A novel framework employing deep multi-attention channels network for the autonomous detection of metastasizing cells through fluorescence microscopy

We developed a transparent computational large-scale imaging-based framework that can distinguish between normal and metastasizing human cells. The method relies on fluorescence microscopy images showing the spatial organization of actin and vimentin filaments in normal and metastasizing single cells, using a combination of multi-attention channels network and global explainable techniques. We test a classification between normal cells (Bj primary fibroblast), and their isogenically matched, transformed and invasive counterpart (BjTertSV40TRasV12). Manual annotation is not trivial to automate due to the intricacy of the biologically relevant features. In this research, we utilized established deep learning networks and our new multi-attention channel architecture. To increase the interpretability of the network - crucial for this application area - we developed an interpretable global explainable approach correlating the weighted geometric mean of the total cell images and their local GradCam scores. The significant results from our analysis unprecedently allowed a more detailed, and biologically relevant understanding of the cytoskeletal changes that accompany oncogenic transformation of normal to invasive and metastasizing cells. We also paved the way for a possible spatial micrometre-level biomarker for future development of diagnostic tools against metastasis (spatial distribution of vimentin)

Probing the dynamic nature of self-assembling cyclic peptide-polymer nanotubes in solution and in mammalian cells

Self-assembling cyclic peptide–polymer nanotubes have emerged as a fascinating supramolecular system, well suited for a diverse range of biomedical applications. Due to their well-defined diameter, tunable peptide anatomy, and ability to disassemble in situ, they have been investigated as promising materials for numerous applications including biosensors, antimicrobials, and drug delivery. Despite this continuous effort, the underlying mechanisms of assembly and disassembly are still not fully understood. In particular, the exchange of units between individual assembled nanotubes has been overlooked so far, despite its knowledge being essential for understanding their behavior in different environments. To investigate the dynamic nature of these systems, cyclic peptide–polymer nanotubes are synthesized, conjugated with complementary dyes, which undergo a Förster resonance energy transfer (FRET) in close proximity. Model conjugates enable to demonstrate not only that their self-assembly is highly dynamic and not kinetically trapped, but also that the self-assembly of the conjugates is strongly influenced by both solvent and concentration. Additionally, the versatility of the FRET system allows studying the dynamic exchange of these systems in mammalian cells in vitro using confocal microscopy, demonstrating the exchange of subunits between assembled nanotubes in the highly complex environment of a cell

An infinite family of superintegrable Hamiltonians with reflection in the plane

We introduce a new infinite class of superintegrable quantum systems in the plane. Their Hamiltonians involve reflection operators. The associated Schr\"odinger equations admit separation of variables in polar coordinates and are exactly solvable. The angular part of the wave function is expressed in terms of little -1 Jacobi polynomials. The spectra exhibit "accidental" degeneracies. The superintegrability of the model is proved using the recurrence relation approach. The (higher-order) constants of motion are constructed and the structure equations of the symmetry algebra obtained.Comment: 19 page

Metastasising Fibroblasts Show an HDAC6-Dependent Increase in Migration Speed and Loss of Directionality Linked to Major Changes in the Vimentin Interactome

Metastasising cells express the intermediate filament protein vimentin, which is used to diagnose invasive tumours in the clinic. We aimed to clarify how vimentin regulates the motility of metastasising fibroblasts. STED super-resolution microscopy, live-cell imaging and quantitative proteomics revealed that oncogene-expressing and metastasising fibroblasts show a less-elongated cell shape, reduced cell spreading, increased cell migration speed, reduced directionality, and stronger coupling between these migration parameters compared to normal control cells. In total, we identified and compared 555 proteins in the vimentin interactome. In metastasising cells, the levels of keratin 18 and Rab5C were increased, while those of actin and collagen were decreased. Inhibition of HDAC6 reversed the shape, spreading and migration phenotypes of metastasising cells back to normal. Inhibition of HDAC6 also decreased the levels of talin 1, tropomyosin, Rab GDI β, collagen and emilin 1 in the vimentin interactome, and partially reversed the nanoscale vimentin organisation in oncogene-expressing cells. These findings describe the changes in the vimentin interactome and nanoscale distribution that accompany the defective cell shape, spreading and migration of metastasising cells. These results support the hypothesis that oncogenes can act through HDAC6 to regulate the vimentin binding of the cytoskeletal and cell–extracellular matrix adhesion components that contribute to the defective motility of metastasising cells

PROPEL: implementation of an evidence based pelvic floor muscle training intervention for women with pelvic organ prolapse: a realist evaluation and outcomes study protocol

Abstract Background Pelvic Organ Prolapse (POP) is estimated to affect 41%–50% of women aged over 40. Findings from the multi-centre randomised controlled “Pelvic Organ Prolapse PhysiotherapY” (POPPY) trial showed that individualised pelvic floor muscle training (PFMT) was effective in reducing symptoms of prolapse, improved quality of life and showed clear potential to be cost-effective. However, provision of PFMT for prolapse continues to vary across the UK, with limited numbers of women’s health physiotherapists specialising in its delivery. Implementation of this robust evidence from the POPPY trial will require attention to different models of delivery (e.g. staff skill mix) to fit with differing care environments. Methods A Realist Evaluation (RE) of implementation and outcomes of PFMT delivery in contrasting NHS settings will be conducted using multiple case study sites. Involving substantial local stakeholder engagement will permit a detailed exploration of how local sites make decisions on how to deliver PFMT and how these lead to service change. The RE will track how implementation is working; identify what influences outcomes; and, guided by the RE-AIM framework, will collect robust outcomes data. This will require mixed methods data collection and analysis. Qualitative data will be collected at four time-points across each site to understand local contexts and decisions regarding options for intervention delivery and to monitor implementation, uptake, adherence and outcomes. Patient outcome data will be collected at baseline, six months and one year follow-up for 120 women. Primary outcome will be the Pelvic Organ Prolapse Symptom Score (POP-SS). An economic evaluation will assess the costs and benefits associated with different delivery models taking account of further health care resource use by the women. Cost data will be combined with the primary outcome in a cost effectiveness analysis, and the EQ-5D-5L data in a cost utility analysis for each of the different models of delivery. Discussion Study of the implementation of varying models of service delivery of PFMT across contrasting sites combined with outcomes data and a cost effectiveness analysis will provide insight into the implementation and value of different models of PFMT service delivery and the cost benefits to the NHS in the longer term

Depth-resolved measurement of the Meissner screening profile in a niobium thin film from spin-lattice relaxation of the implanted β\beta-emitter 8^{8}Li

We report measurements of the Meissner screening profile in a Nb(300 nm)/Al$_{2}$O$_{3}$ thin film using $^{8}$Li $\beta$-detected nuclear magnetic resonance ($\beta$-NMR). The NMR probe $^{8}$Li was ion-implanted into the Nb film at energies $\leq$ 20 keV, corresponding to mean stopping depths comparable to Nb's magnetic penetration depth $\lambda$. $^{8}$Li's strong dipole-dipole coupling with the host $^{93}$Nb nuclei provided a "cross-relaxation" channel that dominated in low magnetic fields, which conferred indirect sensitivity to the local magnetic field via the spin-lattice relaxation (SLR) rate $1/T_{1}$. From a fit of the $1/T_{1}$ data to a model accounting for its dependence on temperature, magnetic field, and $^{8}$Li$^{+}$ implantation energy, we obtained a magnetic penetration depth $\lambda_{0}$ = 51.5(22) nm, consistent with a relatively short carrier mean-free-path $\ell$ = 18.7(29) nm typical of similarly prepared Nb films. The results presented here constitute an important step towards using $^{8}$Li $\beta$-NMR to characterize bulk Nb samples with engineered surfaces, which are often used in the fabrication of particle accelerators.Comment: 16 pages, 4 figure

Supersymmetric Quantum Mechanics with Reflections

We consider a realization of supersymmetric quantum mechanics where supercharges are differential-difference operators with reflections. A supersymmetric system with an extended Scarf I potential is presented and analyzed. Its eigenfunctions are given in terms of little -1 Jacobi polynomials which obey an eigenvalue equation of Dunkl type and arise as a q-> -1 limit of the little q-Jacobi polynomials. Intertwining operators connecting the wave functions of extended Scarf I potentials with different parameters are presented.Comment: 17 page

Nuclear magnetic resonance of ion implanted 8^8Li in ZnO

We report on the stability and magnetic state of ion implanted $^8$Li in single crystals of the semiconductor ZnO using $\beta$-detected nuclear magnetic resonance. At ultradilute concentrations, the spectra reveal distinct Li sites from 7.6 to 400 K. Ionized shallow donor interstitial Li is stable across the entire temperature range, confirming its ability to self-compensate the acceptor character of its (Zn) substitutional counterpart. Above 300 K, spin-lattice relaxation indicates the onset of correlated local motion of interacting defects, and the spectra show a site change transition from disordered configurations to substitutional. Like the interstitial, the substitutional shows no resolved hyperfine splitting, indicating it is also fully ionized above 210 K. The electric field gradient at the interstitial $^8$Li exhibits substantial temperature dependence with a power law typical of non-cubic metals.Comment: 15 pages and 11 figure

International, multidisciplinary Delphi consensus recommendations on non-pharmacological interventions for fibromyalgia

Funding Information: The Republic of Turkey Ministry of National Education for the PhD studentship. Publisher Copyright: © 2022 The Author(s)Objectives: To develop evidence-based expert recommendations for non-pharmacological treatments for pain, fatigue, sleep problems, and depression in fibromyalgia. Methods: An international, multidisciplinary Delphi exercise was conducted. Authors of EULAR and the Canadian Fibromyalgia Guidelines Group, members of the American Pain Society and clinicians with expertise in fibromyalgia were invited. Participants were asked to select non-pharmacological interventions that could be offered for specific fibromyalgia symptoms and to classify them as either core or adjunctive treatments. An evidence summary was provided to aid the decision making. Items receiving >70% votes were accepted, those receiving <30% votes were rejected and those obtaining 30-70% votes were recirculated for up to two additional rounds. Results: Seventeen experts participated (Europe (n = 10), North America (n = 6), and Israel (n = 1)) in the Delphi exercise and completed all three rounds. Aerobic exercise, education, sleep hygiene and cognitive behavioural therapy were recommended as core treatments for all symptoms. Mind-body exercises were recommended as core interventions for pain, fatigue and sleep problems. Mindfulness was voted core treatment for depression, and adjunctive treatment for other symptoms. Other interventions, namely music, relaxation, hot bath, and local heat were voted as adjunctive treatments, varying between symptoms. Conclusions: This study provided evidence-based expert consensus recommendations on non-pharmacological treatments for fibromyalgia that may be used to individualise treatments in clinical practice targeting the diverse symptoms associated with fibromyalgia.publishersversionepub_ahead_of_prin

Randomised controlled trial of GM-CSF in critically ill patients with impaired neutrophil phagocytosis

Background. Critically ill patients with impaired neutrophil phagocytosis have significantly increased risk of nosocomial infection. Granulocyte-macrophage colony-stimulating factor (GM-CSF) improves phagocytosis by neutrophils ex vivo. This study tested the hypothesis that GM-CSF improves neutrophil phagocytosis in critically ill patients in whom phagocytosis is known to be impaired Methods. This was a multi-centre, phase 2a randomised, placebo-controlled clinical trial Using a personalised medicine approach, only critically ill patients with impaired neutrophil phagocytosis were included. Patients were randomised 1:1 to subcutaneous GM-CSF (3 microgrammws/kg/day) or placebo, once daily for 4 days. The primary outcome measure was neutrophil phagocytosis 2 days after initiation of GM-CSF. Secondary outcomes included neutrophil phagocytosis over time, neutrophil functions other than phagocytosis, monocyte HLA-DR expression, and safety. Results. Thirty-eight patients were recruited from 5 intensive care units (17 randomised to GM-CSF). Mean neutrophil phagocytosis at day 2 was 57.2% (SD 13.2%) in the GM-CSF group and 49.8% (13.4%) in the placebo group, p=0.73. The proportion of patients with neutrophil phagocytosis >50% at day 2, and monocyte HLA-DR, appeared significantly higher in the GM-CSF group. Neutrophil functions other than phagocytosis did not appear significantly different between the groups. The most common adverse event associated with GM-CSF was pyrexia. Conclusions. GM-CSF did not improve mean neutrophil phagocytosis at day 2, but was safe and appeared to increase the proportion of patients with adequate phagocytosis. The study suggests proof of principle for a pharmacological effect on neutrophil function in a subset of critically ill patients.This work was funded by a grant from the Medical Research Council (G1100233), with additional support from the National Institute for Health Research (NIHR) Newcastle Biomedical Research Centre. It was sponsored by Newcastle Universit