Automated identification of flagella from videomicroscopy via the medial axis transform

Ubiquitous in eukaryotic organisms, the flagellum is a well-studied organelle that is well-known to be responsible for motility in a variety of organisms. Commonly necessitated in their study is the capability to image and subsequently track the movement of one or more flagella using videomicroscopy, requiring digital isolation and location of the flagellum within a sequence of frames. Such a process in general currently requires some researcher input, providing some manual estimate or reliance on an experiment-specific heuristic to correctly identify and track the motion of a flagellum. Here we present a fully-automated method of flagellum identification from videomicroscopy based on the fact that the flagella are of approximately constant width when viewed by microscopy. We demonstrate the effectiveness of the algorithm by application to captured videomicroscopy of Leishmania mexicana, a parasitic monoflagellate of the family Trypanosomatidae. ImageJ Macros for flagellar identification are provided, and high accuracy and remarkable throughput are achieved via this unsupervised method, obtaining results comparable in quality to previous studies of closely-related species but achieved without the need for precursory measurements or the development of a specialised heuristic, enabling in general the automated generation of digitised kinematic descriptions of flagellar beating from videomicroscopy.Comment: 10 pages, 5 figures. Author accepted manuscript. Supplementary Material available at https://doi.org/10.1038/s41598-019-41459-

Boundary behaviours of Leishmania mexicana: a hydrodynamic simulation study

It is well established that the parasites of the genus Leishmania exhibit complex surface interactions with the sandfly vector midgut epithelium, but no prior study has considered the details of their hydrodynamics. Here, the boundary behaviours of motile Leishmania mexicana promastigotes are explored in a computational study using the boundary element method, with a model flagellar beating pattern that has been identified from digital videomicroscopy. In particular a simple flagellar kinematics is observed and quantified using image processing and mode identification techniques, suggesting a simple mechanical driver for the Leishmania beat. Phase plane analysis and long-time simulation of a range of Leishmania swimming scenarios demonstrate an absence of stable boundary motility for an idealised model promastigote near passive or repulsive surfaces, with behaviours ranging from boundary capture to deflection into the bulk. Indeed, the inclusion of a repulsive surface force results in the deflection of all surface-bound promastigotes, suggesting that the documented surface detachment of infective metacyclic promastigotes may be the result of morphological adaptation and simple hydrodynamics. Further, simulation elucidates a remarkable morphology-dependent hydrodynamic mechanism of boundary approach, hypothesised to be the cause of the well-established phenomenon of tip-first epithelial attachment of Leishmania promastigotes to the sandfly vector midgut.Comment: 12 pages, 9 figures. Supplementary Material available upon reques

Facilitators and barriers to the successful implementation of pediatric antibacterial drug trials: Findings from CTTI's survey of investigators.

An urgent need exists to develop new antibacterial drugs for children. We conducted research with investigators of pediatric antibacterial drug trials to identify facilitators and barriers in the conduct of these trials. Seventy-three investigators completed an online survey assessing the importance of 15 facilitators (grouped in 5 topical categories) and the severity of 36 barriers (grouped in 6 topical categories) to implementing pediatric antibacterial drug trials. Analysis focused on the identification of key factors that facilitate the successful implementation of pediatric antibacterial drug trials and the key barriers to implementation. Almost all investigators identified two factors as very important facilitators: having site personnel for enrollment and having adequate funding. Other top factors were related to staffing. Among the barriers, factors related to parent concerns and consent were prominent, particularly obtaining parental consent when there was disagreement between parents, concerns about the number of blood draws, and concerns about the number of invasive procedures. Having overly narrow eligibility criteria was also identified as a major barrier. The survey findings suggest three areas in which to focus efforts to help facilitate ongoing drug development: (1) improving engagement with parents of children who may be eligible to enroll in a pediatric antibacterial drug trial, (2) broadening inclusion criteria to allow more participants to enroll, and (3) ensuring adequate staffing and establishing sustainable financial strategies, such as funding pediatric trial networks. The pediatric antibacterial drug trials enterprise is likely to benefit from focused efforts by all stakeholders to remove barriers and enhance facilitation

Directions of zero thermal expansion in anisotropic oxides

Figure 13. – Quadric surface visualizing the coefficients of thermal expansion of HfTiO4 at room temperature. Blue is positive, red is negative and yellow represents directions of zero thermal expansion. Oxide materials often have anisotropic crystal structures, which can result in direction-dependent material properties. While they typically have positive coefficients of thermal expansion, it has been observed that some oxide materials can have directions of negative thermal expansion over certain temperature ranges. Such materials, having both positive and negative coefficients of thermal expansion, must also have particular directions in which the thermal expansion is zero. Using the Quadrupole Lamp Furnace (QLF) developed in the Kriven group at the University of Illinois at Urbana Champaign, high-temperature in-situ x-ray diffraction has been performed at the National Synchrotron Light Source II (NSLS II) X-ray powder diffraction beamline (XPD – 28-ID) to track directions of zero thermal expansion in orthorhombic HfTiO4. These results have important implications for the design of composites for high-temperature applications. Please click Additional Files below to see the full abstract

Candidate genes mediating magnetoreception in rainbow trout ( Oncorhynchus mykiss )

Diverse animals use Earth's magnetic field in orientation and navigation, but little is known about the molecular mechanisms that underlie magnetoreception. Recent studies have focused on two possibilities: (i) magnetite-based receptors; and (ii) biochemical reactions involving radical pairs. We used RNA sequencing to examine gene expression in the brain of rainbow trout ( Oncorhynchus mykiss ) after exposure to a magnetic pulse known to disrupt magnetic orientation behaviour. We identified 181 differentially expressed genes, including increased expression of six copies of the frim gene, which encodes a subunit of the universal iron-binding and trafficking protein ferritin. Functions linked to the oxidative effects of free iron (e.g. oxidoreductase activity, transition metal ion binding, mitochondrial oxidative phosphorylation) were also affected. These results are consistent with the hypothesis that a magnetic pulse alters or damages magnetite-based receptors and/or other iron-containing structures, which are subsequently repaired or replaced through processes involving ferritin. Additionally, some genes that function in the development and repair of photoreceptive structures (e.g. crggm3 , purp , prl , gcip , crabp1 and pax6 ) were also differentially expressed, raising the possibility that a magnetic pulse might affect structures and processes unrelated to magnetite-based magnetoreceptors

Leeches (Annelida: Hirudinida) of Northern Arkansas

Twenty-one lotic and lentic environments throughout central and northern Arkansas were surveyed for the presence of leeches during June 2004 and April, July - October 2005. Fourteen species of leeches {Helobdella elongata, Helobdella papillata, Helobdella stagnalis, Placobdella cryptobranchii, Placobdella multilineata, Placobdella ornata, Placobdella papillifera, Placobdella parasitica, Placobdella phaler a, Placobdella picta, Haemopis marmorata, Erpobdella fervida, Erpobdella microstoma, and Erpobdella punctata) representing 3 families were collected. Five species (H. elongata, P. cryptobranchii, P. multilineata, H. marmorata, and E. fervida) are reported from Arkansas for the first time. The natural history of the 22 species of leeches now known from Arkansas is reviewed

Perceived barriers to pediatrician and family practitioner participation in pediatric clinical trials: Findings from the Clinical Trials Transformation Initiative.

Despite legislation to stimulate pediatric drug development through clinical trials, enrolling children in trials continues to be challenging. Non-investigator (those who have never served as a clinical trial investigator) providers are essential to recruitment of pediatric patients, but little is known regarding the specific barriers that limit pediatric providers from participating in and referring their patients to clinical trials. We conducted an online survey of pediatric providers from a wide variety of practice types across the United States to evaluate their attitudes and awareness of pediatric clinical trials. Using a 4-point Likert scale, providers described their perception of potential barriers to their practice serving as a site for pediatric clinical trials. Of the 136 providers surveyed, 52/136 (38%) had previously referred a pediatric patient to a trial, and only 17/136 (12%) had ever been an investigator for a pediatric trial. Lack of awareness of existing pediatric trials was a major barrier to patient referral by providers, in addition to consideration of trial risks, distance to the site, and time needed to discuss trial participation with parents. Overall, providers perceived greater challenges related to parental concerns and parent or child logistical barriers than study implementation and ethics or regulatory barriers as barriers to their practice serving as a trial site. Providers who had previously been an investigator for a pediatric trial were less likely to be concerned with potential barriers than non-investigators. Understanding the barriers that limit pediatric providers from collaboration or inhibit their participation is key to designing effective interventions to optimize pediatric trial participation

Surfing, sweeping, and assembly of particles by a moving liquid crystal phase boundary

Non-equilibrium transport of particles embedded in a liquid crystal host can, by cooling through a phase transition, be exploited to create a remarkable variety of structures including shells, foams, and gels. Due to the complexity of the multicomponent system and protocol-dependent experimental results, the physical mechanisms behind structure selection remain only partially understood. Here we formulate a new model coupling LC physics to a Fokker-Planck equation as is commonly used in studies of transport. The resulting model allows us to draw an analogy between the LC-nanocomposite system and chemotaxis, enriching the space of possible target structures that could be produced. We study the model in one dimension both analytically and numerically to identify different parameter regimes where soliton-like pulses of particles ``surf'' the phase boundary or where the interface ``sweeps'' particles from one domain to another. We also consider an extended model that includes agglomeration of the particles and observe formation of periodic structures as a prototypical example of hierarchical self assembly. Results are compared with experimental observations of transport by isolated phase boundaries.Comment: 11 pages, 6 figure