Construction, testing and in-situ operation of the T2K ND280 electromagnetic calorimeter

The T2K experiment is a long baseline, second generation neutrino oscillation experiment located in Japan. Its aim is to measure the $\theta_{23}$ and $\theta_{13}$ neutrino oscillation mixing angles, as well as to make precision measurements of the atmospheric mass squared difference $\Delta m_{23}^2$ . Along with its other commitments, the UK was responsible for the design, assembly, testing and commissioning of the near detector’s electromagnetic calorimeters, as well as the development of the detector’s reconstruction software. Some of the processes by which these objectives were achieved are highlighted within, with a specific focus on physical assembly and testing of the detectors, as well as the development of software designed to estimate the energy of interaction byproducts which arrive in the detector’s fiducial volume

Fourier-Net+: Leveraging Band-Limited Representation for Efficient 3D Medical Image Registration

U-Net style networks are commonly utilized in unsupervised image registration to predict dense displacement fields, which for high-resolution volumetric image data is a resource-intensive and time-consuming task. To tackle this challenge, we first propose Fourier-Net, which replaces the costly U-Net style expansive path with a parameter-free model-driven decoder. Instead of directly predicting a full-resolution displacement field, our Fourier-Net learns a low-dimensional representation of the displacement field in the band-limited Fourier domain which our model-driven decoder converts to a full-resolution displacement field in the spatial domain. Expanding upon Fourier-Net, we then introduce Fourier-Net+, which additionally takes the band-limited spatial representation of the images as input and further reduces the number of convolutional layers in the U-Net style network's contracting path. Finally, to enhance the registration performance, we propose a cascaded version of Fourier-Net+. We evaluate our proposed methods on three datasets, on which our proposed Fourier-Net and its variants achieve comparable results with current state-of-the art methods, while exhibiting faster inference speeds, lower memory footprint, and fewer multiply-add operations. With such small computational cost, our Fourier-Net+ enables the efficient training of large-scale 3D registration on low-VRAM GPUs. Our code is publicly available at \url{https://github.com/xi-jia/Fourier-Net}.Comment: Under review. arXiv admin note: text overlap with arXiv:2211.1634

Local and population-level responses of Greater sage-grouse to oil and gas development and climatic variation in Wyoming

Background Spatial scale is important when studying ecological processes. The Greater sage-grouse (Centrocercus urophasianus) is a large sexually dimorphic tetraonid that is endemic to the sagebrush biome of western North America. The impacts of oil and gas (OAG) development at individual leks has been well-documented. However, no previous studies have quantified the population-level response. Methods Hierarchical models were used to estimate the effects of the areal disturbance due to well pads as well as climatic variation on individual lek counts and Greater sage-grouse populations (management units) over 32 years. The lek counts were analyzed using generalized linear mixed models while the management units were analyzed using Gompertz population dynamic models. The models were fitted using frequentist and Bayesian methods. An information-theoretic approach was used to identify the most important spatial scale and time lags. The relative importance of OAG and climate at the local and population-level scales was assessed using information-theoretic (Akaike’s weights) and estimation (effect size) statistics. Results At the local scale, OAG was an important negative predictor of the lek count. At the population scale, there was only weak support for OAG as a predictor of density changes but the estimated impacts on the long-term carrying capacity were consistent with summation of the local impacts. Regional climatic variation, as indexed by the Pacific Decadal Oscillation, was an important positive predictor of density changes at both the local and population level (particularly in the most recent part of the time series). Conclusions Additional studies to reduce the uncertainty in the range of possible effects of OAG at the population scale are required. Wildlife agencies need to account for the effects of regional climatic variation when managing sage-grouse populations

Public Health Response to Imported Case of Poliomyelitis, Australia, 2007

Inactivated polio vaccine was offered, and the index case-patient and household contacts were quarantined

The role of CD8+ T cell clones in immune thrombocytopenia

Immune thrombocytopenia (ITP) is traditionally considered an antibody-mediated disease. However, a number of features suggest alternative mechanisms of platelet destruction. In this study, we use a multi-dimensional approach to explore the role of cytotoxic CD8+ T cells in ITP. We characterised patients with ITP and compared them to age-matched controls using immunophenotyping, next-generation sequencing of T cell receptor (TCR) genes, single-cell RNA sequencing, and functional T cell and platelet assays. We found that adults with chronic ITP have increased polyfunctional, terminally differentiated effector memory CD8+ T cells (CD45RA+CD62L-) expressing intracellular interferon-g, tumour necrosis factor-a, and Granzyme B defining them as TEMRA cells. These TEMRA cells expand when the platelet count falls and show no evidence of physiological exhaustion. Deep sequencing of the T cell receptor showed expanded T cell clones in patients with ITP. T cell clones persisted over many years, were more prominent in patients with refractory disease, and expanded when the platelet count was low. Combined single-cell RNA and TCR sequencing of CD8+ T cells confirmed that the expanded clones are TEMRA cells. Using in vitro model systems, we show that CD8+ T cells from patients with ITP form aggregates with autologous platelets, release interferon-g and trigger platelet activation and apoptosis through TCR-mediated release of cytotoxic granules. These findings of clonally expanded CD8+ T cells causing platelet activation and apoptosis provide an antibody-independent mechanism of platelet destruction, indicating that targeting specific T-cell clones could be a novel therapeutic approach for patients with refractory ITP

‘Scrutinised, judged and sabotaged’: A qualitative video diary study of first-time breastfeeding mothers

Objective To explore how support impacted on mothers’ breastfeeding experiences in the first few weeks following birth. Design A qualitative approach explored real-time experiences of breastfeeding captured by five first-time mothers in the South of England on camcorder as video diaries. A multi-dimensional approach involving thematic analysis ensured both the audio and visual elements of the data were analysed. Findings Mothers felt ‘under surveillance’ by the biomedical approach to support from the healthcare team. At best mothers felt reassured that they were ‘on the right track’. When mothers felt their breastfeeding was constantly being examined, criticised and threatened they felt ‘scrutinised, judged and sabotaged’. When they found it difficult to access healthcare support, or they avoided it altogether to circumvent further scrutiny, they felt ‘abandoned and alone’. Key conclusions Collecting audio-visual data in real-time adds fresh insights into how support impacts mothers’ experiences of breastfeeding. The biomedical approach to support for breastfeeding is not effective. Scrutinising, judging and/or sabotaging mothers’ attempts to breastfeed can have long-lasting effects on maternal emotional wellbeing. Implications for practice Breastfeeding support might be improved by adopting a more social model of care. Future research needs to explore how relationship-based support can be provided by the health service

Risk factors for Epstein Barr virus-associated cancers: a systematic review, critical appraisal, and mapping of the epidemiological evidence

Background Epstein Barr Virus (EBV) infects 90%-95% of all adults globally and causes~1% of all cancers. Differing proportions of Burkitt’s lymphoma (BL), gastric carcinoma (GC), Hodgkin’s lymphoma (HL) and nasopharyngeal carcinoma (NPC) are associated with EBV. We sought to systematically review the global epidemiological evidence for risk factors that (in addition to EBV) contribute to the development of the EBV-associated forms of these cancers, assess the quality of the evidence, and compare and contrast the cancers. Methods MEDLINE, Embase and Web of Science were searched for studies of risk factors for EBV-associated BL, GC, HL and NPC without language or temporal restrictions. Studies were excluded if there was no cancer-free comparator group or where analyses of risk factors were inadequately documented. After screening and reference list searching, data were extracted into standardised spreadsheets and quality assessed. Due to heterogeneity, a narrative synthesis was undertaken. Results 9916 hits were retrieved. 271 papers were retained: two BL, 24 HL, one GC and 244 NPC. The majority of studies were from China, North America and Western Europe. Risk factors were categorised as dietary, environmental/non-dietary, human genetic, and infection and clinical. Anti-EBV antibody load was associated with EBV-associated GC and BL. Although the evidence could be inconsistent, HLA-A alleles, smoking, infectious mononucleosis and potentially other infections were risk factors for EBV-associated HL. Rancid dairy products; anti-EBV antibody and EBV DNA load; history of chronic ear, nose and/or throat conditions; herbal medicine use; family history; and human genetics were risk factors for NPC. Fresh fruit and vegetable and tea consumption may be protective against NPC. Conclusions Many epidemiological studies of risk factors in addition to EBV for the EBV-associated forms of BL, GC, HL and NPC have been undertaken, but there is a dearth of evidence for GC and BL. Available evidence is of variable quality. The aetiology of EBV-associated cancers likely results from a complex intersection of genetic, clinical, environmental and dietary factors, which is difficult to assess with observational studies. Large, carefully designed, studies need to be strategically undertaken to harmonise and clarify the evidence. Registration PROSPERO CRD4201705980

The effect of ring expansion in thienobenzo[b]indacenodithiophene polymers for organic field-effect transistors

A fused donor, thienobenzo[b]indacenodithiophene (TBIDT), was designed and synthesized using a novel acid-promoted cas-cade ring closure strategy, and copolymerized with a benzothiadiazole (BT) monomer. The backbone of TBIDT is an expan-sion of the well-known indacenodithiophene (IDT) unit and was expected to enhance the charge carrier mobility, by improving backbone planarity and facilitating short-contacts between polymer chains. However, the optimized field-effect transistors demonstrated an average saturation hole mobility of 0.9 cm2 V−1s−1, lower than the performance of IDT-BT (~1.5 cm2 V−1s−1). Mobilities extracted from time-resolved microwave conductivity (TRMC) measurements were consistent with the trend in hole mobilities in OFET devices. Scanning Tunneling Microscopy (STM) measurements and computational modelling illustrated that TBIDT-BT exhibits a less ordered microstructure in comparison to IDT-BT. This reveals that a regular side chain pack-ing density, independent of conformational isomers, is critical to avoid local free volume due to irregular packing, which can host trapping impurities. DFT calculations indicated that TBIDT-BT, despite containing a larger, planar unit, showed less stabilization of planar backbone geometries, in comparison to IDT-BT. This is due to the reduced electrostatic stabilizing inter-actions between the peripheral thiophene of the fused core with the BT unit, resulting in a reduction of the barrier to rotation around the single bond. These insights provide a greater understanding of the general structure-property relationships required for semiconducting polymer repeat units to ensure optimal backbone planarization, as illustrated with IDT-type units, guiding the design of novel semiconducting polymers with extended fused backbones for high-performance field-effect transistors

Learn2Reg: comprehensive multi-task medical image registration challenge, dataset and evaluation in the era of deep learning

Image registration is a fundamental medical image analysis task, and a wide variety of approaches have been proposed. However, only a few studies have comprehensively compared medical image registration approaches on a wide range of clinically relevant tasks. This limits the development of registration methods, the adoption of research advances into practice, and a fair benchmark across competing approaches. The Learn2Reg challenge addresses these limitations by providing a multi-task medical image registration data set for comprehensive characterisation of deformable registration algorithms. A continuous evaluation will be possible at https://learn2reg.grand-challenge.org. Learn2Reg covers a wide range of anatomies (brain, abdomen, and thorax), modalities (ultrasound, CT, MR), availability of annotations, as well as intra- and inter-patient registration evaluation. We established an easily accessible framework for training and validation of 3D registration methods, which enabled the compilation of results of over 65 individual method submissions from more than 20 unique teams. We used a complementary set of metrics, including robustness, accuracy, plausibility, and runtime, enabling unique insight into the current state-of-the-art of medical image registration. This paper describes datasets, tasks, evaluation methods and results of the challenge, as well as results of further analysis of transferability to new datasets, the importance of label supervision, and resulting bias. While no single approach worked best across all tasks, many methodological aspects could be identified that push the performance of medical image registration to new state-of-the-art performance. Furthermore, we demystified the common belief that conventional registration methods have to be much slower than deep-learning-based methods