but is more general than, the popular Yule distribution on trees). We derive fast algorithms for computing the probability that (i) any given vertex in the tree was the j--th speciation event (for each j), and (ii) any one given vertex is earlier in the tree than a second given vertex. We show how the first algorithm can be used to calculate the expected length of any given interior edge in any given tree that has been generated under either a constant-rate speciation model, or the coalescent model

Normal stresses in semiflexible polymer hydrogels

Biopolymer gels such as fibrin and collagen networks are known to develop tensile axial stress when subject to torsion. This negative normal stress is opposite to the classical Poynting effect observed for most elastic solids including synthetic polymer gels, where torsion provokes a positive normal stress. As recently shown, this anomalous behavior in fibrin gels depends on the open, porous network structure of biopolymer gels, which facilitates interstitial fluid flow during shear and can be described by a phenomenological two-fluid model with viscous coupling between network and solvent. Here we extend this model and develop a microscopic model for the individual diagonal components of the stress tensor that determine the axial response of semi-flexible polymer hydrogels. This microscopic model predicts that the magnitude of these stress components depends inversely on the characteristic strain for the onset of nonlinear shear stress, which we confirm experimentally by shear rheometry on fibrin gels. Moreover, our model predicts a transient behavior of the normal stress, which is in excellent agreement with the full time-dependent normal stress we measure.Comment: 12 pages, 8 figure

Experimental phage therapy of burn wound infection : difficult first steps

Antibiotic resistance has become a major public health problem and the antibiotics pipeline is running dry. Bacteriophages (phages) may offer an ‘innovative’ means of infection treatment, which can be combined or alternated with antibiotic therapy and may enhance our abilities to treat bacterial infections successfully. Today, in the Queen Astrid Military Hospital, phage therapy is increasingly considered as part of a salvage therapy for patients in therapeutic dead end, particularly those with multidrug resistant infections. We describe the application of a well-defined and quality controlled phage cocktail, active against Pseudomonas aeruginosa and Staphylococcus aureus, on colonized burn wounds within a modest clinical trial (nine patients, 10 applications), which was approved by a leading Belgian Medical Ethical Committee. No adverse events, clinical abnormalities or changes in laboratory test results that could be related to the application of phages were observed. Unfortunately, this very prudent ‘clinical trial’ did not allow for an adequate evaluation of the efficacy of the phage cocktail. Nevertheless, this first ‘baby step’ revealed several pitfalls and lessons for future experimental phage therapy and helped overcome the psychological hurdles that existed to the use of viruses in the treatment of patients in our burn unit

Stability of bacteriophages in burn wound care products

Bacteriophages could be used along with burn wound care products to enhance antimicrobial pressure during treatment. However, some of the components of the topical antimicrobials that are traditionally used for the prevention and treatment of burn wound infection might affect the activity of phages. Therefore, it is imperative to determine the counteraction of therapeutic phage preparations by burn wound care products before application in patients. Five phages, representatives of two morphological families (Myoviridae and Podoviridae) and active against 3 common bacterial burn wound pathogens (Acinetobacter baumannii, Pseudomonas aeruginosa and Staphylococcus aureus) were tested against 13 different products commonly used in the treatment of burn wounds. The inactivation of the phages was quite variable for different phages and different products. Majority of the anti-infective products affected phage activity negatively either immediately or in the course of time, although impact was not always significant. Products with high acidity had the most adverse effect on phages. Our findings demonstrate that during combined treatment the choice of phages and wound care products must be carefully defined in advance

Introduction to fungal physiology

This chapter describes some basic aspects of fungal cell physiology, focusing primarily on nutrition, growth, metabolism in unicellular yeasts and filamentous fungi, and cell death. It considers the most common growth forms, the filamentous fungi and unicellular yeasts. Fungal growth involves transport and assimilation of nutrients, followed by their integration into cellular components, followed by biomass increase and eventual cell division or septation. The physiology of vegetative reproduction and its control in fungi has been most widely studied in two model eukaryotes, the budding yeast, Saccharomyces cerevisiae, and the fission yeast, Schizosaccharomyces pombe. An understanding of the death of fungal cells is important from a fundamental viewpoint because fungi, especially yeasts, represent valuable model systems for the study of cellular aging and apoptosis (programed cell death). Recycling and redeployment of cellular material also helps drive the apical growth of filamentous fungi and the mycelium explores and extends through the environment

Characterization of newly isolated lytic bacteriophages active against Acinetobacter baumannii

Based on genotyping and host range, two newly isolated lytic bacteriophages, myovirus vB_AbaM_Acibel004 and podovirus vB_AbaP_Acibel007, active against Acinetobacter baumannii clinical strains, were selected from a new phage library for further characterization. The complete genomes of the two phages were analyzed. Both phages are characterized by broad host range and essential features of potential therapeutic phages, such as short latent period (27 and 21 min, respectively), high burst size (125 and 145, respectively), stability of activity in liquid culture and low frequency of occurrence of phage-resistant mutant bacterial cells. Genomic analysis showed that while Acibel004 represents a novel bacteriophage with resemblance to some unclassified Pseudomonas aeruginosa phages, Acibel007 belongs to the well-characterized genus of the Phikmvlikevirus. The newly isolated phages can serve as potential candidates for phage cocktails to control A. baumannii infections

Some of the Other Works of the Torah: Boundaries and Inheritance as Legal Metaphors in the Hebrew Bible and Hellenistic Jewish Literature

Thesis advisor: David S. VanderhooftIn this dissertation, I explore the metaphorical value of law in the Hebrew Bible and Hellenistic Jewish literature. While the study of biblical law and Hellenistic Jewish halakah is well established, less attention has been paid to the intentional use of legal diction to create legal metaphors—metaphors that draw upon legal language for the sake of generating new ethical and theological insights. My argument is based upon Roger White’s theory of metaphor which states that a metaphor juxtaposes two otherwise unrelated vocabularies in order to produce new meaning. Thus, I draw upon comparative study of ancient Near Eastern law as a means of understanding the register of biblical Hebrew legal diction concerning land tenure and inheritance. With the legal background established, I investigate three sets of metaphors, one drawn from the prohibition against violating established property boundaries and two drawn from the legal domain of inheritance: the inheritance of wisdom and the inheritance of glory. These legal metaphors demonstrate the profitability of attending to legal diction. The boundary metaphor demonstrates that when attempting to describe the good or virtuous life, law served not only to provide a description of obligations, it also shaped the way in which early Jewish communities understood reality itself. The inheritance of wisdom metaphors demonstrate that sophisticated comparisons could be drawn between legal concepts and scribal learning, particularly when wisdom was thought of as a document. The inheritance of glory metaphors demonstrate the way in which semantic shifting impacts the meaning of a metaphor.Thesis (PhD) — Boston College, 2020.Submitted to: Boston College. Graduate School of Arts and Sciences.Discipline: Theology

Cost-Effectiveness of Interventions to Promote Fruit and Vegetable Consumption

Background: Fruits and vegetables are an essential part of the human diet, but many people do not consume the recommended serves to prevent cardiovascular disease and cancer. In this research, we evaluate the cost-effectiveness of interventions to promote fruit and vegetable consumption to determine which interventions are good value for money, and by how much current strategies can reduce the population disease burden

A natural orbital method for the electron momentum distribution in matter

A variational method for many electron system is applied to momentum distribution calculations. The method uses a generating two-electron geminal and the amplitudes of the occupancies of one particle natural orbitals as variational parameters. It introduces correlation effects beyond the free fermion nodal structure.Comment: 3 pages, Latex, revised paper with new reference