The ZX calculus is a language for surface code lattice surgery

A leading choice of error correction for scalable quantum computing is the surface code with lattice surgery. The basic lattice surgery operations, the merging and splitting of logical qubits, act non-unitarily on the logical states and are not easily captured by standard circuit notation. This raises the question of how best to design, verify, and optimise protocols that use lattice surgery, in particular in architectures with complex resource management issues. In this paper we demonstrate that the operations of the ZX calculus --- a form of quantum diagrammatic reasoning based on bialgebras --- match exactly the operations of lattice surgery. Red and green ``spider'' nodes match rough and smooth merges and splits, and follow the axioms of a dagger special associative Frobenius algebra. Some lattice surgery operations require non-trivial correction operations, which are captured natively in the use of the ZX calculus in the form of ensembles of diagrams. We give a first taste of the power of the calculus as a language for lattice surgery by considering two operations (T gates and producing a CNOT) and show how ZX diagram re-write rules give lattice surgery procedures for these operations that are novel, efficient, and highly configurable

Pauli Fusion : a computational model to realise quantum transformations from ZX terms

We present an abstract model of quantum computation, the Pauli Fusion model, whose primitive operations correspond closely to generators of the ZX calculus (a formal graphical language for quantum computing). The fundamental operations of Pauli Fusion are also straightforward abstractions of basic processes in some leading proposed quantum technologies. These operations have non-deterministic heralded effects, similarly to measurement-based quantum computation. We describe sufficient conditions for Pauli Fusion procedures to be deterministically realisable, so that it performs a given transformation independently of its non-deterministic outcomes. This provides an operational model to realise ZX terms beyond the circuit model

TF Target Mapper: A BLAST search tool for the identification of Transcription Factor target genes

BACKGROUND: In the current era of high throughput genomics a major challenge is the genome-wide identification of target genes for specific transcription factors. Chromatin immunoprecipitation (ChIP) allows the isolation of in vivo binding sites of transcription factors and provides a powerful tool for examining gene regulation. Crosslinked chromatin is immunoprecipitated with antibodies against specific transcription factors, thus enriching for sequences bound in vivo by these factors in the immunoprecipitated DNA. Cloning and sequencing the immunoprecipitated sequences allows identification of transcription factor target genes. Routinely, thousands of such sequenced clones are used in BLAST searches to map their exact location in the genome and the genes located in the vicinity. These genes represent potential targets of the transcription factor of interest. Such bioinformatics analysis is very laborious if performed manually and for this reason there is a need for developing bioinformatic tools to automate and facilitate it. RESULTS: In order to facilitate this analysis we generated TF Target Mapper (Transcription Factor Target Mapper). TF Target Mapper is a BLAST search tool allowing rapid extraction of annotated information on genes around each hit. It combines sequence cleaning/filtering, pattern searching and BLAST searches with extraction of information on genes located around each BLAST hit and comparisons of the output list of genes or gene ontology IDs with user-implemented lists. We successfully applied and tested TF Target Mapper to analyse sequences bound in vivo by the transcription factor GATA-1. We show that TF Target Mapper efficiently extracted information on genes around ChIPed sequences, thus identifying known (e.g. α-globin and ζ-globin) and potentially novel GATA-1 gene targets. CONCLUSION: TF Target Mapper is a very efficient BLAST search tool that allows the rapid extraction of annotated information on the genes around each hit. It can contribute to the comprehensive bioinformatic transcriptome/regulome analysis, by providing insight into the mechanisms of action of specific transcription factors, thus helping to elucidate the pathways these factors regulate

Application of Big Data to Support Evidence-Based Public Health Policy Decision-Making for Hearing

Ideally, public health policies are formulated from scientific data; however, policy-specific data are often unavailable. Big data can generate ecologically-valid, high-quality scientific evidence, and therefore has the potential to change how public health policies are formulated. Here, we discuss the use of big data for developing evidence-based hearing health policies, using data collected and analyzed with a research prototype of a data repository known as EVOTION (EVidence-based management of hearing impairments: public health pOlicy-making based on fusing big data analytics and simulaTION), to illustrate our points. Data in the repository consist of audiometric clinical data, prospective real-world data collected from hearing aids and an app, and responses to questionnaires collected for research purposes. To date, we have used the platform and a synthetic dataset to model the estimated risk of noise-induced hearing loss and have shown novel evidence of ways in which external factors influence hearing aid usage patterns. We contend that this research prototype data repository illustrates the value of using big data for policy-making by providing high-quality evidence that could be used to formulate and evaluate the impact of hearing health care policies

The psychosocial cost burden of cancer : A systematic literature review

BACKGROUND AND OBJECTIVE: Psychosocial costs, or quality of life costs, account for psychological distress, pain, suffering and other negative experiences associated with cancer. They contribute to the overall economic burden of cancer that patients experience. But this category of costs remains poorly understood. This hinders opportunities to make the best cancer control policy decisions. This study explored the psychosocial cost burden associated with cancer, how studies measure psychosocial costs and the impact of this burden. METHODS: A systematic literature review of academic and grey literature published from 2008 to 2018 was conducted by searching electronic databases, guided by the Institute of Medicine's conceptualization of psychosocial burden. Results were analyzed using a narrative synthesis and a weighted proportion of populations affected was calculated. Study quality was assessed using the Ottawa-Newcastle instrument. RESULTS: A total of 25 studies were included. There was variation in how psychosocial costs were conceptualized and an inconsistent approach to measurement. Most studies measured social dimensions and focused on the financial consequences of paying for care. Fewer studies assessed costs associated with the other domains of this burden, including psychological, physical, and spiritual dimensions. Fourty-four percent of cancer populations studied were impacted by psychosocial costs and this varied by disease site (38%-71%). Two studies monetized the psychosocial cost burden, estimating a lifetime cost per case ranging from CAD$427753 to CAD$528769. Studies were of varying quality; 60% of cross-sectional studies had a high risk of bias. CONCLUSIONS: Consistency in approach to measurement would help to elevate this issue for researchers and decision makers. At two-thirds of the total economic burden of cancer, economic evaluations should account for psychosocial costs to better inform decision-making. More support is needed to address the psychosocial cost burden faced by patients and their families

Integration of advanced methods and models to study drug absorption and related processes : An UNGAP perspective

Funding Information: AI acknowledges the support of projects icp009 (ALKOOL) of PRACE-ICEI (grant agreement 800858) for awarding access to Piz Daint, at the Swiss National Supercomputing Centre (CSCS), Switzerland and BG05M2OP001–1.001–0004 (UNITe) of the Bulgarian Ministry of Education and Science. For further details on points raised in this article, please contact [email protected]. Funding Information: Acknowledgements. JAGH is supported by the Biocenter Finland, the Helsinki Institute of Life Sciences, and the Faculty of Pharmacy, University of Helsinki. Publisher Copyright: © 2021 The AuthorsThis collection of contributions from the European Network on Understanding Gastrointestinal Absorption-related Processes (UNGAP) community assembly aims to provide information on some of the current and newer methods employed to study the behaviour of medicines. It is the product of interactions in the immediate pre-Covid period when UNGAP members were able to meet and set up workshops and to discuss progress across the disciplines. UNGAP activities are divided into work packages that cover special treatment populations, absorption processes in different regions of the gut, the development of advanced formulations and the integration of food and pharmaceutical scientists in the food-drug interface. This involves both new and established technical approaches in which we have attempted to define best practice and highlight areas where further research is needed. Over the last months we have been able to reflect on some of the key innovative approaches which we were tasked with mapping, including theoretical, in silico, in vitro, in vivo and ex vivo, preclinical and clinical approaches. This is the product of some of us in a snapshot of where UNGAP has travelled and what aspects of innovative technologies are important. It is not a comprehensive review of all methods used in research to study drug dissolution and absorption, but provides an ample panorama of current and advanced methods generally and potentially useful in this area. This collection starts from a consideration of advances in a priori approaches: an understanding of the molecular properties of the compound to predict biological characteristics relevant to absorption. The next four sections discuss a major activity in the UNGAP initiative, the pursuit of more representative conditions to study lumenal dissolution of drug formulations developed independently by academic teams. They are important because they illustrate examples of in vitro simulation systems that have begun to provide a useful understanding of formulation behaviour in the upper GI tract for industry. The Leuven team highlights the importance of the physiology of the digestive tract, as they describe the relevance of gastric and intestinal fluids on the behaviour of drugs along the tract. This provides the introduction to microdosing as an early tool to study drug disposition. Microdosing in oncology is starting to use gamma-emitting tracers, which provides a link through SPECT to the next section on nuclear medicine. The last two papers link the modelling approaches used by the pharmaceutical industry, in silico to Pop-PK linking to Darwich and Aarons, who provide discussion on pharmacometric modelling, completing the loop of molecule to man.Peer reviewe

Seprase: An overview of an important matrix serine protease

Seprase or Fibroblast Activation Protein (FAP) is an integral membrane serine peptidase, which has been shown to have gelatinase activity. Seprase has a dual function in tumour progression. The proteolytic activity of Seprase has been shown to promote cell invasiveness towards the ECM and also to support tumour growth and proliferation. Seprase appears to act as a proteolytically active 170-kDa dimer, consisting of two 97- kDa subunits. It is a member of the group type II integral serine proteases, which includes dipeptidyl peptidase IV (DPPIV/CD26) and related type II transmembrane prolyl serine peptidases, which exert their mechanisms of action on the cell surface. DPPIV and Seprase exhibit multiple functions due to their abilities to form complexes with each other and to interact with other membrane-associated molecules. Localisation of these protease complexes at cell surface protrusions, called invadopodia, may have a prominent role in processing soluble factors and in the degradation of extracellular matrix components that are essential to the cellular migration and matrix invasion that occur during tumour invasion, metastasis and angiogenesis

Are mice good models for human neuromuscular disease? Comparing muscle excursions in walking between mice and humans

The mouse is one of the most widely used animal models to study neuromuscular diseases and test new therapeutic strategies. However, findings from successful pre-clinical studies using mouse models frequently fail to translate to humans due to various factors. Differences in muscle function between the two species could be crucial but often have been overlooked. The purpose of this study was to evaluate and compare muscle excursions in walking between mice and humans

Sequence dependent antitumour efficacy of the vascular disrupting agent ZD6126 in combination with paclitaxel

The clinical success of small-molecule vascular disrupting agents (VDAs) depends on their combination with conventional therapies. Scheduling and sequencing remain key issues in the design of VDA–chemotherapy combination treatments. This study examined the antitumour activity of ZD6126, a microtubule destabilising VDA, in combination with paclitaxel (PTX), a microtubule-stabilising cytotoxic drug, and the influence of schedule and sequence on the efficacy of the combination. Nude mice bearing MDA-MB-435 xenografts received weekly cycles of ZD6126 (200 mg kg−1 i.p.) administered at different times before or after PTX (10, 20, and 40 mg kg−1 i.v.). ZD6126 given 2 or 24 h after PTX showed no significant benefit, a result that was attributed to a protective effect of PTX against ZD6126-induced vascular damage and tumour necrosis, a hallmark of VDA activity. Paclitaxel counteracting activity was reduced by distancing drug administrations, and ZD6126 given 72 h after PTX potentiated the VDA's antitumour activity. Schedules with ZD6126 given before PTX improved therapeutic activity, which was paralleled by a VDA-induced increase in cell proliferation in the viable tumour tissue. Paclitaxel given 72 h after ZD6126 yielded the best response (50% tumours regressing). A single treatment with ZD6126 followed by weekly administration of PTX was sufficient to achieve a similar response (57% remissions). These findings show that schedule, sequence and timing are crucial in determining the antitumour efficacy of PTX in combination with ZD6126. Induction of tumour necrosis and increased proliferation in the remaining viable tumour tissue could be exploited as readouts to optimise schedules and maximise therapeutic efficacy

The effect of thermal dose on hyperthermia-mediated inhibition of DNA repair through homologous recombination

Hyperthermia has a number of biological effects that sensitize tumors to radiotherapy in the range between 40-44 °C. One of these effects is heat-induced degradation of BRCA2 that in turn causes reduced RAD51 focus formation, which results in an attenuation of DNA repair through homologous recombination. Prompted by this molecular insight into how hyperthermia attenuates homologous recombination, we now quantitatively explore time and temperature dynamics of hyperthermia on BRCA2 levels and RAD51 focus formation in cell culture models, and link this to their clonogenic survival capacity after irradiation (0-6 Gy). For treatment temperatures above 41 °C, we found a decrease in cell survival, an increase in sensitization towards irradiation, a decrease of BRCA2 protein levels, and altered RAD51 focus formation. When the temperatures exceeded 43 °C, we found that hyperthermia alone killed more cells directly, and that processes other than homologous recombination were affected by the heat. This study demonstrates that optimal inhibition of HR is achieved by subjecting cells to hyperthermia at 41-43 °C for 30 to 60 minutes. Our data provides a guideline for the clinical application of novel combination treatments that could exploit hyperthermia's attenuation of homologous recombination, such as the combination of hyperthermia with PARP-inhibitors for non-BRCA mutations carriers