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In image-based profiling, software extracts thousands of morphological features of cells from multi-channel fluorescence microscopy images, yielding single-cell profiles that can be used for basic research and drug discovery. Powerful applications have been proven, including clustering chemical and genetic perturbations on the basis of their similar morphological impact, identifying disease phenotypes by observing differences in profiles between healthy and diseased cells and predicting assay outcomes by using machine learning, among many others. Here, we provide an updated protocol for the most popular assay for image-based profiling, Cell Painting. Introduced in 2013, it uses six stains imaged in five channels and labels eight diverse components of the cell: DNA, cytoplasmic RNA, nucleoli, actin, Golgi apparatus, plasma membrane, endoplasmic reticulum and mitochondria. The original protocol was updated in 2016 on the basis of several years’ experience running it at two sites, after optimizing it by visual stain quality. Here, we describe the work of the Joint Undertaking for Morphological Profiling Cell Painting Consortium, to improve upon the assay via quantitative optimization by measuring the assay’s ability to detect morphological phenotypes and group similar perturbations together. The assay gives very robust outputs despite various changes to the protocol, and two vendors’ dyes work equivalently well. We present Cell Painting version 3, in which some steps are simplified and several stain concentrations can be reduced, saving costs. Cell culture and image acquisition take 1–2 weeks for typically sized batches of ≤20 plates; feature extraction and data analysis take an additional 1–2 weeks. This protocol is an update to Nat. Protoc . 11, 1757–1774 (2016): https://doi.org/10.1038/nprot.2016.105 We provide an updated protocol for image-based profiling with Cell Painting. A detailed procedure, with standardized conditions for the assay, is presented, along with a comprehensive description of parameters to be considered when optimizing the assay.

In image-based profiling, software extracts thousands of morphological features of cells from multi-channel fluorescence microscopy images, yielding single-cell profiles that can be used for basic research and drug discovery. Powerful applications have been proven, including clustering chemical and genetic perturbations based on their similar morphological impact, identifying disease phenotypes by observing differences in profiles between healthy and diseased cells, and predicting assay outcomes using machine learning, among many others. Here we provide an updated protocol for the most popular assay for image-based profiling, Cell Painting. Introduced in 2013, it uses six stains imaged in five channels and labels eight diverse components of the cell: DNA, cytoplasmic RNA, nucleoli, actin, golgi apparatus, plasma membrane, endoplasmic reticulum, and mitochondria. The original protocol was updated in 2016 based on several years' experience running it at two sites, after optimizing it by visual stain quality. Here we describe the work of the Joint Undertaking for Morphological Profiling (JUMP) Cell Painting Consortium, aiming to improve upon the assay via quantitative optimization, based on the measured ability of the assay to detect morphological phenotypes and group similar perturbations together. We find that the assay gives very robust outputs despite a variety of changes to the protocol and that two vendors' dyes work equivalently well. We present Cell Painting version 3, in which some steps are simplified and several stain concentrations can be reduced, saving costs. Cell culture and image acquisition take 1 to 2 weeks for a typically sized batch of 20 or fewer plates; feature extraction and data analysis take an additional 1 to 2 weeks.Competing Interest StatementS.S. and A.E.C. serve as scientific advisors for companies that use image-based profiling and Cell Painting (AEC: Recursion, SS: Waypoint Bio, Dewpoint Therapeutics) and receive honoraria for occasional talks at pharmaceutical and biotechnology companies. D.G. is an employee of Bayer, AG, Pharmaceuticals. S.G., B.Z., G.H. are employees of Merck Healthcare KGaA, Darmstadt, Germany J.D.B. and T.G. were employed at Pfizer for the duration of this work. S.Y. was employed at Takeda for the duration of this work. S.E.S. was employed at Biogen for the duration of her contributions to this work. C.-H.L. was employed at Janssen Pharmaceutica at the time of writing. J.B.C & P.J.A. are employees of the Novartis Institutes for Biomedical Research, Cambridge MA, USA and declare no competing financial interests E.M., G.W., T.M, L.M. & J.P. are employees of AstraZeneca, Cambridge, UK K.J. was employed at AstraZeneca for the duration of this work. D.J.L. and S.H. are employees of Pfizer, Inc.Footnotes* Author name fixed* https://github.com/carpenterlab/2022_Cimini_NatureProtocols

Tropical ozone destruction: Halogens tidy up Tropospheric ozone is an important greenhouse gas in addition to its influence on air quality, on the photochemical processing of atmospheric chemicals and on ecosystem viability. Increasing tropospheric ozone levels over the past 150 years have led to a significant climate perturbation and a full understanding of the factors controlling the tropospheric ozone budget is required. The tropical marine boundary layer is the most important global region for loss of ozone, because of its high water vapour content, high solar radiation levels and large geographical extent. Surface atmospheric observations in this region are extremely sparse, hence the importance of a new year-round dataset from Cape Verde Observatory in the tropical North Atlantic Ocean. The observations reveal that the photochemical destruction rate of ozone in the tropical marine boundary layer is about 50% greater than predicted by current global models, and that this destruction is caused by halogen chemistry. This paper reports eight months of spectroscopic measurements at the Cape Verde Observatory indicative of the ubiquitous daytime presence of bromine monoxide and iodine monoxide in the tropical marine boundary layer. A year-round data set of co-located in situ surface trace gas measurements made in conjunction with low level aircraft observations show that the mean daily observed ozone loss is ∼50 per cent greater than that simulated by a global chemistry model using a classical photochemistry scheme that excludes halogen chemistry. Increasing tropospheric ozone levels over the past 150 years have led to a significant climate perturbation 1 ; the prediction of future trends in tropospheric ozone will require a full understanding of both its precursor emissions and its destruction processes. A large proportion of tropospheric ozone loss occurs in the tropical marine boundary layer 2 , 3 and is thought to be driven primarily by high ozone photolysis rates in the presence of high concentrations of water vapour. A further reduction in the tropospheric ozone burden through bromine and iodine emitted from open-ocean marine sources has been postulated by numerical models 4 , 5 , 6 , 7 , but thus far has not been verified by observations. Here we report eight months of spectroscopic measurements at the Cape Verde Observatory indicative of the ubiquitous daytime presence of bromine monoxide and iodine monoxide in the tropical marine boundary layer. A year-round data set of co-located in situ surface trace gas measurements made in conjunction with low-level aircraft observations shows that the mean daily observed ozone loss is ∼50 per cent greater than that simulated by a global chemistry model using a classical photochemistry scheme that excludes halogen chemistry. We perform box model calculations that indicate that the observed halogen concentrations induce the extra ozone loss required for the models to match observations. Our results show that halogen chemistry has a significant and extensive influence on photochemical ozone loss in the tropical Atlantic Ocean boundary layer. The omission of halogen sources and their chemistry in atmospheric models may lead to significant errors in calculations of global ozone budgets, tropospheric oxidizing capacity and methane oxidation rates, both historically and in the future.

Neoantigens are peptides derived from non-synonymous mutations presented by human leukocyte antigens (HLAs), which are recognized by antitumour T cells 1 – 14 . The large HLA allele diversity and limiting clinical samples have restricted the study of the landscape of neoantigen-targeted T cell responses in patients over their treatment course. Here we applied recently developed technologies 15 – 17 to capture neoantigen-specific T cells from blood and tumours from patients with metastatic melanoma with or without response to anti-programmed death receptor 1 (PD-1) immunotherapy. We generated personalized libraries of neoantigen–HLA capture reagents to single-cell isolate the T cells and clone their T cell receptors (neoTCRs). Multiple T cells with different neoTCR sequences (T cell clonotypes) recognized a limited number of mutations in samples from seven patients with long-lasting clinical responses. These neoTCR clonotypes were recurrently detected over time in the blood and tumour. Samples from four patients with no response to anti-PD-1 also demonstrated neoantigen-specific T cell responses in the blood and tumour to a restricted number of mutations with lower TCR polyclonality and were not recurrently detected in sequential samples. Reconstitution of the neoTCRs in donor T cells using non-viral CRISPR–Cas9 gene editing demonstrated specific recognition and cytotoxicity to patient-matched melanoma cell lines. Thus, effective anti-PD-1 immunotherapy is associated with the presence of polyclonal CD8 + T cells in the tumour and blood specific for a limited number of immunodominant mutations, which are recurrently recognized over time. Effective anti-PD-1 immunotherapy is associated with the presence of polyclonal CD8 + T cells in the tumour and blood specific for a limited number of immunodominant mutations, which are recurrently recognized over time.

Measurements of OH reactivity were made at the Weybourne Atmospheric Observatory on the North Norfolk coast, UK in May 2004. A wide range of supporting species was also measured concurrently as part of the TORCH-2 field campaign, allowing a detailed study of the OH oxidation chemistry to be carried out. Measurements were made in a variety of air masses, with the 3 most prevalent being air from the Atlantic that arrived at the site from over mainland UK in a South Westerly direction, and much cleaner Northerly air that originated over the far North Sea or Arctic, passed over the North Sea and arrived at the site from a North/North Easterly direction. Direct OH reactivity measurements were made on 6 days during the campaign and with influence of 2 of the 3 air masses prevalent during the study period. The average, minimum and maximum measured OH reactivity are: 4.9, 1.3 and 9.7 respectively. The measured OH reactivity was compared to key OH sinks such as NO₂ and CO and a general positive correlation was observed. OH reactivity (k′) was then calculated using the full range of OH sinks species that were measured (including >30 NMHCs) and their pseudo first order rate constants for reaction with OH. For much of the measurement period there is a significant difference between the measured and calculated k′, with an average value of k′meas- k′calc = 1.9 s⁻¹, indicative of unmeasured OH sinks. A zero-dimensional box model containing a subset of the Master Chemical Mechanism was used to calculate the OH reactivity more accurately. The simultaneously measured trace species were used as inputs to the model and their oxidative degradation was described by a chemical mechanism containing ~5,000 species. The extra OH sinks species produced by the model, resulted in an improvement in the agreement between k′meas and k′calc, however the averaged missing OH reactivity across the entire measurement period remained at 1.4 s⁻¹. Speculation is made as to the source of this missing reactivity, including reference to studies showing that a potentially large number of high molecular weight aromatic species could be unmeasured by standard instrumentation.

Stigma of mental health conditions hinders recovery and well-being. The Honest, Open, Proud (HOP) program shows promise in reducing stigma but there is uncertainty about the feasibility of a randomized trial to evaluate a peer-delivered, individual adaptation of HOP for psychosis (Let's Talk). A multi-site, Prospective Randomized Open Blinded Evaluation (PROBE) design, feasibility randomised controlled trial (RCT) comparing the peer-delivered intervention (Let's Talk) to treatment as usual (TAU). Follow-up was 2.5 and 6 months. Randomization was via a web-based system, with permuted blocks of random size. Up to 10 sessions of the intervention over 10 weeks were offered. The primary outcome was feasibility data (recruitment, retention, intervention attendance). Primary outcomes were analyzed by intention to treat. Safety outcomes were reported by as treated status. The study was prospectively registered: https://doi.org/10.1186/ISRCTN17197043. 149 patients were referred to the study and 70 were recruited. 35 were randomly assigned to intervention + TAU and 35 to TAU. Recruitment was 93% of the target sample size. Retention rate was high (81% at 2.5 months primary endpoint), and intervention attendance rate was high (83%). 21% of 33 patients in Let's talk + TAU had an adverse event and 16% of 37 patients in TAU. One serious adverse event (pre-randomization) was partially related and expected. This is the first trial to show that it is feasible and safe to conduct a RCT of HOP adapted for people with psychosis and individual delivery. An adequately powered trial is required to provide robust evidence.

Background Improving the quality of care in community settings for people with ‘Complex Emotional Needs’ (CEN—our preferred working term for services for people with a “personality disorder” diagnosis or comparable needs) is recognised internationally as a priority. Plans to improve care should be rooted as far as possible in evidence. We aimed to take stock of the current state of such evidence, and identify significant gaps through a scoping review of published investigations of outcomes of community-based psychosocial interventions designed for CEN. Methods We conducted a scoping review with systematic searches. We searched six bibliographic databases, including forward and backward citation searching, and reference searching of relevant systematic reviews. We included studies using quantitative methods to test for effects on any clinical, social, and functioning outcomes from community-based interventions for people with CEN. The final search was conducted in November 2020. Results We included 226 papers in all (210 studies). Little relevant literature was published before 2000. Since then, publications per year and sample sizes have gradually increased, but most studies are relatively small, including many pilot or uncontrolled studies. Most studies focus on symptom and self-harm outcomes of various forms of specialist psychotherapy: most result in outcomes better than from inactive controls and similar to other specialist psychotherapies. We found large evidence gaps. Adaptation and testing of therapies for significant groups (e.g. people with comorbid psychosis, bipolar disorder, post-traumatic stress disorder, or substance misuse; older and younger groups; parents) have for the most part only reached a feasibility testing stage. We found little evidence regarding interventions to improve social aspects of people’s lives, peer support, or ways of designing effective services. Conclusions Compared with other longer term mental health problems that significantly impair functioning, the evidence base on how to provide high quality care for people with CEN is very limited. There is good evidence that people with CEN can be helped when specialist therapies are available and when they are able to engage with them. However, a much more methodologically robust and substantial literature addressing a much wider range of research questions is urgently needed to optimise treatment and support across this group.