Nanoscale electrical conductivity imaging using a nitrogen-vacancy center in diamond

The electrical conductivity of a material can feature subtle, nontrivial, and spatially-varying signatures with critical insight into the material's underlying physics. Here we demonstrate a conductivity imaging technique based on the atom-sized nitrogen-vacancy (NV) defect in diamond that offers local, quantitative, and noninvasive conductivity imaging with nanoscale spatial resolution. We monitor the spin relaxation rate of a single NV center in a scanning probe geometry to quantitatively image the magnetic fluctuations produced by thermal electron motion in nanopatterned metallic conductors. We achieve 40-nm scale spatial resolution of the conductivity and realize a 25-fold increase in imaging speed by implementing spin-to-charge conversion readout of a shallow NV center. NV-based conductivity imaging can probe condensed-matter systems in a new regime, and as a model example, we project readily achievable imaging of nanoscale phase separation in complex oxides.Comment: Supplementary information at en

Applicability of frozen-viscosity models of unsteady wall shear stress

The validity of assumed frozen-viscosity conditions underpinning an important class of theoretical models of unsteady wall shear stress in transient flows in pipes and channels is assessed using detailed computational fluid dynamics (CFD) simulations. The need for approximate one-dimensional ð1DÞfx; tg models of the wall stress is unavoidable in analyses of transient flows in extensive pipe networks because it would be economically impracticable to use higher order methods of analysis. However, the bases of the various models have never been established rigorously. It is shown herein that a commonly used approach developed by the first authors is flawed in the case of smoothwall flows although it is more plausible for rough-wall flows. The assessment process is undertaken for a particular, but important, unsteady flow case, namely, a uniform acceleration from an initially steady turbulent flow. First, detailed predictions from a validated CFD method are used to derive baseline solutions with which predictions based on approximate models can be compared. Then, alternative solutions are obtained using various prescribed frozen-viscosity distributions. Differences between these solutions and the baseline solutions are used to determine which frozen-viscosity distributions are the most promising starting points for developing 1Dfx; tg models of unsteady components of wall shear stress. It is shown that no frozen-viscosity distribution performs well for large times after the commencement of an acceleration. However, even the simplest approximation (laminar) performs well for short durations—which is when the greatest amplitudes of the unsteady components occu

Unsteady skin friction experimentation in a large diameter pipe

Experimental data for the validation of theoretical models of unsteady skin friction are limited and are available only for a few low Reynolds number flow cases. There is a strong need for detailed measurements in flows at high Reynolds numbers. In addition, there is a need for a wider range of well-controlled acceleration/deceleration rates and detailed visualization of flow structure and profiles. To address these needs, a large-scale pipeline apparatus at Deltares, Delft, The Netherlands, has been used for unsteady skin friction experiments including acceleration, deceleration and acoustic resonance tests. The apparatus consists of a constant head tank, a horizontal 200 mm diameter pipe of changeable length (44 to 49 metres) and a control valve at the downstream end. In addition to standard instrumentation, two distinctive instruments have been used: hot-film wall shear stress sensors ("direct" measurement of wall shear stress) and a PIV set-up for measurement of unsteady flow profiles. This paper describes the test rig, the instrumentation layout and the test programme. Finally, some initial test results are presented and discussed

A comparative study of turbulence models in a transient channel flow

Open Access funded by Engineering and Physical Sciences Research Council Under a Creative Commons license The authors would like to acknowledge the financial support provided by the Engineering and Physical Sciences Research Council (EPSRC) through the Grant No. EP/G068925/1.Peer reviewedPublisher PD

Genomic and epidemiological analysis of SARS-CoV-2 viruses in Sri Lanka

Background: In order to understand the molecular epidemiology of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) in Sri Lanka, since March 2020, we carried out genomic sequencing overlaid on available epidemiological data until April 2021. Methods: Whole genome sequencing was carried out on diagnostic sputum or nasopharyngeal swabs from 373 patients with COVID-19. Molecular clock phylogenetic analysis was undertaken to further explore dominant lineages. Results: The B.1.411 lineage was most prevalent, which was established in Sri Lanka and caused outbreaks throughout the country until March 2021. The estimated time of the most recent common ancestor (tMRCA) of this lineage was June 1, 2020 (with 95% lower and upper bounds March 30 to July 27) suggesting cryptic transmission may have occurred, prior to a large epidemic starting in October 2020. Returning travellers were identified with infections caused by lineage B.1.258, as well as the more transmissible B.1.1.7 lineage, which has replaced B.1.411 to fuel the ongoing large outbreak in the country. Conclusions: The large outbreak that started in early October, is due to spread of a single virus lineage, B.1.411 until the end of March 2021, when B.1.1.7 emerged and became the dominant lineage

Comparing De Novo Genome Assembly: The Long and Short of It

Recent advances in DNA sequencing technology and their focal role in Genome Wide Association Studies (GWAS) have rekindled a growing interest in the whole-genome sequence assembly (WGSA) problem, thereby, inundating the field with a plethora of new formalizations, algorithms, heuristics and implementations. And yet, scant attention has been paid to comparative assessments of these assemblers' quality and accuracy. No commonly accepted and standardized method for comparison exists yet. Even worse, widely used metrics to compare the assembled sequences emphasize only size, poorly capturing the contig quality and accuracy. This paper addresses these concerns: it highlights common anomalies in assembly accuracy through a rigorous study of several assemblers, compared under both standard metrics (N50, coverage, contig sizes, etc.) as well as a more comprehensive metric (Feature-Response Curves, FRC) that is introduced here; FRC transparently captures the trade-offs between contigs' quality against their sizes. For this purpose, most of the publicly available major sequence assemblers – both for low-coverage long (Sanger) and high-coverage short (Illumina) reads technologies – are compared. These assemblers are applied to microbial (Escherichia coli, Brucella, Wolbachia, Staphylococcus, Helicobacter) and partial human genome sequences (Chr. Y), using sequence reads of various read-lengths, coverages, accuracies, and with and without mate-pairs. It is hoped that, based on these evaluations, computational biologists will identify innovative sequence assembly paradigms, bioinformaticists will determine promising approaches for developing “next-generation” assemblers, and biotechnologists will formulate more meaningful design desiderata for sequencing technology platforms. A new software tool for computing the FRC metric has been developed and is available through the AMOS open-source consortium

Dynamics of notch pathway expression during mouse testis post-natal development and along the spermatogenic cycle

Articles in International JournalsThe transcription and expression patterns of Notch pathway components (Notch 1–3, Delta1 and 4, Jagged1) and effectors (Hes1, Hes2, Hes5 and Nrarp) were evaluated (through RT-PCR and IHC) in the mouse testis at key moments of post-natal development, and along the adult spermatogenic cycle. Notch pathway components and effectors are transcribed in the testis and expressed in germ, Sertoli and Leydig cells, and each Notch component shows a specific cell-type and timewindow expression pattern. This expression at key testis developmental events prompt for a role of Notch signaling in prepubertal spermatogonia quiescence, onset of spermatogenesis, and regulation of the spermatogenic cycle

Phenotyping male infertility in the mouse: how to get the most out of a ‘non-performer’

BACKGROUND: Functional male gametes are produced through complex processes that take place within the testis, epididymis and female reproductive tract. A breakdown at any of these phases can result in male infertility. The production of mutant mouse models often yields an unexpected male infertility phenotype. It is with this in mind that the current review has been written. The review aims to act as a guide to the 'non-reproductive biologist' to facilitate a systematic analysis of sterile or subfertile mice and to assist in extracting the maximum amount of information from each model. METHODS: This is a review of the original literature on defects in the processes that take a mouse spermatogonial stem cell through to a fully functional spermatozoon, which result in male infertility. Based on literature searches and personal experience, we have outlined a step-by-step strategy for the analysis of an infertile male mouse line. RESULTS: A wide range of methods can be used to define the phenotype of an infertile male mouse. These methods range from histological methods such as electron microscopy and immunohistochemistry, to hormone analyses and methods to assess sperm maturation status and functional competence. CONCLUSION: With the increased rate of genetically modified mouse production, the generation of mouse models with unexpected male infertility is increasing. This manuscript will help to ensure that the maximum amount of information is obtained from each mouse model and, by extension, will facilitate the knowledge of both normal fertility processes and the causes of human infertility

Fetal programming of adult Leydig cell function by androgenic effects on stem/progenitor cells

status: publishe