Note on recruitment as an ethical question: lessons from a project on asexuality

This short piece considers how participant recruitment can have ethical elements. With reference to a qualitative research project on asexuality we explore the challenges associated with recruiting from an emerging, and politically charged, identity group. In our attempt to broaden the representation of asexual stories we sought to recruit people who may not fully identify with the emerging term ‘asexual’ as a sexual orientation while also not equating this with a lifestyle choice of abstinence. This was attempted through crafting suitable recruitment materials via the use of the Mass Observation archive and expanded sampling criteria. Our efforts met with mixed success, on which we reflect. We conclude by suggesting how such ethical questions related to recruitment will remain ‘gaps’ in ethical regulation, calling for a greater reflexive approach from researchers about sampling criteria

Evolution: functional evolution of nuclear structure.

The evolution of the nucleus, the defining feature of eukaryotic cells, was long shrouded in speculation and mystery. There is now strong evidence that nuclear pore complexes (NPCs) and nuclear membranes coevolved with the endomembrane system, and that the last eukaryotic common ancestor (LECA) had fully functional NPCs. Recent studies have identified many components of the nuclear envelope in living Opisthokonts, the eukaryotic supergroup that includes fungi and metazoan animals. These components include diverse chromatin-binding membrane proteins, and membrane proteins with adhesive lumenal domains that may have contributed to the evolution of nuclear membrane architecture. Further discoveries about the nucleoskeleton suggest that the evolution of nuclear structure was tightly coupled to genome partitioning during mitosis

Eight unique basal bodies in the multi-flagellated diplomonad Giardia lamblia.

Giardia lamblia is an intestinal parasitic protist that causes significant acute and chronic diarrheal disease worldwide. Giardia belongs to the diplomonads, a group of protists in the supergroup Excavata. Diplomonads are characterized by eight motile flagella organized into four bilaterally symmetric pairs. Each of the eight Giardia axonemes has a long cytoplasmic region that extends from the centrally located basal body before exiting the cell body as a membrane-bound flagellum. Each basal body is thus unique in its cytological position and its association with different cytoskeletal features, including the ventral disc, axonemes, and extra-axonemal structures. Inheritance of these unique and complex cytoskeletal elements is maintained through basal body migration, duplication, maturation, and their subsequent association with specific spindle poles during cell division. Due to the complex composition and inheritance of specific basal bodies and their associated structures, Giardia may require novel basal body-associated proteins. Thus, protists such as Giardia may represent an undiscovered source of novel basal body-associated proteins. The development of new tools that make Giardia genetically tractable will enable the composition, structure, and function of the eight basal bodies to be more thoroughly explored

State-space model identification and feedback control of unsteady aerodynamic forces

Unsteady aerodynamic models are necessary to accurately simulate forces and develop feedback controllers for wings in agile motion; however, these models are often high dimensional or incompatible with modern control techniques. Recently, reduced-order unsteady aerodynamic models have been developed for a pitching and plunging airfoil by linearizing the discretized Navier-Stokes equation with lift-force output. In this work, we extend these reduced-order models to include multiple inputs (pitch, plunge, and surge) and explicit parameterization by the pitch-axis location, inspired by Theodorsen's model. Next, we investigate the na\"{\i}ve application of system identification techniques to input--output data and the resulting pitfalls, such as unstable or inaccurate models. Finally, robust feedback controllers are constructed based on these low-dimensional state-space models for simulations of a rigid flat plate at Reynolds number 100. Various controllers are implemented for models linearized at base angles of attack $\alpha_0=0^\circ, \alpha_0=10^\circ$, and $\alpha_0=20^\circ$. The resulting control laws are able to track an aggressive reference lift trajectory while attenuating sensor noise and compensating for strong nonlinearities.Comment: 20 pages, 13 figure

Calculating NMR parameters in aluminophosphates : evaluation of dispersion correction schemes

Periodic density functional theory (DFT) calculations have recently emerged as a popular tool for assigning solid-state nuclear magnetic resonance (NMR) spectra. However, in order for the calculations to yield accurate results, accurate structural models are also required. In many cases the structural model (often derived from crystallographic diffraction) must be optimised (i.e., to an energy minimum) using DFT prior to the calculation of NMR parameters. However, DFT does not reproduce weak long-range "dispersion'' interactions well, and optimisation using some functionals can expand the crystallographic unit cell, particularly when dispersion interactions are important in defining the structure. Recently, dispersion-corrected DFT (DFT-D) has been extended to periodic calculations, to compensate for these missing interactions. Here, we investigate whether dispersion corrections are important for aluminophosphate zeolites (AlPOs) by comparing the structures optimised by DFT and DFT-D (using the PBE functional). For as-made AlPOs (containing cationic structure-directing agents (SDAs) and framework-bound anions) dispersion interactions appear to be important, with significant changes between the DFT and DFT-D unit cells. However, for calcined AlPOs, where the SDA-anion pairs are removed, dispersion interactions appear much less important, and the DFT and DFT-D unit cells are similar. We show that, while the different optimisation strategies yield similar calculated NMR parameters (providing that the atomic positions are optimised), the DFT-D optimisations provide structures in better agreement with the experimental diffraction measurements. Therefore, it appears that DFT-D calculations can, and should, be used for the optimisation of calcined and as-made AlPOs, in order to provide the closest agreement with all experimental measurements.PostprintPeer reviewe

On non-normality and classification of amplification mechanisms in stability and resolvent analysis

We seek to quantify non-normality of the most amplified resolvent modes and predict their features based on the characteristics of the base or mean velocity profile. A 2-by-2 model linear Navier-Stokes (LNS) operator illustrates how non-normality from mean shear distributes perturbation energy in different velocity components of the forcing and response modes. The inverse of their inner product, which is unity for a purely normal mechanism, is proposed as a measure to quantify non-normality. In flows where there is downstream spatial dependence of the base/mean, mean flow advection separates the spatial support of forcing and response modes which impacts the inner product. Success of mean stability analysis depends on the normality of amplification. If the amplification is normal, the resolvent operator written in its dyadic representation reveals that the adjoint and forward stability modes are proportional to the forcing and response resolvent modes. If the amplification is non-normal, then resolvent analysis is required to understand the origin of observed flow structures. Eigenspectra and pseudospectra are used to characterize these phenomena. Two test cases are studied: low Reynolds number cylinder flow and turbulent channel flow. The first deals mainly with normal mechanisms and quantification of non-normality using the inverse inner product of the leading forcing and response modes agrees well with the product of the resolvent norm and distance between the imaginary axis and least stable eigenvalue. In turbulent channel flow, structures result from both normal and non-normal mechanisms. Mean shear is exploited most efficiently by stationary disturbances while bounds on the pseudospectra illustrate how non-normality is responsible for the most amplified disturbances at spatial wavenumbers and temporal frequencies corresponding to well-known turbulent structures

Characterizing and correcting for the effect of sensor noise in the dynamic mode decomposition

Dynamic mode decomposition (DMD) provides a practical means of extracting insightful dynamical information from fluids datasets. Like any data processing technique, DMD's usefulness is limited by its ability to extract real and accurate dynamical features from noise-corrupted data. Here we show analytically that DMD is biased to sensor noise, and quantify how this bias depends on the size and noise level of the data. We present three modifications to DMD that can be used to remove this bias: (i) a direct correction of the identified bias using known noise properties, (ii) combining the results of performing DMD forwards and backwards in time, and (iii) a total least-squares-inspired algorithm. We discuss the relative merits of each algorithm, and demonstrate the performance of these modifications on a range of synthetic, numerical, and experimental datasets. We further compare our modified DMD algorithms with other variants proposed in recent literature