Post-translational modification-centric base editor screens to assess phosphorylation site functionality in high throughput.

Signaling pathways that drive gene expression are typically depicted as having a dozen or so landmark phosphorylation and transcriptional events. In reality, thousands of dynamic post-translational modifications (PTMs) orchestrate nearly every cellular function, and we lack technologies to find causal links between these vast biochemical pathways and genetic circuits at scale. Here we describe the high-throughput, functional assessment of phosphorylation sites through the development of PTM-centric base editing coupled to phenotypic screens, directed by temporally resolved phosphoproteomics. Using T cell activation as a model, we observe hundreds of unstudied phosphorylation sites that modulate NFAT transcriptional activity. We identify the phosphorylation-mediated nuclear localization of PHLPP1, which promotes NFAT but inhibits NFκB activity. We also find that specific phosphosite mutants can alter gene expression in subtle yet distinct patterns, demonstrating the potential for fine-tuning transcriptional responses. Overall, base editor screening of PTM sites provides a powerful platform to dissect PTM function within signaling pathways.

Colonisation of hospital surfaces from low- and middle-income countries by extended spectrum ß-lactamase- and carbapenemase-producing bacteria.

Hospital surfaces can harbour bacterial pathogens, which may disseminate and cause nosocomial infections, contributing towards mortality in low- and middle-income countries (LMICs). During the BARNARDS study, hospital surfaces from neonatal wards were sampled to assess the degree of environmental surface and patient care equipment colonisation by Gram-negative bacteria (GNB) carrying antibiotic resistance genes (ARGs). Here, we perform PCR screening for extended-spectrum ß-lactamases (blaCTX-M-15) and carbapenemases (blaNDM, blaOXA-48-like and blaKPC), MALDI-TOF MS identification of GNB carrying ARGs, and further analysis by whole genome sequencing of bacterial isolates. We determine presence of consistently dominant clones and their relatedness to strains causing neonatal sepsis. Higher prevalence of carbapenemases is observed in Pakistan, Bangladesh, and Ethiopia, compared to other countries, and are mostly found in surfaces near the sink drain. Klebsiella pneumoniae, Enterobacter hormaechei, Acinetobacter baumannii, Serratia marcescens and Leclercia adecarboxylata are dominant; ST15 K. pneumoniae is identified from the same ward on multiple occasions suggesting clonal persistence within the same environment, and is found to be identical to isolates causing neonatal sepsis in Pakistan over similar time periods. Our data suggests persistence of dominant clones across multiple time points, highlighting the need for assessment of Infection Prevention and Control guidelines.

Climate Change and Children's Health: Building a Healthy Future for Every Child.

Observed changes in temperature, precipitation patterns, sea level, and extreme weather are destabilizing major determinants of human health. Children are at higher risk of climate-related health burdens than adults because of their unique behavior patterns; developing organ systems and physiology; greater exposure to air, food, and water contaminants per unit of body weight; and dependence on caregivers. Climate change harms children through numerous pathways, including air pollution, heat exposure, floods and hurricanes, food insecurity and nutrition, changing epidemiology of infections, and mental health harms. As the planet continues to warm, climate change's impacts will worsen, threatening to define the health and welfare of children at every stage of their lives. Children who already bear higher burden of disease because of living in low-wealth households and communities, lack of access to high quality education, and experiencing racism and other forms of unjust discrimination bear greater risk of suffering from climate change hazards. Climate change solutions, advanced through collaborative work of pediatricians, health systems, communities, corporations, and governments lead to immediate gains in child health and equity and build a foundation for generations of children to thrive. This technical report reviews the nature of climate change and its associated child health effects and supports the recommendations in the accompanying policy statement on climate change and children's health.

Climate Change and Children's Health: Building a Healthy Future for Every Child.

The warming of our planet matters to every child. Driven by fossil fuel-generated greenhouse gas emissions, climate conditions stable since the founding of modern pediatrics in the mid-nineteenth century have shifted, and old certainties are falling away. Children's physical and mental health are threatened by climate change through its effects on temperature, precipitation, and extreme weather; ecological disruption; and community disruption. These impacts expose and amplify existing inequities and create unprecedented intergenerational injustice. Fossil fuel extraction and combustion cause harm today and reach centuries into the future, jeopardizing the health, safety, and prosperity of today's children and future generations. Appreciating the unique vulnerability of their patients, pediatricians have become leading health advocates for climate actions necessary to protect all living and future children. Policies that reduce reliance on fossil fuels and promote cleaner air, facilitate walking and bicycling, encourage more sustainable diets, increase access to nature, and develop more connected communities lead to immediate gains in child health and equity, and build a foundation for generations of children to thrive.

TET Enzymes in the Immune System: From DNA Demethylation to Immunotherapy, Inflammation, and Cancer.

Ten-eleven translocation (TET) proteins are iron-dependent and α-ketoglutarate-dependent dioxygenases that sequentially oxidize the methyl group of 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC). All three epigenetic modifications are intermediates in DNA demethylation. TET proteins are recruited by transcription factors and by RNA polymerase II to modify 5mC at enhancers and gene bodies, thereby regulating gene expression during development, cell lineage specification, and cell activation. It is not yet clear, however, how the established biochemical activities of TET enzymes in oxidizing 5mC and mediating DNA demethylation relate to the known association of TET deficiency with inflammation, clonal hematopoiesis, and cancer. There are hints that the ability of TET deficiency to promote cell proliferation in a signal-dependent manner may be harnessed for cancer immunotherapy. In this review, we draw upon recent findings in cells of the immune system to illustrate established as well as emerging ideas of how TET proteins influence cellular function. Expected final online publication date for the Annual Review of Immunology, Volume 42 is April 2024. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Time-motion observations to characterize the developmental environment in a paediatric post-acute care hospital.

BACKGROUND: Chronically hospitalized children are at risk for neurodevelopmental delay, compounded by restricted social interactions, movement and environmental stimulation. We measured patients' movements and interactions to characterize developmentally relevant aspects of our inpatient environment and identify opportunities for developmental enrichment. METHODS: As part of a quality improvement initiative to inform neurodevelopmental programming for children with medical complexity at our paediatric post-acute care specialty hospital, we conducted >232 hours of time-motion observations. Trained observers followed 0- to 5-year-old inpatients from 7 am to 7 pm on weekdays, categorizing observations within five domains: Where, With, Position, State and Environment. Observations were collected continuously utilizing REDCap on iPads. A change in any domain initiated a new observation. RESULTS: Patients were median 1 year and 8 months of age (range 2 months to 3 years 9 months) with a median length of hospitalization of 514 days (range 66-1298). In total, 2636 unique observations (or median 134 observations per patient-day [range 95-210]) were collected. Patients left their rooms up to 4 times per day for median 1 h and 34 min (range 41 min to 4 h:30 min). Patients spent 4 h:6 min (2 h:57 min to 6 h:30 min) interacting with someone and 3 h:51 min (57 min to 6 h:36 min) out of bed each day. Patients were simultaneously out of their beds, interacting with someone and awake for 2 h:21 min (51 min to 4 h:19 min) each day. CONCLUSIONS: Despite a care model prioritizing time out of bed and social interaction, time-motion observations indicate patients spent many of their waking hours in bed and alone. Quantifying our inpatients developmental opportunities will inform neurodevelopmental programming initiatives.

Proteome-wide base editor screens to assess phosphorylation site functionality in high-throughput.

Signaling pathways that drive gene expression are typically depicted as having a dozen or so landmark phosphorylation and transcriptional events. In reality, thousands of dynamic post-translational modifications (PTMs) orchestrate nearly every cellular function, and we lack technologies to find causal links between these vast biochemical pathways and genetic circuits at scale. Here, we describe "signaling-to-transcription network" mapping through the development of PTM-centric base editing coupled to phenotypic screens, directed by temporally-resolved phosphoproteomics. Using T cell activation as a model, we observe hundreds of unstudied phosphorylation sites that modulate NFAT transcriptional activity. We identify the phosphorylation-mediated nuclear localization of the phosphatase PHLPP1 which promotes NFAT but inhibits NFκB activity. We also find that specific phosphosite mutants can alter gene expression in subtle yet distinct patterns, demonstrating the potential for fine-tuning transcriptional responses. Overall, base editor screening of PTM sites provides a powerful platform to dissect PTM function within signaling pathways.

Staphylococcus aureus Bacteremia in Pediatric Patients: Uncovering a Rural Health Challenge.

Background: Staphylococcus aureus bacteremia poses significant risk for morbidity and mortality. This may be exacerbated in rural populations facing unique health challenges. Methods: To investigate factors influencing S. aureus bacteremia outcomes, we conducted a retrospective cohort study of children admitted to St. Louis Children's Hospital (SLCH) from 2011 to 2019. Exposures included rurality (defined by the Rural-Urban Continuum Code), Area Deprivation Index, and outside hospital (OSH) admission before SLCH admission. The primary outcome was treatment failure, a composite of 90-day all-cause mortality and hospital readmission. Results: Of 251 patients, 69 (27%) were from rural areas; 28 (11%) were initially admitted to an OSH. Treatment failure occurred in 39 (16%) patients. Patients from rural areas were more likely to be infected with methicillin-resistant S. aureus (45%) vs urban children (29%; P = .02). Children initially admitted to an OSH, vs those presenting directly to SLCH, were more likely to require intensive care unit-level (ICU) care (57% vs 29%; P = .002), have an endovascular source of infection (32% vs 12%; P = .004), have a longer duration of illness before hospital presentation (4.1 vs 3.0 days; P = .04), and have delayed initiation of targeted antibiotic therapy (3.9 vs 2.6 days; P = .01). Multivariable analysis revealed rural residence (adjusted odds ratio [aOR], 2.3; 95% CI, 1.1-5.0), comorbidities (aOR, 2.9; 95% CI, 1.3-6.2), and ICU admission (aOR, 3.9; 95% CI, 1.9-8.3) as predictors of treatment failure. Conclusions: Children from rural areas face barriers to specialized health care. These challenges may contribute to severe illness and worse outcomes among children with S. aureus bacteremia.

TET2, tumor control, and CAR T cell hyperproliferation.

A recent study by Jain et al. published in Nature followed up on evidence suggesting that depletion of 5-methylcytosine dioxygenase TET2 in chimeric antigen receptor CAR T cells could enhance their expansion, persistence, and antitumor efficacy. Their findings are cautionary, but offer hope of a path forward.

Extremes of baseline cognitive function determine the severity of delirium: a population study.

Although delirium is a significant clinical and public health problem, little is understood about how specific vulnerabilities underlie the severity of its presentation. Our objective was to quantify the relationship between baseline cognition and subsequent delirium severity. We prospectively investigated a population-representative sample of 1510 individuals aged ≥70 years, of whom 209 (13.6%) were hospitalized across 371 episodes (1999 person-days assessment). Baseline cognitive function was assessed using the modified Telephone Interview for Cognitive Status, supplemented by verbal fluency measures. We estimated the relationship between baseline cognition and delirium severity [Memorial Delirium Assessment Scale (MDAS)] and abnormal arousal (Observational Scale of Level of Arousal), adjusted by age, sex, frailty and illness severity. We conducted further analyses examining presentations to specific hospital settings and common precipitating aetiologies. The median time from baseline cognitive assessment to admission was 289 days (interquartile range 130 to 47 days). In admitted patients, delirium was present on at least 1 day in 45% of admission episodes. The average number of days with delirium (consecutively positive assessments) was 3.9 days. Elective admissions accounted for 88 bed days (4.4%). In emergency (but not elective) admissions, we found a non-linear U-shaped relationship between baseline global cognition and delirium severity using restricted cubic splines. Participants with baseline cognition 2 standard deviations below average (z-score = -2) had a mean MDAS score of 14 points (95% CI 10 to 19). Similarly, those with baseline cognition z-score = + 2 had a mean MDAS score of 7.9 points (95% CI 4.9 to 11). Individuals with average baseline cognition had the lowest MDAS scores. The association between baseline cognition and abnormal arousal followed a comparable pattern. C-reactive protein ≥20 mg/l and serum sodium <125 mM/l were associated with more severe delirium. Baseline cognition is a critical determinant of the severity of delirium and associated changes in arousal. Emergency admissions with lowest and highest baseline cognition who develop delirium should receive enhanced clinical attention.

The Ocean Carbon and Acidification Data System.

The Ocean Carbon and Acidification Data System (OCADS) is a data management system at the National Oceanic and Atmospheric Administration (NOAA) National Centers for Environmental Information (NCEI). It manages a wide range of ocean carbon and acidification data, including chemical, physical, and biological observations collected from research vessels, ships of opportunity, and uncrewed platforms, as well as laboratory experiment results, and model outputs. Additionally, OCADS serves as a repository for related Global Ocean Observing System (GOOS) biogeochemistry Essential Ocean Variables (EOVs), e.g., oxygen, nutrients, transient tracers, and stable isotopes. OCADS endeavors to be one of the world's leading providers of ocean carbon and acidification data, information, products, and services. To provide the best data management services to the ocean carbon and acidification research community, OCADS prioritizes adopting a customer-centric approach and gathering knowledge and expertise from the research community to improve its data management practices. OCADS aims to make all ocean carbon and acidification data accessible via a single portal, and welcomes submissions from around the world: https://www.ncei.noaa.gov/products/ocean-carbon-acidification-data-system/.

Simulation, stories, and fictional worlds.

The authors explain our attraction to strange, literary places as resulting from our attraction to strange places in real life. I believe this is correct and important. The aim of the following commentary is to show that their main conclusion is closely related to - even (retrospectively) predictable from - the operation of simulation and the consequences of that operation for storytelling.

Non-linearity in event runoff generation in a small agricultural catchment.

Understanding the role of soil moisture and other controls in runoff generation is important for predicting runoff across scales. This paper aims to identify the degree of non-linearity of the relationship between event peak runoff and potential controls for different runoff generation mechanisms in a small agricultural catchment. The study is set in the 66 ha Hydrological Open Air Laboratory, Austria, where discharge was measured at the catchment outlet and for 11 sub-catchments or hillslopes with different runoff generation mechanisms. Peak runoff of 73 events was related to three potential controls: event precipitation, soil moisture and groundwater levels. The results suggest that the hillslopes dominated by ephemeral overland flow exhibit the most non-linear runoff generation behaviour for its controls; runoff is only generated above a threshold of 95% of the maximum soil moisture. Runoff generation through tile drains and in wetlands is more linear. The largest winter and spring events at the catchment outlet are caused by runoff from hillslopes with shallow flow paths (ephemeral overland flow and tile drainage mechanisms), while the largest summer events are caused by other hillslopes, those with deeper flow paths or with saturation areas throughout the year. Therefore, the response of the entire catchment is a mix of the various mechanisms, and the groundwater contribution makes the response more linear. The implications for hydrological modelling are discussed.

The impact of infectious diseases consultation for children with Staphylococcus aureus bacteremia.

BACKGROUND: Despite clear benefit of improved outcomes in adults, the impact of infectious diseases (ID) consultation for Staphylococcus aureus bacteremia in children remains understudied. METHODS: To assess the impact of pediatric ID consultation on management and outcomes, we conducted a cohort study of children with S. aureus bacteremia at St. Louis Children's Hospital from 2011 to 2018. We assessed adherence to six established quality-of-care indicators (QCIs). We applied propensity score methodology to examine the impact of ID consultation on risk of treatment failure, a composite of all-cause mortality or hospital readmission within 90 days. RESULTS: Of 306 patients with S. aureus bacteremia, 193 (63%) received ID consultation. ID consultation was associated with increased adherence to all QCIs, including proof-of-cure blood cultures, indicated laboratory studies, echocardiography, source control, targeted antibiotic therapy, and antibiotic duration. Obtaining proof-of-cure blood cultures and all indicated laboratory studies were associated with improved outcomes. In propensity score-weighted analyses, risk of treatment failure was similar among patients who did and did not receive ID consultation. However, the number of events was small and risk estimates were imprecise. CONCLUSIONS: For children with S. aureus bacteremia, ID consultation improved adherence to QCIs, some of which were associated with improved clinical outcomes. IMPACT: In children with Staphylococcus aureus bacteremia, consultation by an infectious diseases (ID) physician improved adherence to established quality-of-care indicators (QCIs). The current literature regarding ID consultation in pediatric S. aureus bacteremia is sparse. Three prior international studies demonstrated improved quality of care with ID consultation, though results were disparate regarding clinical outcomes. This article impacts the current literature by strengthening the evidence that ID consultation in children improves adherence to QCIs, and demonstrates that adherence to QCIs improves clinical outcomes.

Skin and Soft Tissue Infection Treatment and Prevention Practices by Pediatric Emergency Medicine Providers.

OBJECTIVE: The aim of the study was to evaluate skin and soft tissue infection (SSTI) treatment and prevention practices among pediatric emergency medicine (PEM) clinicians in the context of current clinical practice guidelines and contemporary evidence. METHODS: This was a cross-sectional survey of PEM clinicians belonging to the American Academy of Pediatrics Section on Emergency Medicine Survey listserv. Four varying hypothetical clinical scenarios of children with SSTI were posed to respondents; subsequent items assessed SSTI treatment and prevention practices. Provider demographics were collected. RESULTS: Of 160 survey respondents, more than half stated that they would prescribe oral antibiotics for each clinical scenario, particularly for more complex presentations (small uncomplicated abscess, 51.8%; large uncomplicated abscess, 71.5%; recurrent abscess, 83.5%; febrile abscess, 90.3%; P < 0.001). Most commonly selected antibiotics were clindamycin and trimethoprim-sulfamethoxazole. Across scenarios, more than 80% selected a duration of treatment 7 days or more. Of the 121 respondents who prescribe preventive measures, 85.1% recommend hygiene measures; 52.5% would prescribe decolonization with topical antibiotic ointment and 77.5% would recommend antiseptic body washes. Half of the respondents reported that their institution has standard guidance for SSTI management. CONCLUSIONS: Although current evidence supports adjuvant antibiotics for all drained SSTI and decolonization for the index patient and household contacts, PEM clinicians do not consistently adhere to these recommendations. In light of these findings, development and implementation of institutional guidelines are necessary to aid PEM clinicians' point-of-care decision making and improving evidence-based practice.

Equal but different! Improving care for older LGBT+ adults.

International human rights movements have improved the visibility and equality of lesbian, gay, bisexual and transgender+ (LGBT+) communities and their members. Health outcomes for LGBT+ people remain, however, worse than for their non-LGBT+ peers. Older LGBT+ people have experienced fewer positive changes, in part due to their lived experience of discrimination and their ongoing, unintentional invisibility in medical and social care. This article highlights the impacts of societal structure, health and social care on the lives of older LGBT+ people including physical and mental health, End of Life, Dementia, Housing and Care Settings, and a focus on the experiences of trans-people. We look at the existing improvements developed by LGBT+ communities (and their allies) and propose refreshing Person-Centred Care to improve inclusivity. Finally, we provide a framework for looking at the areas in which service challenges arise and suggest ways to address these to make health and social care services more ready to meet the needs of older LGBT+ people.

Longitudinal Dynamics of Skin Bacterial Communities in the Context of Staphylococcus aureus Decolonization.

Decolonization with topical antimicrobials is frequently prescribed in health care and community settings to prevent Staphylococcus aureus infection. However, effects on commensal skin microbial communities remains largely unexplored. Within a household affected by recurrent methicillin-resistant S. aureus skin and soft tissue infections (SSTI), skin swabs were collected from the anterior nares, axillae, and inguinal folds of 14 participants at 1- to 3-month intervals over 24 months. Four household members experienced SSTI during the first 12-months (observational period) and were prescribed a 5-day decolonization regimen with intranasal mupirocin and bleach water baths at the 12-month study visit. We sequenced the 16S rRNA gene V1-V2 region and compared bacterial community characteristics between the pre- and post-intervention periods and between younger and older subjects. The median Shannon diversity index was stable during the 12-month observational period at all three body sites. Bacterial community characteristics (diversity, stability, and taxonomic composition) varied with age. Among all household members, not exclusively among the four performing decolonization, diversity was unstable throughout the year post-intervention. In the month after decolonization, bacterial communities were changed. Although communities largely returned to their baseline states, relative abundance of some taxa remained changed throughout the year following decolonization (e.g., more abundant Bacillus; less abundant Cutibacterium). This 5-day decolonization regimen caused disruption of skin bacteria, and effects differed in younger and older subjects. Some effects were observed throughout the year post-intervention, which emphasizes the need for better understanding of the collateral effects of decolonization for S. aureus eradication. IMPORTANCE Decolonization with topical antimicrobials is frequently prescribed to prevent Staphylococcus aureus infection, but the effects on commensal skin bacteria are undetermined. We found that decolonization with mupirocin and bleach water baths leads to sustained disruption of bacterial communities.

BATF and IRF4 cooperate to counter exhaustion in tumor-infiltrating CAR T cells.

The transcription factors nuclear factor of activated T cells (NFAT) and activator protein 1 (AP-1; Fos-Jun) cooperate to promote the effector functions of T cells, but NFAT in the absence of AP-1 imposes a negative feedback program of T cell hyporesponsiveness (exhaustion). Here, we show that basic leucine zipper ATF-like transcription factor (BATF) and interferon regulatory factor 4 (IRF4) cooperate to counter T cell exhaustion in mouse tumor models. Overexpression of BATF in CD8+ T cells expressing a chimeric antigen receptor (CAR) promoted the survival and expansion of tumor-infiltrating CAR T cells, increased the production of effector cytokines, decreased the expression of inhibitory receptors and the exhaustion-associated transcription factor TOX and supported the generation of long-lived memory T cells that controlled tumor recurrence. These responses were dependent on BATF-IRF interaction, since cells expressing a BATF variant unable to interact with IRF4 did not survive in tumors and did not effectively delay tumor growth. BATF may improve the antitumor responses of CAR T cells by skewing their phenotypes and transcriptional profiles away from exhaustion and towards increased effector function.