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Abstract Activating transcription factor 4 (ATF4) plays a central role in the integrated stress response (ISR) and one overlapping branch of the unfolded protein response (UPR). We recently reported that the splicing inhibitor isoginkgetin (IGG) induced ATF4 protein along with several known ATF4-regulated transcripts in a response that resembled the ISR and UPR. However, the contribution of ATF4-dependent and -independent transcriptional responses to IGG exposure was not known. Here we used RNA-sequencing in HCT116 colon cancer cells and an isogenic subline lacking ATF4 to investigate the contribution of ATF4 to IGG-induced changes in gene expression. Approximately 85% of the IGG-responsive DEGs in HCT116 cells were also differentially expressed in response to the ER stressor thapsigargin (Tg) and these were enriched for genes associated with the UPR and ISR. Most of these were positively regulated by IGG with impaired responses in the ATF4-deficient cells. Nonetheless, there were DEGs that responded similarly in both cell lines. The ATF4-independent IGG-induced DEGs included several metal responsive transcripts encoding metallothionines and a zinc transporter. Taken together, the predominant IGG response was ATF4-dependent in these cells and resembled the UPR and ISR while a second less prominent response involved the ATF4-independent regulation of metal responsive mRNAs.

Background Thapsigargin (Tg) is a compound that inhibits the SERCA calcium transporter leading to decreased endoplasmic reticulum (ER) Ca2+ levels. Many ER chaperones are required for proper folding of membrane-associated and secreted proteins, and they are Ca2+ dependent. Therefore, Tg leads to the accumulation of misfolded proteins in the ER, activating the unfolded protein response (UPR) to help restore homeostasis. Tg reportedly induces cell cycle arrest and apoptosis in many cell types but how these changes are linked to the UPR remains unclear. The activating transcription factor 4 (ATF4) plays a key role in regulating ER stress-induced gene expression so we sought to determine if ATF4 is required for Tg-induced cell cycle arrest and apoptosis using ATF4-deficient cells. Methods Two-parameter flow cytometric analysis of DNA replication and DNA content was used to assess the effects of Tg on cell cycle distribution in isogenic HCT116-derived cell lines either expressing or lacking ATF4. For comparison, we similarly assessed the Tg response in isogenic cell lines deleted of the p53 tumour suppressor and the p53-regulated p21WAF1 cyclin-dependent kinase inhibitor important in G1 and G2 arrests induced by DNA damage. Results Tg led to a large depletion of the S phase population with a prominent increase in the proportion of HCT116 cells in the G1 phase of the cell cycle. Importantly, this effect was largely independent of ATF4. We found that loss of p21WAF1 but not p53 permitted Tg treated cells to enter S phase and synthesize DNA. Therefore, p21WAF1plays an important role in these Tg-induced cell cycle alterations while ATF4 and p53 do not. Remarkably, the ATF4-, p53-and p21WAF1-deficient cell lines were all more sensitive to Tg-induced apoptosis. Taken together, p21WAF1 plays a larger role in regulating Tg-induced G1 and G2 arrests than ATF4 or p53 but these proteins similarly contribute to protection from Tg-induced apoptosis. This work highlights the complex network of stress responses that are activated in response to ER stress.

When a record hot month occurs, timely and credible attribution and contextualisation information can enhance public understanding and future preparedness. This is particularly effective if provided in real time by a National Meteorological and Hydrological Service (NMHS). Many NMHSs are working to integrate research-based attribution methods into their operational services. In this study, researchers and climate service staff collaborated to assess the feasibility of delivering such information swiftly and aligned with standard NMHS data and procedures. The record warm July (winter) temperatures of Tasmania, Australia in 2023 were chosen to illustrate the trial. Rapid results were available three days after the event. Approximately half of the unusual warmth was attributed to climate change, with the likelihood of breaking the previous record at least 17 times higher in the current climate compared to a stationary pre-industrial climate (14% vs. 0.4%). The warming trend became evident in the 1980s, and by 2060, average July temperatures in Tasmania match the record temperature of July 2023 under a high emissions scenario. However, average July minimum temperatures were not well modelled, necessitating the addition of a higher-resolution forecast-based attribution method. In subsequent analysis, almost all the forecast temperature anomaly, and reduced storm activity, was attributable to climate change. Statistical analysis revealed that a weak El Niño partly offset the unusual warmth. To expedite these additional approaches, information drawn from real-time forecasts could be used. Lessons learnt from this trial include technical improvements to align better with NMHS protocols including using consistent datasets and baselines, and refining and automating the method suite. Logistical and communication enhancements included training staff to run the suite, improving communication materials, and developing delivery channels. These learnings provide key considerations for NMHSs as they move towards providing timely and credible climate attribution and contextualisation information as part of their operational services.

Extreme event attribution (EEA) information is increasingly in demand from climate services. EEA messages can: raise awareness about the effect climate change has already imposed, inform climate change liability conversations, and be combined with climate projections to inform adaptation. However, due to limitations in observations, models and methods, there are barriers towards operationalising EEA in practice. Operational services will need EEA to be done transparently and using preset formats. Here we review recent experience and practice in EEA in Australia and New Zealand with a view to inform the design of an EEA component of climate services. We present a flow chart of the processes involved, noting particular care is needed on the trigger, event definition, and climate model evaluation, with effective stage gates. We also promote the use of tailored causal network diagrams as a standard tool to inform an EEA study and communicate results, with particular care needed for messages on events with lower confidence or complex sets of influences, including tropical cyclones and extratropical cyclones. We suggest that extending EEA to impact attribution is essential for making EEA messages salient but requires an uplift in forming interdisciplinary teams and in granular exposure and vulnerability datasets and is likely to raise new interdisciplinary methodological questions. Finally, we suggest communication of EEA messages can learn more from its origins in medical epidemiology.

Extreme maximum temperatures during Australian spring can have deleterious impacts on a range of sectors from health to wine grapes to planning for wildfires but are studied relatively little compared to spring rainfall. Spring maximum temperatures in Australia have been rising over recent decades, and it is important to understand how Australian spring maximum temperatures develop in the present and warming climate. Australia's climate is influenced by variability in the tropics and extratropics, but some of this influence impacts Australia differently from winter to summer and, consequently, may have different impacts on Australia as spring evolves. Using linear regression analysis, this paper explores the atmospheric dynamics and remote drivers of high maximum temperatures over the individual months of spring. We find that the drivers of early spring maximum temperatures in Australia are more closely related to low-level wind changes, which in turn are more related to the Southern Annular Mode than variability in the tropics. By late spring, Australia's maximum temperatures are proportionally more related to warming through subsidence than low-level wind changes and more closely related to tropical variability. This increased relationship with the tropical variability is linked with the breakdown of the subtropical jet through spring and an associated change in tropically forced Rossby wave teleconnections. An improved understanding of how the extratropics and tropics project onto the mechanisms that drive high maximum temperatures through spring may lead to improved sub-seasonal prediction of high temperatures in the future.

This article presents findings from a four-year collaborative research project on immigrant and mixed-status families in Santa Cruz County, California. The project employed a new model of critical community-engaged scholarship called Community Initiated Student Engaged Research (CISER) in order to gain access to and build trust with this vulnerable population. The study used an overarching theoretical framework of “belonging” to identify six key factors most consequential for belonging and/or exclusion, including access to education, economic security, legal immigration status, health services, opportunities for youth, and social networks. The findings reveal the complex and interconnected nature of these factors and demonstrate how exclusion experienced due to a lack of legal immigration status had far-reaching effects on interviewees’ job prospects and experiences of economic, health, and housing insecurity. The article highlights the importance of using an assets-based approach to draw out the myriad ways interviewees and communities create spaces, networks, and ways to promote and enhance both material and emotional forms of belonging. The CISER model and its participatory approach also provide tangible benefits for community partners and undergraduate researchers. This article contributes to the literature on immigrant experiences and critical community-engaged research while offering insights into sources of and systemic barriers to collective belonging.

Isoginkgetin (IGG) is a compound originally derived from the leaves of Ginkgo biloba trees. It was subsequently identified through a chemical screen to be an inhibitor of both the major and minor spliceosome, with an IC50 value of 30 µM [1]. Little is currently known about the overall effects of spliceosome inhibition on human cells. Here, we treated HCT116 and a p53 null subline of colon cancer cells with 30 µM IGG for 8 hours. Total RNA was isolated, and Affymetrix oligonucleotide microarray analysis was completed using samples from two biologically independent experiments. A relatively small number of transcripts were differentially expressed in these cell lines. There was considerable overlap in the upregulated but not the downregulated transcripts. PANTHER Reactome analysis of these shared upregulated transcripts identified enriched pathways involving the ATF4 transcription factor important in the integrated stress response [2].

Abstract Background Conducting research in partnership with stakeholders (e.g. policy-makers, practitioners, organisations, patients) is a promising and popular approach to improving the implementation of research findings in policy and practice. This study aimed to identify the principles, strategies, outcomes and impacts reported in different types of reviews of research partnerships in order to obtain a better understanding of the scope of the research partnership literature. Methods This review of reviews is part of a Coordinated Multicenter Team approach to synthesise the research partnership literature with five conceptually linked literature reviews. The main research question was ‘What principles, strategies, outcomes and impacts are reported in different types of research partnership approaches?’. We included articles describing a literature review of research partnerships using a systematic search strategy. We used an adapted version of the Revised Assessment of Multiple Systematic Reviews tool to assess quality. Nine electronic databases were searched from inception to April 2018. Principles, strategies, outcomes and impacts were extracted from the included reviews and analysed using direct content analysis. Results We included 86 reviews using terms describing several research partnership approaches (e.g. community-based participatory research, participatory research, integrated knowledge translation). After the analyses, we synthesised 17 overarching principles and 11 overarching strategies and grouped them into one of the following subcategories: relationship between partners; co-production of knowledge; meaningful stakeholder engagement; capacity-building, support and resources; communication process; and ethical issues related to the collaborative research activities. Similarly, we synthesised 20 overarching outcomes and impacts on researchers, stakeholders, the community or society, and the research process. Conclusions This review of reviews is the first that presents overarching principles, strategies, outcomes and impacts of research partnerships. This review is unique in scope as we synthesised literature across multiple research areas, involving different stakeholder groups. Our findings can be used as a first step to guide the initiation and maintenance of research partnerships and to create a classification system of the key domains of research partnerships, which may improve reporting consistency in the research partnership literature. Trial registration This study is registered via Open Science Framework: https://doi.org/10.17605/OSF.IO/GVR7Y .

Mid-circuit measurements are a key component in many quantum information computing protocols, including quantum error correction, fault-tolerant logical operations, and measurement based quantum computing. As such, techniques to quickly and efficiently characterize or benchmark their performance are of great interest. Beyond the measured qubit, it is also relevant to determine what, if any, impact mid-circuit measurement has on adjacent, unmeasured, spectator qubits. Here, we present a mid-circuit measurement benchmarking suite developed from the ubiquitous paradigm of randomized benchmarking. We show how our benchmarking suite can be used to both detect as well as quantify errors on both measured and spectator qubits, including measurement-induced errors on spectator qubits and entangling errors between measured and spectator qubits. We demonstrate the scalability of our suite by simultaneously characterizing mid-circuit measurement on multiple qubits from an IBM Quantum Falcon device, and support our experimental results with numerical simulations. Further, using a mid-circuit measurement tomography protocol we establish the nature of the errors identified by our benchmarking suite.

Objectives Studies have demonstrated high rates of mortality in people with proximal femoral fracture and SARS-CoV-2, but there is limited published data on the factors that influence mortality for clinicians to make informed treatment decisions. This study aims to report the 30-day mortality associated with perioperative infection of patients undergoing surgery for proximal femoral fractures and to examine the factors that influence mortality in a multivariate analysis.Setting Prospective, international, multicentre, observational cohort study.Participants Patients undergoing any operation for a proximal femoral fracture from 1 February to 30 April 2020 and with perioperative SARS-CoV-2 infection (either 7 days prior or 30-day postoperative).Primary outcome 30-day mortality. Multivariate modelling was performed to identify factors associated with 30-day mortality.Results This study reports included 1063 patients from 174 hospitals in 19 countries. Overall 30-day mortality was 29.4% (313/1063). In an adjusted model, 30-day mortality was associated with male gender (OR 2.29, 95% CI 1.68 to 3.13, p80 years (OR 1.60, 95% CI 1.1 to 2.31, p=0.013), preoperative diagnosis of dementia (OR 1.57, 95% CI 1.15 to 2.16, p=0.005), kidney disease (OR 1.73, 95% CI 1.18 to 2.55, p=0.005) and congestive heart failure (OR 1.62, 95% CI 1.06 to 2.48, p=0.025). Mortality at 30 days was lower in patients with a preoperative diagnosis of SARS-CoV-2 (OR 0.6, 95% CI 0.6 (0.42 to 0.85), p=0.004). There was no difference in mortality in patients with an increase to delay in surgery (p=0.220) or type of anaesthetic given (p=0.787).Conclusions Patients undergoing surgery for a proximal femoral fracture with a perioperative infection of SARS-CoV-2 have a high rate of mortality. This study would support the need for providing these patients with individualised medical and anaesthetic care, including medical optimisation before theatre. Careful preoperative counselling is needed for those with a proximal femoral fracture and SARS-CoV-2, especially those in the highest risk groups.Trial registration number NCT04323644

Abstract Background Genome wide association studies have identified > 200 susceptibility loci accounting for much of the heritability of multiple sclerosis (MS). Epstein-Barr virus (EBV), a memory B cell tropic virus, has been identified as necessary but not sufficient for development of MS. The molecular and immunological basis for this has not been established. Infected B cell proliferation is driven by signalling through the EBV produced cell surface protein LMP1, a homologue of the MS risk gene CD40. Methods We have investigated transcriptomes of B cells and EBV-infected B cells at Latency III (LCLs) and identified MS risk genes with altered expression on infection and with expression levels associated with the MS risk genotype (LCLeQTLs). The association of LCLeQTL genomic burden with EBV phenotypes in vitro and in vivo was examined. The risk genotype effect on LCL proliferation with CD40 stimulation was assessed. Results These LCLeQTL MS risk SNP:gene pairs (47 identified) were over-represented in genes dysregulated between B and LCLs (p

The oxytocin receptor (OXTR) is a G protein-coupled receptor with a diverse repertoire of intracellular signaling pathways, which are activated in response to binding oxytocin (OXT) and a similar nonapeptide, vasopressin. This review summarizes the cell and molecular biology of the OXTR and its downstream signaling cascades, particularly focusing on the vasoactive functions of OXTR signaling in humans and animal models, as well as the clinical applications of OXTR targeting cerebrovascular accidents.

The spliceosome assembles on pre-mRNA in a stepwise manner through five successive pre-spliceosome complexes. The spliceosome functions to remove introns from pre-mRNAs to generate mature mRNAs that encode functional proteins. Many small molecule inhibitors of the spliceosome have been identified and they are cytotoxic. However, little is known about genetic determinants of cell sensitivity. Activating transcription factor 3 (ATF3) is a transcription factor that can stimulate apoptotic cell death in response to a variety of cellular stresses. Here, we used a genetic approach to determine if ATF3 was important in determining the sensitivity of mouse embryonic fibroblasts (MEFs) to two splicing inhibitors: pladienolide B (PB) and isoginkgetin (IGG), that target different pre-spliceosome complexes. Both compounds led to increased ATF3 expression and apoptosis in control MEFs while ATF3 null cells were significantly protected from the cytotoxic effects of these drugs. Similarly, ATF3 was induced in response to IGG and PB in the two human tumour cell lines tested while knockdown of ATF3 protected cells from both drugs. Taken together, ATF3 appears to contribute to the cytotoxicity elicited by these spliceosome inhibitors in both murine and human cells.

Despite their versatility, superconducting qubits such as transmons still have limited coherence times compared to resonators. Here, the authors show how to use a single transmon to implement universal one-qubit and two-qubit operations among nine qubits encoded in superconducting resonators’ eigenmodes.

Hardware-efficient transpilation of quantum circuits to a quantum device native gate set is essential for the execution of quantum algorithms on noisy quantum computers. Typical quantum devices utilize a gate set with a single two-qubit Clifford entangling gate per pair of coupled qubits; however, in some applications access to a non-Clifford two-qubit gate can result in more optimal circuit decompositions and also allows more flexibility in optimizing over noise. We demonstrate calibration of a low-error non-Clifford controlled-π/2 phase (cs) gate on a cloud-based IBM Quantum system using the Qiskit Pulse framework. To measure the gate error of the calibrated cs gate we perform non-Clifford cnot-dihedral interleaved randomized benchmarking. We are able to obtain a gate error of 5.9(7)×10^{−3} at a gate length 263 ns, which is close to the coherence limit of the associated qubits, and lower error than the back-end standard calibrated cnot gate.

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Emissions of methane (CH4) from dairy production systems are environmentally detrimental and represent an energy cost to the cow. This study evaluated the effect of varying C18 fatty acid sources on CH4 emissions, milk production and rumen methanogen populations in grazing lactating dairy cows. Forty-five Holstein Friesian cows were randomly allocated to one of three treatments (n = 15). Cows were offered 15 kg dry matter (DM)/d of grazed pasture plus supplementary concentrates (4 kg DM/d) containing either stearic acid (SA), linseed oil (LO), or soy oil (SO). Cows offered LO and SO had lower pasture DM intake (DMI) than those offered SA (11.3, 11.5 vs. 12.6 kg/d). Cows offered LO and SO had higher milk yield (21.0, 21.3 vs. 19.7 kg/d) and milk protein yield (0.74, 0.73 vs. 0.67 kg/d) than those offered SA. Emissions of CH4 (245 vs. 293, 289 g/d, 12.4 vs. 15.7, 14.8 g/kg of milk and 165 vs. 207, 195 g/kg of milk solids) were lower for cows offered LO than those offered SA or SO. Methanobrevibacter ruminantium abundance was reduced in cows offered LO compared to SA. Offering supplementary concentrates containing LO can reduce enteric CH4 emissions from pasture fed dairy cows.