The UK Clinical Research Collaboration (UKCRC) Tissue Directory and Coordination Centre: the UK’s centre for facilitating the usage of human samples for medical research

The UKCRC Tissue Directory and Coordination Centre was established to improve access to and utilisation of UK human tissue samples for medical research. The key output of the Centre is the creation of the UK’s first pan-disease Tissue Directory (https://directory.biobankinguk.org/). Any researcher can search the Directory based on a series of simple key words including disease classification, age, sex, sample type, preservation details, quality indicators and datasets available. The Directory as of April 2017 contains 100 Bioresources. Researchers seeking fresh samples can also search for facilities that offer bespoke collection services. Future work of the Centre will be to explore greater standardisation of biobanking activities across the UK and to facilitate an inter-connected research infrastructure related to the use of human biosamples

Optimized schwarz methods for Maxwell equations with discontinuous coefficients

We study non-overlapping Schwarz methods for solving time-harmonic Maxwell’s equations in heterogeneous media. We show that the classical Schwarz algorithm is always divergent when coefficient jumps are present along the interface. In the case of transverse magnetic or transverse electric two dimensional formulations, convergence can be achieved in specific configurations only. We then develop optimized Schwarz methods which can take coefficient jumps into account in their transmission conditions. These methods exhibit rapid convergence, and sometimes converge independently of the mesh parameter, even without overlap. We illustrate our analysis with numerical experiments

In vitro cell compatibility and antibacterial activity of microencapsulated doxycycline designed for improved localized therapy of septic arthritis

OBJECTIVES: For the treatment of septic arthritis in large animals, the local application of antibiotics as a slow release system may be an appropriate means to reach high local bioactivity and low systemic side effects and drug residues. In this study, doxycycline microspheres were developed and tested in vitro for their drug-release properties, suitability for intra-articular application and antimicrobial activity. METHODS: The development of a slow release system was achieved by microencapsulation of the drug into poly(lactide-co-glycolide) microspheres by a novel ultrasonic atomization method. Drug elution was evaluated from microspheres dispersed in elution medium at pre-defined time points by HPLC. Joint-tissue compatibility was tested on cultured bovine synoviocytes by evaluating the expression of pro-inflammatory cytokine mRNA and the production of nitric oxide (NO). Finally, the antimicrobial activity of the released antibiotic was assessed with gram-negative and gram-positive bacteria exposed to release medium sampled at days 1, 7 and 12 after microsphere suspension. RESULTS: An adequate size of the microspheres, sufficient stabilization of doxycycline in aqueous environment and drug release (25 mg microspheres in 4 mL medium) above MIC for bacteria usually isolated in bovine and equine joints were obtained over 15 days. Although the cytokine mRNA expression reflected the excellent tissue compatibility, the results with NO yielded contradictory results. Antimicrobial tests of the release medium proved to match perfectly the activity of non-encapsulated, free doxycycline as reported in the literature. CONCLUSIONS: The newly developed doxycycline delivery system achieved the target specifications and is ready for in vivo testin

Control of human cytomegalovirus replication by liver resident natural killer cells

Natural killer cells are considered to be important for control of human cytomegalovirus– a major pathogen in immune suppressed transplant patients. Viral infection promotes the development of an adaptive phenotype in circulating natural killer cells that changes their anti-viral function. In contrast, less is understood how natural killer cells that reside in tissue respond to viral infection. Here we show natural killer cells resident in the liver have an altered phenotype in cytomegalovirus infected individuals and display increased anti-viral activity against multiple viruses in vitro and identify and characterise a subset of natural killer cells responsible for control. Crucially, livers containing natural killer cells with better capacity to control cytomegalovirus replication in vitro are less likely to experience viraemia post-transplant. Taken together, these data suggest that virally induced expansion of tissue resident natural killer cells in the donor organ can reduce the chance of viraemia post-transplant

Fourier Method for Approximating Eigenvalues of Indefinite Stekloff Operator

We introduce an efficient method for computing the Stekloff eigenvalues associated with the Helmholtz equation. In general, this eigenvalue problem requires solving the Helmholtz equation with Dirichlet and/or Neumann boundary condition repeatedly. We propose solving the related constant coefficient Helmholtz equation with Fast Fourier Transform (FFT) based on carefully designed extensions and restrictions of the equation. The proposed Fourier method, combined with proper eigensolver, results in an efficient and clear approach for computing the Stekloff eigenvalues.Comment: 12 pages, 4 figure

Need for adjuvant radiotherapy in oral cancer: depth of invasion rather than tumor diameter

PURPOSE The 8th edition of the TNM Cancer Staging Manual incorporates depth of invasion (DOI) into the pathologic tumor classification for oral squamous cell carcinoma (OSSC). While deep invading tumors with small tumor diameters (TD) have been categorized as early stage tumors in the 7th edition, they are now upstaged, potentially influencing the decision to initiate adjuvant radiotherapy (RT). METHODS OSCC patients surgically treated with curative intent between 2010 and 2019 were consecutively included. Tumors were staged based on TD only (according to the 7th edition TNM Cancer Staging Manual), then restaged based solely on DOI. RESULTS Of the 133 included patients, 58 patients (43.6%) had a different pT-stage when using DOI instead of TD for staging (upstaging in 23.3%). Overall survival (OS) was significantly worse in patients who were upstaged with DOI. In addition, stratification by adjuvant RT showed significant worse OS in upstaged patients without receiving adjuvant RT. CONCLUSIONS DOI seems to be an import indicator for adjuvant RT in OSCC-patients

Sequence learning modulates neural responses and oscillatory coupling in human and monkey auditory cortex

Learning complex ordering relationships between sensory events in a sequence is fundamental for animal perception and human communication. While it is known that rhythmic sensory events can entrain brain oscillations at different frequencies, how learning and prior experience with sequencing relationships affect neocortical oscillations and neuronal responses is poorly understood. We used an implicit sequence learning paradigm (an “artificial grammar”) in which humans and monkeys were exposed to sequences of nonsense words with regularities in the ordering relationships between the words. We then recorded neural responses directly from the auditory cortex in both species in response to novel legal sequences or ones violating specific ordering relationships. Neural oscillations in both monkeys and humans in response to the nonsense word sequences show strikingly similar hierarchically nested low-frequency phase and high-gamma amplitude coupling, establishing this form of oscillatory coupling—previously associated with speech processing in the human auditory cortex—as an evolutionarily conserved biological process. Moreover, learned ordering relationships modulate the observed form of neural oscillatory coupling in both species, with temporally distinct neural oscillatory effects that appear to coordinate neuronal responses in the monkeys. This study identifies the conserved auditory cortical neural signatures involved in monitoring learned sequencing operations, evident as modulations of transient coupling and neuronal responses to temporally structured sensory input

Stain-free identification of tissue pathology using a generative adversarial network to infer nanomechanical signatures

Intraoperative frozen section analysis can be used to improve the accuracy of tumour margin estimation during cancer resection surgery through rapid processing and pathological assessment of excised tissue. Its applicability is limited in some cases due to the additional risks associated with prolonged surgery, largely from the time-consuming staining procedure. Our work uses a measurable property of bulk tissue to bypass the staining process: as tumour cells proliferate, they influence the surrounding extra-cellular matrix, and the resulting change in elastic modulus provides a signature of the underlying pathology. In this work we accurately localise atomic force microscopy measurements of human liver tissue samples and train a generative adversarial network to infer elastic modulus from low-resolution images of unstained tissue sections. Pathology is predicted through unsupervised clustering of parameters characterizing the distributions of inferred values, achieving 89% accuracy for all samples based on the nominal assessment (n = 28), and 95% for samples that have been validated by two independent pathologists through post hoc staining (n = 20). Our results demonstrate that this technique could increase the feasibility of intraoperative frozen section analysis for use during resection surgery and improve patient outcomes

Fast interior point solution of quadratic programming problems arising from PDE-constrained optimization

Interior point methods provide an attractive class of approaches for solving linear, quadratic and nonlinear programming problems, due to their excellent efficiency and wide applicability. In this paper, we consider PDE-constrained optimization problems with bound constraints on the state and control variables, and their representation on the discrete level as quadratic programming problems. To tackle complex problems and achieve high accuracy in the solution, one is required to solve matrix systems of huge scale resulting from Newton iteration, and hence fast and robust methods for these systems are required. We present preconditioned iterative techniques for solving a number of these problems using Krylov subspace methods, considering in what circumstances one may predict rapid convergence of the solvers in theory, as well as the solutions observed from practical computations

Euclidean Structure from N>=2 Parallel Circles: Theory and Algorithms

International audienceOur problem is that of recovering, in one view, the 2D Euclidean structure, induced by the projections of N parallel circles. This structure is a prerequisite for camera calibration and pose computation. Until now, no general method has been described for N > 2. The main contribution of this work is to state the problem in terms of a system of linear equations to solve.We give a closed-form solution as well as bundle adjustment-like refinements, increasing the technical applicability and numerical stability. Our theoretical approach generalizes and extends all those described in existing works for N = 2 in several respects, as we can treat simultaneously pairs of orthogonal lines and pairs of circles within a unified framework. The proposed algorithm may be easily implemented, using well-known numerical algorithms. Its performance is illustrated by simulations and experiments with real images