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Background The SARS-Cov-2 Omicron variant demonstrates rapid spread but with reduced disease severity. Studies evaluating the lung imaging findings of Omicron infection versus non-Omicron variants remain lacking. Purpose To compare Omicron and Delta variants of SARS-CoV-2 by their chest CT radiological pattern, biochemical parameters, clinical severity and hospital outcomes after adjusting for vaccination status. Materials and Methods Retrospective study of hospitalized adult patients rt-PCR positive for SARS-CoV-2 with CT pulmonary angiography performed within 7 days of admission between December 1, 2021 and January 14, 2022. Blinded radiological analysis with multiple readers including RSNA CT classification, chest CT severity score (CT-SS, range 0 least severe to 25 most severe) and CT imaging features including bronchial wall thickening. Results 106 patients (Delta n=66, Omicron n=40) were evaluated (mean age, 58 years ± 18, 58 men). In the Omicron group, 37% (15/40) of CT pulmonary angiograms were categorized as normal compared with 15% (10/66) in the Delta group (p=.016). Using a generalized linear model to control for confounding variables, including vaccination status, Omicron variant infection was associated with a CT-SS that was lower by 7.2 points compared to infection with Delta variant (β=-7.2, 95%CI: -9.9, -4.5; p

Permanently implanted devices that deliver electrical stimulation are increasingly used to treat patients with drug-resistant epilepsy. Primary care physicians, neurologists, and epilepsy clinicians may encounter patients with a variety of implanted neuromodulation devices in the course of clinical care. Due to the rapidly changing landscape of available epilepsy-related neurostimulators, there may be uncertainty related to how these devices should be handled during imaging procedures and perioperative care. We review the safety and management of epilepsy-related implanted neurostimulators that may be encountered during imaging and surgery. We provide a summary of approved device labeling and recommendations for the practical management of these devices to help guide clinicians as they care for patients treated with bioelectronic medicine.

The Dead Sea is a hypersaline terminal lake whose level has been declining due to anthropogenic stresses since the 1960s. At its eastern shore, near Ghor-Al-Haditha in Jordan, over 1200 collapse sinkholes have been mapped roughly parallel to the shoreline from the 1980s until 2017. This mapping also documented five larger karstic depressions (uvalas), that formed in close spatial-temporal association with the sinkholes, and demonstrated that sinkhole and uvala formation during this period has migrated laterally, both in the direction of shoreline retreat (from east to west) and parallel with the shoreline from south to north.Here, we use new, high-resolution optical satellite imagery from the Pleiades and PNEO satellites, to show that over 500 new sinkholes have formed between 2018-2022. Furthermore, three new uvalas have developed to the north in accordance with the appearance of the sinkholes. Our study indicates quantitatively that the coalescence of sinkholes to form larger compound sinkholes is a subsequent stage of uvala development. New mapping confirms a previously established link between sinkhole size distribution and the mechanical properties of the sedimentary materials in which they form, with holes formed in salt-dominated morphologies being smaller in diameter than those in alluvium and lacustrine mudflats. Initial comparison to local meteorological records has shown that a temporal link between periods of high rainfall and enhanced sinkhole formation is not readily apparent at the resolution of the sinkhole mapping. Moreover, as previous studies had hypothesized, growth of the sinkhole population and the uvalas continues towards the north and is diminished to the south. Our results help to inform hazard monitoring and mitigation strategies at Ghor Al-Haditha: for example, presently growing areas of surface depressions are within 130 meters of a 700-meter-long stretch of the western main highway connecting the north and south of Jordan. Therefore, we suggest that infrastructure such as the highway continue to be monitored in light of the observed subsidence.

In early 2020, a group of geoscientists and other experts came together, within the framework of the Irish Centre for Research in Applied Geoscience (iCRAG), to learn about the challenges experienced by researchers in iCRAG, and to identify ways to work together to create a more inclusive environment. However, it was swiftly realised that these issues were manifest across the geosciences, and that any meaningful changes would need to be structural and widespread. This led to the formation of the Equity, Diversity and Inclusion in Geoscience (EDIG) project: a volunteer-led, virtual initiative, aiming to make geoscience more inclusive, accessible, and equitable. The EDIG project strives to improve awareness of the impact of prejudice, bias, exclusion, discrimination and other experiences within the larger geoscience community and to create strategies and networks to tackle inequities within geoscience.To help us better understand the challenges faced across the geoscience community, we ran an anonymous survey asking people about their experiences (or lack of) with equality, diversity, and inclusion related topics. The results of the survey helped to structure an online, free conference run over three days in December 2020. This inaugural event aimed to amplify the voices and experiences of underrepresented groups in geoscience in regard to equity, diversity and inclusion, drawing on the knowledge of 17 speakers from geoscience communities around the world.From the conversations at the 2020 event, we decided to expand outwards, opening our committee up to new volunteers and developing new projects to address barriers and challenges holistically. Many of these projects have involved collaborations with other initiatives and groups, including focused workshops (e.g., early career researcher barriers in Ireland) and are leading to new resources to help reach a wider network. In November 2022, we ran our second virtual conference, which sought to shift the conversation beyond increasing awareness toward strategies for action, and along with our original focus on improving awareness included sessions on data (collection, use, challenges) and how we might influence the future of equity, diversity and inclusion in geoscience.Going forward, our focus is to grow our network by building greater international links with other like-minded organisations (we’ve discovered that many people want to be involved, which is great!). We want to create a platform for us all to come together to work towards a more equitable and just geoscientific community. We also aim to raise awareness of the vital contributions of minoritized groups to geoscientific knowledge and the damaging consequences of their marginalisation and oppression in the history of our science. Only by creating a global network of supporters and activists can we hope to improve the diversity and inclusivity of our science. Let’s all come together to listen, learn and move forward together.

There is a growing appreciation for membraneless organelles (MLOs) in regulating cellular stress responses. Here, we demonstrate a role for the nuclear paraspeckle, a highly ordered biomolecular condensate that nucleates on theNeat1lncRNA, in both activating and repressing innate immune gene expression in murine macrophages. In response to a variety of innate agonists, macrophages rapidly upregulate and then downregulate paraspeckles. Paraspeckle maintenance and aggregation requires active transcription and MAPK signaling. Downregulation of paraspeckles, an adaptation seemingly unique to macrophages, is mediated by the nuclear RNA exosome, via degradation ofNeat1. Primary macrophages lackingNeat1(Neat1KO) misregulate many critical inflammatory cytokines, with a failure to upregulate genes likeIl6andCxcl9and to downregulate others (e.g.,Csf3andVegfa), at the transcript and protein levels in response to lipopolysaccharide (LPS) treatment. We propose that dynamic assembly and disassembly of paraspeckles help macrophages mount an innate immune response by controlling the availability of RNA processing machineries in the nucleus. Collectively, these data argue that stress-responsive biomolecular condensates play a prominent role in modulating immune cell function.

While the signaling cascades and transcription factors that turn on expression of innate immune genes are well-characterized, the role of RNA binding proteins in activating and sustaining the innate immune response is poorly understood. Members of the serine/arginine-rich (SR) family of mRNA processing factors play diverse roles in transcription, pre-mRNA splicing, export, and translation. Transcriptomic analysis of murine macrophage cell lines revealed that one such SR protein, SRSF7, is required for optimal expression of interferon stimulated genes (ISGs) at rest and in response to a variety of innate immune stimuli in a splicing-independent fashion. We demonstrate that SRSF7 is necessary and sufficient to drive expression of interferon regulatory transcription factor 7 (IRF7), an important activator of the type I IFN response in resting and LPS-treated macrophages. By associating with theIrf7promoter, SRSF7 maximizes binding of the STAT1 transcription factor and promotes RNA polymerase II elongation. These studies define an unorthodox role for an SR protein in activating transcription and highlight the importance of RNA binding proteins in shaping the macrophage innate immune response to pathogens.

IFNγ is an immune mediator with concomitant pro- and anti-tumor functions. Here, we provide evidence that IFNγ directly acts on intra-tumoral CD8 T cells to restrict anti-tumor responses. We report that expression of the IFNγ receptor β chain (IFNγR2) in CD8 T cells negatively correlates with clinical responsiveness to checkpoint blockade in metastatic melanoma patients, suggesting that the loss of sensitivity to IFNγ contributes to successful antitumor immunity. Indeed, specific deletion of IFNγR in CD8 T cells promotes tumor control in a mouse model of melanoma. Chronic IFNγ inhibits the maintenance, clonal diversity and proliferation of stem-like T cells. This leads to decreased generation of T cells with intermediate expression of exhaustion markers, previously associated with beneficial anti-tumor responses. This study provides evidence of a negative feedback loop whereby IFNγ depletes stem-like T cells to restrict anti-tumor immunity. Targeting this pathway might represent an alternative strategy to enhance T cell-based therapies.

Immune checkpoint blockade (ICB) has markedly improved outcomes across a range of tumours, including metastatic melanoma (MM). However, peripheral biomarkers of response remain lacking and underlying mechanisms of action incompletely described. A number of studies have demonstrated the value of T cell receptor (TCR) repertoire analysis in determining associations with response, however identifying key groups of T cells based on their TCR usage has remained elusive. Here we performed deep sequencing of the TCR of CD8+T cells isolated from peripheral blood of patients receiving ICB for MM (n=91) at multiple time points, along with healthy control samples (n=42) and resected tumour specimens (from n=7 patients). Using the GLIPH2 algorithm to cluster TCR based on putative shared antigen specificity, we describe groups of TCR which expand post-ICB in responding patients which we term ‘Emergent Responder’ (ER) clones. We find that these ER clones are typically large and of a memory phenotype, with increased expression of genes encoding cytotoxic proteins. Analysis of tumours resected in advance of ICB demonstrates ER clones are enriched and expanded within the tumour compared to the periphery at pre-treatment. Significantly, we note the proportion of the peripheral repertoire occupied by ER clones strongly correlates with long-term clinical response. Clinical outcome further associated with HLA type and, crucially, can be validated across replication and independent datasets. This work provides the first-in-kind description of TCR-defined CD8+T cells that mediate the response to ICB in MM, demonstrating the prognostic utility of the peripheral immune repertoire with potential widespread therapeutic and prognostic applications.

Cocirculation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and influenza viruses could pose unpredictable risks to health systems globally, with recent studies suggesting more severe disease outcomes in coinfected patients. The initial lack of a readily available coronavirus disease 2019 (COVID-19) vaccine has reinforced the importance of influenza vaccine programs during the COVID-19 pandemic. Live attenuated influenza vaccine (LAIV) is an important tool in protecting against influenza, particularly in children. However, it is unknown whether LAIV administration influences the outcomes of acute SARS-CoV-2 infection or disease. To investigate this, quadrivalent LAIV was administered to ferrets 3 days before or after SARS-CoV-2 infection. LAIV administration did not exacerbate the SARS-CoV-2 disease course or lung pathology with either regimen. In addition, LAIV administered before SARS-CoV-2 infection significantly reduced SARS-CoV-2 replication and shedding in the upper respiratory tract. This study demonstrated that LAIV administration in close proximity to SARS-CoV-2 infection does not exacerbate mild disease and can reduce SARS-CoV-2 shedding.

SARS-CoV-2 remains a global threat to human health particularly as escape mutants emerge. There is an unmet need for effective treatments against COVID-19 for which neutralizing single domain antibodies (nanobodies) have significant potential. Their small size and stability mean that nanobodies are compatible with respiratory administration. We report four nanobodies (C5, H3, C1, F2) engineered as homotrimers with pmolar affinity for the receptor binding domain (RBD) of the SARS-CoV-2 spike protein. Crystal structures show C5 and H3 overlap the ACE2 epitope, whilst C1 and F2 bind to a different epitope. Cryo Electron Microscopy shows C5 binding results in an all down arrangement of the Spike protein. C1, H3 and C5 all neutralize the Victoria strain, and the highly transmissible Alpha (B.1.1.7 first identified in Kent, UK) strain and C1 also neutralizes the Beta (B.1.35, first identified in South Africa). Administration of C5-trimer via the respiratory route showed potent therapeutic efficacy in the Syrian hamster model of COVID-19 and separately, effective prophylaxis. The molecule was similarly potent by intraperitoneal injection., Neutralizing nanobodies (Nb) are of considerable interest as therapeutic agents for COVID-19 treatment. Here, the authors functionally and structurally characterize Nbs that bind with high affinity to the receptor binding domain of the SARS-CoV-2 spike protein and show that an engineered homotrimeric Nb prevents disease progression in a Syrian hamster model of COVID-19 when administered intranasally.

Development of anti-drug antibodies (ADAs) can interfere with therapeutic monoclonal antibodies and may lead to drug neutralisation and clinical disease progression. Measurement of circulating drug levels and development of ADAs in the setting of anti-programmed cell death-1 agent pembrolizumab has not been well-studied. Enzyme-linked immunosorbent assays were used to measure pembrolizumab drug level and ADAs in 41 patients with melanoma at baseline, Time-point 1 (3 weeks) and Time-point 2 (21 weeks). Assay results were related to patient demographics and clinical outcome data at 6 months. The median pembrolizumab drug level at 3 weeks was 237 ng/μL and did not correlate with age, sex or body surface area.17/41 patients had an ADA detected at any timepoint, with the highest prevalence at Timepoint 1 (median concentration = 17 ng/μL). The presence of an ADA did not correlate with clinical progression at 6 months. 3/41 (7%) of patients displayed a falling pembrolizumab drug level and rising ADA titre between Timepoint 1 and 2 suggestive of a neutralising ADA. Pembrolizumab drug levels and ADAs can be readily measured. The rates of total and treatment-emergent ADAs may be higher in “real-word” settings than those previously reported. Larger studies are needed to determine effect of neutralising ADAs on long-term clinical outcome.

Map-making is an important step for the data analysis of cosmic microwave background (CMB) experiments. It consists of converting the data, which are typically a long, complex, and noisy collection of measurements, into a map, which is an image of the observed sky. We present in this paper a new map-making code named PICASSO (Polarization and Intensity CArtographer for Scanned Sky Observations), which was implemented to construct intensity and polarization maps from the Multi Frequency Instrument (MFI) of the QUIJOTE (Q-U-I Joint TEnerife) CMB polarization experiment. PICASSO is based on the destriping algorithm, and is suited to address specific issues of ground-based microwave observations, with a technique that allows the fit of a template function in the time domain, during the map-making step. This paper describes the PICASSO code, validating it with simulations and assessing its performance. For this purpose, we produced realistic simulations of the QUIJOTE-MFI survey of the northern sky (approximately ∼20 000 deg2), and analysed the reconstructed maps with PICASSO, using real and harmonic space statistics. We show that, for this sky area, PICASSO is able to reconstruct, with high fidelity, the injected signal, recovering all the scales with ℓ > 10 in TT, EE, and BB. The signal error is better than 0.001 per cent at 20 < ℓ < 200. Finally, we validated some of the methods that will be applied to the real wide-survey data, like the detection of the CMB anisotropies via cross-correlation analyses. Despite that the implementation of PICASSO is specific for QUIJOTE-MFI data, it could be adapted to other experiments., Partial financial support is provided by the Spanish Ministry of Science, Innovation and Universities under the projects AYA2007-68058-C03-01, AYA2010-21766-C03-02, AYA2014-60438-P, AYA2017-84185-P, IACA13-3E-2336, IACA15-BE-3707, EQC2018-004918-P, the Severo Ochoa Program SEV-2015-0548, and also by the Consolider-Ingenio project CSD2010-00064 (EPI: Exploring the Physics of Inflation). This project has received funding from the European Union’s Horizon 2020 research and innovation program under grant agreement number 687312 (RADIOFOREGROUNDS). RBB and JDBA acknowledge the Spanish Agencia Estatal de Investigación (AEI, MICIU) for the financial support provided under the projects with references PID2019-110610RB-C21, ESP2017-83921-C2-1-R, and AYA2017-90675-REDC, co-funded with EU FEDER funds, and also acknowledge the funding from Unidad de Excelencia María de Maeztu (MDM-2017-0765).

Second-generation bromodomain and extra terminal (BET) inhibitors, which selectively target one of the two bromodomains in the BET proteins, have begun to emerge in the literature. These inhibitors aim to help determine the roles and functions of each domain and assess whether they can demonstrate an improved safety profile in clinical settings compared to pan-BET inhibitors. Herein, we describe the discovery of a novel BET BD2-selective chemotype using a structure-based drug design from a hit identified by DNA-encoded library technologies, showing a structural differentiation from key previously reported greater than 100-fold BD2-selective chemotypes GSK620, GSK046, and ABBV-744. Following a structure-based hypothesis for the selectivity and optimization of the physicochemical properties of the series, we identified 60 (GSK040), an in vitro ready and in vivo capable BET BD2-inhibitor of unprecedented selectivity (5000-fold) against BET BD1, excellent selectivity against other bromodomains, and good physicochemical properties. This novel chemical probe can be added to the toolbox used in the advancement of epigenetics research.

Domain-specific BET bromodomain ligands represent an attractive target for drug discovery with the potential to unlock the therapeutic benefits of antagonizing these proteins without eliciting the toxicological aspects seen with pan-BET inhibitors. While we have reported several distinct classes of BD2 selective compounds, namely, GSK620, GSK549, and GSK046, only GSK046 shows high aqueous solubility. Herein, we describe the lead optimization of a further class of highly soluble compounds based upon a picolinamide chemotype. Focusing on achieving >1000-fold selectivity for BD2 over BD1 ,while retaining favorable physical chemical properties, compound 36 was identified as being 2000-fold selective for BD2 over BD1 (Brd4 data) with >1 mg/mL solubility in FaSSIF media. 36 represents a valuable new in vivo ready molecule for the exploration of the BD2 phenotype.

Event: SPIE Astronomical Telescopes + Instrumentation, 2022, Montréal, Québec, Canada., et al., The QUIJOTE (Q-U-I joint Tenerife) experiment combines the operation of two radio-telescopes and three instruments working in the microwave bands 10–20 GHz, 26–36 GHz and 35–47 GHz at the Teide Observatory, Tenerife, and has already been presented in previous SPIE meetings (Hoyland, R. J. et al, 2012; Rubi˜no-Mart´ın et al., 2012). The Cosmology group at the IAC have designed a new upgrade to the MFI instrument in the band 10–20 GHz. The aim of the QUIJOTE telescopes is to characterise the polarised emission of the cosmic microwave background (CMB), as well as galactic and extra-galactic sources, at medium and large angular scales. This MFI2 will continue the survey at even higher sensitivity levels. The MFI2 project led by the Instituto de Astrof´ısica de Canarias (IAC) consists of five polarimeters, three of them operating in the sub-band 10–15 GHz, and two in the sub-band 15–20 GHz. The MFI2 instrument is expected to be a full two–three times more sensitive than the former MFI. The microwave complex correlator design has been replaced by a simple correlator design with a digital back-end based on the latest Xilinx FPGAs (ZCU111). During the first half of 2019 the manufacture of the new cryostat was completed and since then the opto-mechanical components have been designed and manufactured. It is expected that the cryogenic front-end will be completed by the end of 2022 along with the FPGA acquisition and observing system. This digital system has been employed to be more robust against stray ground-based and satellite interference, having a frequency resolution of 1 MHz., Partial financial support is provided by the Spanish Ministry of Science and Innovation (MICINN), under the projects AYA2017-84185-P, IACA15-BE-3707, EQC2018-004918-P and the FEDER Agreement INSIDE-OOCC (ICTS-2019-03-IAC-12). We also acknowledge financial support of the Severo Ochoa Programs SEV-2015-0548 and CEX2019-000920-S.

Background SP140 is a bromodomain-containing protein expressed predominantly in immune cells. Genetic polymorphisms and epigenetic modifications in the SP140 locus have been linked to Crohn’s disease (CD), suggesting a role in inflammation. Results We report the development of the first small molecule SP140 inhibitor (GSK761) and utilize this to elucidate SP140 function in macrophages. We show that SP140 is highly expressed in CD mucosal macrophages and in in vitro-generated inflammatory macrophages. SP140 inhibition through GSK761 reduced monocyte-to-inflammatory macrophage differentiation and lipopolysaccharide (LPS)-induced inflammatory activation, while inducing the generation of CD206+ regulatory macrophages that were shown to associate with a therapeutic response to anti-TNF in CD patients. SP140 preferentially occupies transcriptional start sites in inflammatory macrophages, with enrichment at gene loci encoding pro-inflammatory cytokines/chemokines and inflammatory pathways. GSK761 specifically reduces SP140 chromatin binding and thereby expression of SP140-regulated genes. GSK761 inhibits the expression of cytokines, including TNF, by CD14+ macrophages isolated from CD intestinal mucosa. Conclusions This study identifies SP140 as a druggable epigenetic therapeutic target for CD.

To mount a protective response to infection while preventing hyperinflammation, gene expression in innate immune cells must be tightly regulated. Despite the importance of pre-mRNA splicing in shaping the proteome, its role in balancing immune outcomes remains understudied. Transcriptomic analysis of murine macrophage cell lines identified Serine/Arginine Rich Splicing factor 6 (SRSF6) as a gatekeeper of mitochondrial homeostasis. SRSF6-dependent orchestration of mitochondrial health is directed in large part by alternative splicing of the pro-apoptosis pore-forming protein BAX. Loss of SRSF6 promotes accumulation of BAX-κ, a variant that sensitizes macrophages to undergo cell death and triggers upregulation of interferon stimulated genes through cGAS sensing of cytosolic mitochondrial DNA. Upon pathogen sensing, macrophages regulate SRSF6 expression to control the liberation of immunogenic mtDNA and adjust the threshold for entry into programmed cell death. This work defines BAX alternative splicing by SRSF6 as a critical node not only in mitochondrial homeostasis but also in the macrophage’s response to pathogens.

Natural Killer cells are innate lymphocytes with central roles in immunosurveillance and are implicated in autoimmune pathogenesis. The degree to which regulatory variants affect Natural Killer cell gene expression is poorly understood. Here we perform expression quantitative trait locus mapping of negatively selected Natural Killer cells from a population of healthy Europeans (n = 245). We find a significant subset of genes demonstrate expression quantitative trait loci specific to Natural Killer cells and these are highly informative of human disease, in particular autoimmunity. A Natural Killer cell transcriptome-wide association study across five common autoimmune diseases identifies further novel associations at 27 genes. In addition to these cis observations, we find novel master-regulatory regions impacting expression of trans gene networks at regions including 19q13.4, the Killer cell Immunoglobulin-like Receptor region, GNLY, MC1R and UVSSA. Our findings provide new insights into the unique biology of Natural Killer cells, demonstrating markedly different expression quantitative trait loci from other immune cells, with implications for disease mechanisms.

A number of reports have recently been published describing the discovery and optimization of bromo and extraterminal inhibitors which are selective for the second bromodomain (BD2); these include our own work toward GSK046 (3) and GSK620 (5). This paper describes our approach to mitigating the genotoxicity risk of GSK046 by replacement of the acetamide functionality with a heterocyclic ring. This was followed by a template-hopping and hybridization approach, guided by structure-based drug design, to incorporate learnings from other BD2-selective series, optimize the vector for the amide region, and explore the ZA cleft, leading to the identification of potent, selective, and bioavailable compounds 28 (GSK452), 39 (GSK737), and 36 (GSK217).

Background Immune checkpoint blockers (ICBs) activate CD8+ T cells, eliciting both anti-cancer activity and immune-related adverse events (irAEs). The relationship of irAEs with baseline parameters and clinical outcome is unclear. Methods Retrospective evaluation of irAEs on survival was performed across primary (N = 144) and secondary (N = 211) independent cohorts of patients with metastatic melanoma receiving single agent (pembrolizumab/nivolumab—sICB) or combination (nivolumab and ipilimumab—cICB) checkpoint blockade. RNA from pre-treatment and post-treatment CD8+ T cells was sequenced and differential gene expression according to irAE development assessed. Results 58.3% of patients developed early irAEs and this was associated with longer progression-free (PFS) and overall survival (OS) across both cohorts (log-rank test, OS: P P = 2.8 × 10−6). Pre-treatment monocyte and neutrophil counts, but not BMI, were additional predictors of clinical outcome. Differential expression of numerous gene pathway members was observed in CD8+ T cells according to irAE development, and patients not developing irAEs demonstrating upregulated CXCR1 pre- and post-treatment. Conclusions Early irAE development post-ICB is associated with favourable survival in MM. Development of irAEs is coupled to expression of numerous gene pathways, suggesting irAE development in-part reflects baseline immune activation.

A novel coronavirus, SARS-CoV-2, has been identified as the causative agent of the current COVID-19 pandemic. Animal models, and in particular non-human primates, are essential to understand the pathogenesis of emerging diseases and to assess the safety and efficacy of novel vaccines and therapeutics. Here, we show that SARS-CoV-2 replicates in the upper and lower respiratory tract and causes pulmonary lesions in both rhesus and cynomolgus macaques. Immune responses against SARS-CoV-2 are also similar in both species and equivalent to those reported in milder infections and convalescent human patients. This finding is reiterated by our transcriptional analysis of respiratory samples revealing the global response to infection. We describe a new method for lung histopathology scoring that will provide a metric to enable clearer decision making for this key endpoint. In contrast to prior publications, in which rhesus are accepted to be the preferred study species, we provide convincing evidence that both macaque species authentically represent mild to moderate forms of COVID-19 observed in the majority of the human population and both species should be used to evaluate the safety and efficacy of interventions against SARS-CoV-2. Importantly, accessing cynomolgus macaques will greatly alleviate the pressures on current rhesus stocks., Non-human primates are important animal models for studying SARS-CoV-2 infection. Here, Salguero et al. directly compare rhesus and cynomolgus macaques and show that both species represent COVID-19 disease of mild clinical cases, and provide a lung histopathology scoring system.

Multiple factors, including tight patient scheduling, complex electronic medical records, and increasing numbers of implanted devices, increase chances of MR imaging safety event occurrence. Several MR imaging safety incidents are described in this article, including the safety conditions and other factors that contributed to the events. MR imaging safety policy and procedural improvements that address these are also described. Specific new revision points in the American College of Radiology Manual on MR Safety are viewed in the context of these events, with emphasis on how their implementation could reduce probability of similar event recurrence.

New implanted medical devices continue to be made available for treatment of medical conditions. Many recipients can benefit from the diagnostic power of MR imaging. Provisions must be made to determine if these patients can be safely scanned. Metal-containing devices can be considered either MR unsafe or conditional. It is essential that all components of an implanted system are completely and accurately identified, with the most restrictive MR safety condition dictating the scanning approach. MR safety considerations for major classes of implanted devices are discussed, recognizing that there have been reports of serious device-related MR safety incidents.

OBJECTIVE To evaluate adverse events and feasibility of performing 1.5-T MRI in patients with cochlear implants (CI) and auditory brainstem implants (ABI). SETTING Single tertiary academic referral center. PATIENTS CI and ABI recipients undergoing 1.5-T MRI without internal magnet removal. INTERVENTION(S) MRI after tight headwrap application. MAIN OUTCOME MEASURES Adverse events, patient tolerance. RESULTS A total of 131 MR studies in 79 patients were performed, with a total of 157 study ears. Sixty-one patients (77%) had unilateral devices. Four patients (5%) underwent MRI with ABI magnets in place. Sixteen patients (20%) had MRI-compatible devices that did not require a head wrap. There were no instances of device stimulation, device malfunction, or excessive heating of the receiver-stimulator package. Magnet tilt requiring manual repositioning occurred during seven studies (4.5%) and magnet displacement requiring operative intervention occurred during seven studies (4.5%). Significant pain where imaging had to be discontinued occurred during three episodes (2%). No adverse events were noted among patients who underwent MRI with an MRI-compatible magnet. CONCLUSIONS MRI with CI or ABI magnets in place is associated with a low prevalence of adverse events when performed in a controlled setting. Many partial magnet displacements can be corrected with firm manual pressure. Devices with magnets that align with the field within their housing were not associated with any adverse events and do not require immobilization of the magnet during the scan. These may be valuable in patients with known or anticipated need for MRI.

FPGA-SoC technology provides a heterogeneous platform for advanced, high-performance systems. The System on Chip (SoC) architecture combines traditional single and multiple core processor topologies with flexible FPGA fabric. Dynamic reconfiguration allows the hardware accelerators to be changed at run-time. This article presents a novel OpenGL compliant GPU design implemented on an FPGA. The design uses an FPGA-SoC environment allowing the embedded processor to offload graphics operation onto a more suitable architecture. To the authors’ knowledge, this is a first. The graphics processor consists of GLSL compliant shaders, an efficient Barycentric Rasterizer, and a draw mode manager. Performance analysis shows the throughput of the shaders to be hundreds of millions of vertices per second. The design uses both pipelining and resource reuse to optimise throughput and resource use, allowing implementation on a low-cost, FPGA device. Pixel processing rates from this implementation are almost 80% higher than other FPGA implementations. Power consumption compared with comparative embedded devices shows the FPGA consuming as little as 2% of the power of a Mali device, and an up to 11.9-fold increase in efficiency compared to an Nvidia RTX 2060 - Turing architecture device.

Objective To provide an initial report that patients with magnetic resonance imaging (MRI) non-conditional cardiac implanted electronic device (CIED) can undergo state-of-the-art magnetic resonance imaging–guided focused (MRgFUS) ablation procedures with careful planning and integration of the procedure into an established CIED MRI practice. Patient and Methods We describe an MRgFUS ablation treatment of lumbar facet joints in a patient with an MRI non-conditional CIED (pacemaker), completed in accordance with our institutional CIED/MRI practice guidelines. Results A risk-benefit analysis by a coordinated multidisciplinary team before this treatment was performed to account for the risks associated with the MRI non-conditional pacemaker in the context of the MRgFUS procedure. Conclusion The patient had no adverse cardiac event during or following this procedure.

The profound efficacy, yet associated toxicity of pan-BET inhibitors is well documented. The possibility of an ameliorated safety profile driven by significantly selective (>100-fold) inhibition of a subset of the eight bromodomains is enticing, but challenging given the close homology. Herein, we describe the X-ray crystal structure-directed optimization of a novel weak fragment ligand with a pan-second bromodomain (BD2) bias, to potent and highly BD2 selective inhibitors. A template hopping approach, enabled by our parallel research into an orthogonal template (15, GSK046), was the basis for the high selectivity observed. This culminated in two tool molecules, 20 (GSK620) and 56 (GSK549), which showed an anti-inflammatory phenotype in human whole blood, confirming their cellular target engagement. Excellent broad selectivity, developability, and in vivo oral pharmacokinetics characterize these tools, which we hope will be of broad utility to the field of epigenetics research.

Pan-bromodomain and extra terminal domain (BET) inhibitors interact equipotently with the eight bromodomains of the BET family of proteins and have shown profound efficacy in a number of in vitro phenotypic assays and in vivo pre-clinical models in inflammation or oncology. A number of these inhibitors have progressed to the clinic where pharmacology-driven adverse events have been reported. To better understand the contribution of each domain to their efficacy and improve their safety profile, selective inhibitors are required. This article discloses the profile of GSK046, also known as iBET-BD2, a highly selective inhibitor of the second bromodomains of the BET proteins that has undergone extensive pre-clinical in vitro and in vivo characterization.

Pan-bromodomain and extra terminal (BET) inhibitors interact equipotently with all eight bromodomains of the BET family of proteins. They have shown profound efficacy in vitro and in vivo in oncology and immunomodulatory models, and a number of them are currently in clinical trials where significant safety signals have been reported. It is therefore important to understand the functional contribution of each bromodomain to assess the opportunity to tease apart efficacy and toxicity. This article discloses the in vitro and cellular activity profiles of GSK789, a potent, cell-permeable, and highly selective inhibitor of the first bromodomains of the BET family.

[Image: see text] Pan-BET inhibitors have shown profound efficacy in a number of in vivo preclinical models and have entered the clinic in oncology trials where adverse events have been reported. These inhibitors interact equipotently with the eight bromodomains of the BET family of proteins. To better understand the contribution of each domain to their efficacy and to improve from their safety profile, selective inhibitors are required. This Letter discloses the profile of GSK973, a highly selective inhibitor of the second bromodomains of the BET proteins that has undergone extensive preclinical in vitro and in vivo characterization.

Tripartite motif-containing proteins (TRIMs) play a variety of recently described roles in innate immunity. Although many TRIMs regulate type I IFN expression following cytosolic nucleic acid sensing of viruses, their contribution to innate immune signaling and gene expression during bacterial infection remains largely unknown. Because Mycobacterium tuberculosis is an activator of cGAS-dependent cytosolic DNA sensing, we set out to investigate a role for TRIM proteins in regulating macrophage responses to M. tuberculosis. In this study, we demonstrate that TRIM14, a noncanonical TRIM that lacks an E3 ubiquitin ligase RING domain, is a critical negative regulator of the type I IFN response in Mus musculus macrophages. We show that TRIM14 interacts with both cGAS and TBK1 and that macrophages lacking TRIM14 dramatically hyperinduce IFN stimulated gene (ISG) expression following M. tuberculosis infection, cytosolic nucleic acid transfection, and IFN-β treatment. Consistent with a defect in resolution of the type I IFN response, Trim14 knockout macrophages have more phospho-Ser754 STAT3 relative to phospho-Ser727 and fail to upregulate the STAT3 target Socs3, which is required to turn off IFNAR signaling. These data support a model whereby TRIM14 acts as a scaffold between TBK1 and STAT3 to promote phosphorylation of STAT3 at Ser727 and resolve ISG expression. Remarkably, Trim14 knockout macrophages hyperinduce expression of antimicrobial genes like Nos2 and are significantly better than control cells at limiting M. tuberculosis replication. Collectively, these data reveal an unappreciated role for TRIM14 in resolving type I IFN responses and controlling M. tuberculosis infection.

This research aims at developing and applying a machine learning based algorithm to detect geological structural features at the exposed Dead Sea shoreline. We focus on sinkhole, stream-channel and crack features that appear in different material at the coastlines, and post partly a threat for the local population and infrastructure. We use high resolution orthophotos and satellite images from the last years, as well as derived topographic models to reach an automatic identification and classification of these structures. The aim is to train a convolutional neural network that can identify these structures on recent datasets from satellite images in order to establish an automated detection of hazardous and active zones in the area. Furthermore, we use the algorithms to detect structures in the shallow waters of the lake.

Treatment with immune checkpoint blockade (ICB) frequently triggers immune-related adverse events (irAEs), causing considerable morbidity. In 214 patients receiving ICB for melanoma, we observed increased severe irAE risk in minor allele carriers of rs16906115, intronic to IL7. We found that rs16906115 forms a B cell-specific expression quantitative trait locus (eQTL) to IL7 in patients. Patients carrying the risk allele demonstrate increased pre-treatment B cell IL7 expression, which independently associates with irAE risk, divergent immunoglobulin expression and more B cell receptor mutations. Consistent with the role of IL-7 in T cell development, risk allele carriers have distinct ICB-induced CD8+ T cell subset responses, skewing of T cell clonality and greater proportional repertoire occupancy by large clones. Finally, analysis of TCGA data suggests that risk allele carriers independently have improved melanoma survival. These observations highlight key roles for B cells and IL-7 in both ICB response and toxicity and clinical outcomes in melanoma.

The mutation profile of the SARS-CoV-2 Omicron (lineage BA.1) variant posed a concern for naturally acquired and vaccine-induced immunity. We investigated the ability of prior infection with an early SARS-CoV-2 ancestral isolate (Australia/VIC01/2020, VIC01) to protect against disease caused by BA.1. We established that BA.1 infection in naïve Syrian hamsters resulted in a less severe disease than a comparable dose of the ancestral virus, with fewer clinical signs including less weight loss. We present data to show that these clinical observations were almost absent in convalescent hamsters challenged with the same dose of BA.1 50 days after an initial infection with ancestral virus. These data provide evidence that convalescent immunity against ancestral SARS-CoV-2 is protective against BA.1 in the Syrian hamster model of infection. Comparison with published pre-clinical and clinical data supports consistency of the model and its predictive value for the outcome in humans. Further, the ability to detect protection against the less severe disease caused by BA.1 demonstrates continued value of the Syrian hamster model for evaluation of BA.1-specific countermeasures.

Pain may be a modifiable risk factor for lower health-related quality of life after pediatric critical illness.To evaluate the association between severe pain experienced in the (pediatrc intensive care unit) and postdischarge health-related quality of life.This was a retrospective cohort study. Children aged 1 month to 18 years admitted to the pediatric intensive care unit and enrolled in the Seattle Children's Hospital Outcomes Assessment Program were included. Pain was assessed every 2 h by bedside nursing staff using a behavioral pain scale or numeric pain scale. A day of severe pain was defined as a pediatric intensive care unit day with ≥25% of pain scores ≥7/10. Baseline (preadmission) and postdischarge (median 6 weeks) health-related quality of life was assessed by the Pediatric Quality of Life Inventory (PedsQL™) or the Stein Jessop Functional Status II-R (FS II-R, for children with developmental disability). The cohort was stratified by diagnosis category (surgical vs. medical), and associations were measured using linear regression models.Among 546 patients, 11.9% experienced ≥1 day of severe pain. In multivariable linear regression, each day of severe pain was independently associated with a lower postdischarge health-related quality of life score by 3.6 points (95% CI -6.3 to -0.9) adjusted for baseline health-related quality of life score, age, baseline cognitive function, days with multi-organ dysfunction, pediatric intensive care unit length of stay, and decline in overall function. This association was stronger among surgical patients than medical patients with each day of severe pain resulting in a lower postdischarge health-related quality of life score by 5.3 points (95% CI -9.6 to -0.9) versus 2.6 points (95% CI -5.8 to 0.6). Surgical patients had lower postdischarge emotional functioning than physical functioning subdomain scores.Children who experience severe pain in the pediatric intensive care unit have lower postdischarge health-related quality of life adjusting for baseline health-related quality of life, particularly among children who have undergone surgery. Attention to pain management may be important to improve postdischarge health-related quality of life.

The mutation profile of the SARS-CoV-2 Omicron variant poses a concern for naturally acquired and vaccine-induced immunity. We investigated the ability of prior infection with an early SARS-CoV-2, 99.99% identical to Wuhan-Hu-1, to protect against disease caused by the Omicron variant. We established that infection with Omicron in naïve Syrian hamsters resulted in a less severe disease than a comparable dose of prototype SARS-CoV-2 (Australia/VIC01/2020), with fewer clinical signs and less weight loss. We present data to show that these clinical observations were almost absent in convalescent hamsters challenged with the same dose of Omicron 50 days after an initial infection with Australia/VIC01/2020. The data provide evidence for immunity raised against prototype SARS-CoV-2 being protective against Omicron in the Syrian hamster model. Further investigation is required to conclusively determine whether Omicron is less pathogenic in Syrian hamsters and whether this is predictive of pathogenicity in humans.

SUMMARYHuman mutations in mitochondrial-associated genes are associated with inflammatory diseases and susceptibility to infection. However, their mechanistic contributions to immune outcomes remain ill-defined. We discovered that the disease-associated gain-of-function allele Lrrk2G2019S (leucine-rich repeat kinase 2) promotes mitochondrial hyper-fission, depolarization, and oxidative stress in macrophages. In the presence of Lrrk2G2019S-dependent mitochondrial perturbations, AIM2 inflammasome activation promotes more cell death but not more pyroptotic IL-1b release. Instead, inflammasome activation in Lrrk2G2019S macrophages triggers gasdermin D (GSDMD)-mediated mitochondrial pores, driving up ROS-mediated RIPK1/RIPK3/MLKL dependent necroptosis. Consequently, infection of Lrrk2G2019S mice with Mycobacterium tuberculosis elicits hyperinflammation and immunopathology via enhanced neutrophil infiltration. By uncovering that GSDMD promotes non-pyroptotic cell death in Lrrk2G2019S macrophages, our findings demonstrate that altered mitochondrial function can reprogram cell death modalities to elicit distinct immune outcomes. This provides mechanistic insights into why mutations in LRRK2 are associated with susceptibility to chronic inflammatory and infectious diseases.HIGHLIGHTSAltered mitochondrial homeostasis reprograms cell death modalitiesGSDMD associates with and depolarizes mitochondrial membranes following AIM2 activationGSDMD initiates a shift from pyroptotic to necroptotic cell death in Lrrk2G2019S macrophagesLrrk2G2019S elicits hyperinflammation and susceptibility to infection in flies and mice

The global pandemic of coronavirus disease (COVID-19) caused by infection with severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has led to an international thrust to study pathogenesis and evaluate interventions. Experimental infection of hamsters and the resulting respiratory disease is one of the preferred animal models since clinical signs of disease and virus shedding are similar to more severe cases of human COVID-19. The main route of challenge has been direct inoculation of the virus via the intranasal route. To resemble the natural infection, we designed a bespoke natural transmission cage system to assess whether recipient animals housed in physically separate adjacent cages could become infected from a challenged donor animal in a central cage, with equal airflow across the two side cages. To optimise viral shedding in the donor animals, a low and moderate challenge dose were compared after direct intranasal challenge, but similar viral shedding responses were observed and no discernible difference in kinetics. The results from our natural transmission set-up demonstrate that most recipient hamsters are infected within the system developed, with variation in the kinetics and levels of disease between individual animals. Common clinical outputs used for the assessment in directly-challenged hamsters, such as weight loss, are less obvious in hamsters who become infected from naturally acquiring the infection. The results demonstrate the utility of a natural transmission model for further work on assessing the differences between virus strains and evaluating interventions using a challenge system which more closely resembles human infection.

Recovery following pediatric critical illness is multifaceted and complex. While most critically ill children survive, many experience morbidities in physical, emotional, cognitive, and social function. We aimed to deeply explore and describe the multidimensional impact of pediatric septic shock for affected children and their families at the granular level using exploratory qualitative methodology. We performed semistructured telephone interviews of adolescents and caregivers of children admitted with community-acquired septic shock to two tertiary pediatric intensive care units in the United States. Interviews were conducted within two years of hospital admission, and were recorded, transcribed, and analyzed using thematic analysis. Two adolescents and 10 caregivers were interviewed. Participants described meaningful and long-lasting outcomes of septic shock on multiple dimensions of their lives. The adolescents and caregivers described substantial negative consequences on physical health and function which resulted in increased medical complexity and heightened caregiver vigilance. The physical impact led to substantial psychosocial consequences for both the child and family, including social isolation. Most caregivers expressed that septic shock was transformational in their lives, with some caregivers describing posttraumatic growth. This preliminary study provides a novel, granular view of the multidimensional impact of septic shock in pediatric patients and their families. Exploring these experiences through qualitative methodology provides greater insight into important patient and family outcomes. Deeper understanding of these outcomes may support the development of meaningful interventions to improve quality of life for children and their families following critical illness.

The antitumor action of immune checkpoint blockade (ICB) is primarily mediated by CD8(+) T cells. How sensitivity to ICB varies across CD8(+) T cell subsets and clonotypes and the relationship of these with clinical outcome is unclear. To explore this, we used single-cell V(D)J and RNA-sequencing to track gene expression changes elicited by ICB across individual peripheral CD8(+) T cell clones, identify baseline markers of CD8(+) T cell clonal sensitivity, and chart how CD8(+) T cell transcriptional changes vary according to phenotypic subset and clonal size. We identified seven subsets of CD8(+) T cells with divergent reactivity to ICB and found that the cytotoxic effector subset showed the greatest number of differentially expressed genes while remaining stable in clonal size after ICB. At the level of CD8(+) T cell clonotypes, we found a relationship between transcriptional changes and clone size, with large clones showing a greater number of differentially regulated genes enriched for pathways including T cell receptor (TCR) signaling. Cytotoxic CD8(+) effector clones were more likely to persist following ICB and were more likely to correspond with public tumor-infiltrating lymphocyte clonotypes. Last, we demonstrated that individuals whose CD8(+) T cell pretreatment showed low cytotoxicity and had fewer expanded clones typically had worse outcomes after ICB treatment. This work further advances understanding of the molecular determinants of ICB response, assisting in the search for peripheral prognostic biomarkers and highlighting the importance of the baseline CD8(+) immune landscape in determining ICB response in metastatic melanoma.

Immune checkpoint blockade (ICB) of PD-1 and CTLA-4 to treat metastatic melanoma (MM) has variable therapeutic benefit. To explore this in peripheral samples, we characterized CD8+ T cell gene expression across a cohort of patients with MM receiving anti-PD-1 alone (sICB) or in combination with anti-CTLA-4 (cICB). Whereas CD8+ transcriptional responses to sICB and cICB involve a shared gene set, the magnitude of cICB response is over fourfold greater, with preferential induction of mitosis- and interferon-related genes. Early samples from patients with durable clinical benefit demonstrated overexpression of T cell receptor–encoding genes. By mapping T cell receptor clonality, we find that responding patients have more large clones (those occupying >0.5% of repertoire) post-treatment than non-responding patients or controls, and this correlates with effector memory T cell percentage. Single-cell RNA-sequencing of eight post-treatment samples demonstrates that large clones overexpress genes implicated in cytotoxicity and characteristic of effector memory T cells, including CCL4, GNLY and NKG7. The 6-month clinical response to ICB in patients with MM is associated with the large CD8+ T cell clone count 21 d after treatment and agnostic to clonal specificity, suggesting that post-ICB peripheral CD8+ clonality can provide information regarding long-term treatment response and, potentially, facilitate treatment stratification. Transcriptomic analysis of peripheral CD8+ T cells in a cohort of patients with metastatic melanoma receiving checkpoint inhibitors shows that the number of large clones early post-treatment is strongly associated with six-month clinical outcome.

The bromodomain and extraterminal (BET) family of bromodomain-containing proteins are important regulators of the epigenome through their ability to recognize N-acetyl lysine (KAc) post-translational modifications on histone tails. These interactions have been implicated in various disease states and, consequently, disruption of BET-KAc binding has emerged as an attractive therapeutic strategy with a number of small molecule inhibitors now under investigation in the clinic. However, until the utility of these advanced candidates is fully assessed by these trials, there remains scope for the discovery of inhibitors from new chemotypes with alternative physicochemical, pharmacokinetic, and pharmacodynamic profiles. Herein, we describe the discovery of a candidate-quality dimethylpyridone benzimidazole compound which originated from the hybridization of a dimethylphenol benzimidazole series, identified using encoded library technology, with an N-methyl pyridone series identified through fragment screening. Optimization via structure- and property-based design led to I-BET469, which possesses favorable oral pharmacokinetic properties, displays activity in vivo, and is projected to have a low human efficacious dose.

OBJECTIVES The aim of this work was to devise mitigation strategies for addressing a range of image artifacts on a clinical 7 T magnetic resonance imaging scanner using the regulatory-approved single-channel radiofrequency transmit mode and vendor-supplied radiofrequency coils to facilitate clinical scanning within reasonable scan times. MATERIALS AND METHODS Optimized imaging sequence protocols were developed for routine musculoskeletal knee and neurological imaging. Sources of severe image nonuniformities were identified, and mitigation strategies were devised. A range of custom-made high permittivity dielectric pads were used to compensate for B1 and B1 inhomogeneities, and also for magnetic susceptibility-induced signal dropouts particularly in the basal regions of the temporal lobes and in the cerebellum. RESULTS Significant improvements in image uniformity were obtained using dielectric pads in the knee and brain. A combination of small voxels, reduced field of view B0 shimming, and high in-plane parallel imaging factors helped to minimize signal loss in areas of high susceptibility-induced field distortions. The high inherent signal-to-noise ratio at 7 T allowed for high receiver bandwidths and thin slices to minimize chemical shift artifacts. Intermittent artifacts due to radiofrequency inversion pulse limitations (power, bandwidth) were minimized with dielectric pads. A patient with 2 implanted metallic cranial fixation devices located within the radiofrequency transmit field was successfully imaged, with minimal image geometric distortions. CONCLUSIONS Challenges relating to severe image artifacts at 7 T using single-channel radiofrequency transmit functionality in the knee and brain were overcome using the approaches described in this article. The resultant high diagnostic image quality paves the way for incorporation of this technology into the routine clinical workflow. Further developmental efforts are required to expand the range of applications to other anatomical areas, and to expand the evidence- and knowledge-base relating to the safety of scanning patients with implanted metallic devices.

Objective To rigorously compare automated atlas‐based and manual tracing hippocampal segmentation for accuracy, repeatability, and clinical acceptability given a relevant range of imaging abnormalities in clinical epilepsy. Methods Forty‐nine patients with hippocampal asymmetry were identified from our institutional radiology database, including two patients with significant anatomic deformations. Manual hippocampal tracing was performed by experienced technologists on 3T MPRAGE images, measuring hippocampal volume up to the tectal plate, excluding the hippocampal tail. The same images were processed using NeuroQuant and FreeSurfer software. Ten subjects underwent repeated manual hippocampal tracings by two additional technologists blinded to previous results to evaluate consistency. Ten patients with two clinical MRI studies had volume measurements repeated using NeuroQuant and FreeSurfer. Results FreeSurfer raw volumes were significantly lower than NeuroQuant (P 0.75) for both automated methods. Asymmetry index reproducibility was excellent (>0.75) for manual tracing and FreeSurfer segmentation and fair (0.4–0.59) for NeuroQuant segmentation. Both automatic segmentation methods failed on the two cases with anatomic deformations. Segmentation errors were visually identified in 25 NeuroQuant and 27 FreeSurfer segmentations, and nine (18%) NeuroQuant and six (12%) FreeSurfer errors were judged clinically significant. Interpretation Automated hippocampal volumes are more reproducible than hand‐traced hippocampal volumes. However, these methods fail in some cases, and significant segmentation errors can occur.

Summary A best evidence topic was written according to a structured protocol. The question addressed was: in patients with inoperable early-stage primary lung cancer does microwave ablation (MWA) or stereotactic ablative body radiotherapy (SBRT) achieve improved outcomes in terms of local control, recurrence, survival and complications? Altogether, more than 550 papers were found using the reported search, of which 12 represented the best evidence to answer the clinical question. The authors, journal, date and country of publication, patient group studied, study type, relevant outcomes and results of these papers are tabulated. No single study directly compared the effects of MWA with SBRT. However, the best available evidence for MWA (7 studies) was compared to that for SBRT (5 studies). The range of 3-year survival reported for MWA was 29.2–84.7%, compared with 42.7–63.5% for SBRT. The range of median survival was 35–60 months for MWA and 32.6–48 months for SBRT. This suggests similar outcomes between these two 2 techniques. Different side-effect profiles were observed between techniques with MWA associated with pneumothorax and fever and SBRT most commonly causing radiation pneumonitis and rib fractures. The evidence base for MWA is less than that for SBRT and is heterogenous in terms of participants and technical design. However, within these limitations, we conclude that MWA appears comparable with SBRT in terms of local control and survival rates.

Background During the five decades since their discovery, filoviruses of four species have caused human hemorrhagic fever outbreaks: Marburg (MARV) marburgvirus, and Zaire (EBOV), Sudan (SUDV) and Bundybugyo (BDBV) ebolaviruses. The largest, devastating EBOV epidemic in West Africa in 2014-16, has been followed by outbreaks of MARV in Uganda, 2017, and EBOV in Democratic Republic of Congo, 2018, emphasizing the need to develop preparedness to diagnose all filoviruses. Objectives The aim of this study was to optimize a new filovirus RT-qPCR to detect all filoviruses, define its limits of detection (LOD) and perform a field evaluation with outbreak samples. Study design A pan-filovirus RT-qPCR targeting the L gene was developed and evaluated within the EbolaMoDRAD (Ebola virus: modern approaches for developing bedside rapid diagnostics) project. Specificity and sensitivity were determined and the effect of inactivation and PCR reagents (liquid and lyophilized format) were tested. Results The LODs for the lyophilized pan-filovirus L-RT-qPCR assay were 9.4 copies per PCR reaction for EBOV, 9.9 for MARV, 1151 for SUDV, 65 for BDBV and 289 for Tai Forest virus. The test was set at the Pasteur Institute, Dakar, Senegal, and 83 Ebola patient samples, with viral load ranging from 5 to 5 million copies of EBOV per reaction, were screened. The results for the patient samples were in 100% concordance with the reference EBOV-specific assay. Discussion Overall, the assay showed good sensitivity and specificity, covered all filoviruses known to be human pathogens, performed well both in lyophilized and liquid-phase formats and with EBOV outbreak clinical samples.