Twirling Elastica: Kinks, Viscous Drag, and Torsional Stress

Biological filaments such as DNA or bacterial flagella are typically curved in their natural states. To elucidate the interplay of viscous drag, twisting, and bending in the overdamped dynamics of such filaments, we compute the steady-state torsional stress and shape of a rotating rod with a kink. Drag deforms the rod, ultimately extending or folding it depending on the kink angle. For certain kink angles and kink locations, both states are possible at high rotation rates. The agreement between our macroscopic experiments and the theory is good, with no adjustable parameters.Comment: 4 pages, 4 figure

Point-of-Care Diagnostics for Infection and Antimicrobial Resistance in Sub-Saharan Africa - A Narrative Review.

INTRODUCTION Sub-Saharan African (SSA) countries are severely impacted by antimicrobial resistance (AMR). Due to gaps in access to diagnostics in SSA the true extent of AMR remains unknown. This diagnostic gap affects patient management and leads to significant antimicrobial overuse. This review explores how point-of-care (POC) testing for pathogen identification and AMR may be used to close the diagnostic gap in SSA countries. METHODS A narrative review exploring current clinical practice and novel developments in the field of point-of-care (POC) testing for infectious diseases and AMR. FINDINGS POC assays for identification of various pathogens have been successfully rolled out in SSA countries. While implementation studies have mostly highlighted impressive test performance of POC assays, there is limited data on effect of implementation on clinical outcomes and cost-effectiveness. We did not encounter local studies of host-directed POC assays relevant to AMR. Novel POC assays using real-time PCR, isothermal amplification, microfluidics and other technologies are in various stages of development. DISCUSSION Available literature shows that POC testing for AMR applications is implementable in SSA and holds the potential to reduce the diagnostic gap. Implementation will require effective regulatory pathways, incorporation of POC testing in clinical and laboratory guidelines, and adequate value capture in existing health financing models

The Viscous Nonlinear Dynamics of Twist and Writhe

Exploiting the "natural" frame of space curves, we formulate an intrinsic dynamics of twisted elastic filaments in viscous fluids. A pair of coupled nonlinear equations describing the temporal evolution of the filament's complex curvature and twist density embodies the dynamic interplay of twist and writhe. These are used to illustrate a novel nonlinear phenomenon: ``geometric untwisting" of open filaments, whereby twisting strains relax through a transient writhing instability without performing axial rotation. This may explain certain experimentally observed motions of fibers of the bacterium B. subtilis [N.H. Mendelson, et al., J. Bacteriol. 177, 7060 (1995)].Comment: 9 pages, 4 figure

Labels for non-individuals

Quasi-set theory is a first order theory without identity, which allows us to cope with non-individuals in a sense. A weaker equivalence relation called ``indistinguishability'' is an extension of identity in the sense that if $x$ is identical to $y$ then $x$ and $y$ are indistinguishable, although the reciprocal is not always valid. The interesting point is that quasi-set theory provides us a useful mathematical background for dealing with collections of indistinguishable elementary quantum particles. In the present paper, however, we show that even in quasi-set theory it is possible to label objects that are considered as non-individuals. We intend to prove that individuality has nothing to do with any labelling process at all, as suggested by some authors. We discuss the physical interpretation of our results.Comment: 11 pages, no figure

A Paraconsistent Higher Order Logic

Classical logic predicts that everything (thus nothing useful at all) follows from inconsistency. A paraconsistent logic is a logic where an inconsistency does not lead to such an explosion, and since in practice consistency is difficult to achieve there are many potential applications of paraconsistent logics in knowledge-based systems, logical semantics of natural language, etc. Higher order logics have the advantages of being expressive and with several automated theorem provers available. Also the type system can be helpful. We present a concise description of a paraconsistent higher order logic with countable infinite indeterminacy, where each basic formula can get its own indeterminate truth value (or as we prefer: truth code). The meaning of the logical operators is new and rather different from traditional many-valued logics as well as from logics based on bilattices. The adequacy of the logic is examined by a case study in the domain of medicine. Thus we try to build a bridge between the HOL and MVL communities. A sequent calculus is proposed based on recent work by Muskens.Comment: Originally in the proceedings of PCL 2002, editors Hendrik Decker, Joergen Villadsen, Toshiharu Waragai (http://floc02.diku.dk/PCL/). Correcte

Semiflexible chains in confined spaces

We develop an analytical method for studying the properties of a noninteracting wormlike chain (WLC) in confined geometries. The mean-field-like theory replaces the rigid constraints of confinement with average constraints, thus allowing us to develop a tractable method for treating a WLC wrapped on the surface of a sphere, and fully encapsulated within it. The efficacy of the theory is established by reproducing the exact correlation functions for a WLC confined to the surface of a sphere. In addition, the coefficients in the free energy are exactly calculated. We also describe the behavior of a surface-confined chain under external tension that is relevant for single molecule experiments on histone-DNA complexes. The force-extension curves display spatial oscillations, and the extension of the chain, whose maximum value is bounded by the sphere diameter, scales as f−1 at large forces, in contrast to the unconfined chain that approaches the contour length as f−1∕2. A WLC encapsulated in a sphere, that is relevant for the study of the viral encapsulation of DNA, can also be treated using the mean-field approach. The predictions of the theory for various correlation functions are in excellent agreement with Langevin simulations. We find that strongly confined chains are highly structured by examining the correlations using a local winding axis. The predicted pressure of the system is in excellent agreement with simulations but, as is known, is significantly lower than the pressures seen for DNA packaged in viral capsids

Cognitive Phenotypes and the Evolution of Animal Decisions

Despite the clear fitness consequences of animal decisions, the science of animal decision making in evolutionary biology is underdeveloped compared with decision science in human psychology. Specifically, the field lacks a conceptual framework that defines and describes the relevant components of a decision, leading to imprecise language and concepts. The ‘judgment and decision-making’ (JDM) framework in human psychology is a powerful tool for framing and understanding human decisions, and we apply it here to components of animal decisions, which we refer to as ‘cognitive phenotypes’. We distinguish multiple cognitive phenotypes in the context of a JDM framework and highlight empirical approaches to characterize them as evolvable traits

Cognitive Phenotypes and the Evolution of Animal Decisions

Despite the clear fitness consequences of animal decisions, the science of animal decision making in evolutionary biology is underdeveloped compared with decision science in human psychology. Specifically, the field lacks a conceptual framework that defines and describes the relevant components of a decision, leading to imprecise language and concepts. The ‘judgment and decision-making’ (JDM) framework in human psychology is a powerful tool for framing and understanding human decisions, and we apply it here to components of animal decisions, which we refer to as ‘cognitive phenotypes’. We distinguish multiple cognitive phenotypes in the context of a JDM framework and highlight empirical approaches to characterize them as evolvable traits