Search

ABSTRACT Thousands of Pseudomonas aeruginosa RNA sequencing (RNA-seq) gene expression profiles are publicly available via the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA). In this work, the transcriptional profiles from hundreds of studies performed by over 75 research groups were reanalyzed in aggregate to create a powerful tool for hypothesis generation and testing. Raw sequence data were uniformly processed using the Salmon pseudoaligner, and this read mapping method was validated by comparison to a direct alignment method. We developed filtering criteria to exclude samples with aberrant levels of housekeeping gene expression or an unexpected number of genes with no reported values and normalized the filtered compendia using the ratio-of-medians method. The filtering and normalization steps greatly improved gene expression correlations for genes within the same operon or regulon across the 2,333 samples. Since the RNA-seq data were generated using diverse strains, we report the effects of mapping samples to noncognate reference genomes by separately analyzing all samples mapped to cDNA reference genomes for strains PAO1 and PA14, two divergent strains that were used to generate most of the samples. Finally, we developed an algorithm to incorporate new data as they are deposited into the SRA. Our processing and quality control methods provide a scalable framework for taking advantage of the troves of biological information hibernating in the depths of microbial gene expression data and yield useful tools for P. aeruginosa RNA-seq data to be leveraged for diverse research goals. IMPORTANCE Pseudomonas aeruginosa is a causative agent of a wide range of infections, including chronic infections associated with cystic fibrosis. These P. aeruginosa infections are difficult to treat and often have negative outcomes. To aid in the study of this problematic pathogen, we mapped, filtered for quality, and normalized thousands of P. aeruginosa RNA-seq gene expression profiles that were publicly available via the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA). The resulting compendia facilitate analyses across experiments, strains, and conditions. Ultimately, the workflow that we present could be applied to analyses of other microbial species.

ABSTRACT Pseudomonas aeruginosa is an opportunistic pathogen that causes difficult-to-treat infections. Two well-studied divergent P. aeruginosa strain types, PAO1 and PA14, have significant genomic heterogeneity, including diverse accessory genes present in only some strains. Genome content comparisons find core genes that are conserved across both PAO1 and PA14 strains and accessory genes that are present in only a subset of PAO1 and PA14 strains. Here, we use recently assembled transcriptome compendia of publicly available P. aeruginosa RNA sequencing (RNA-seq) samples to create two smaller compendia consisting of only strain PAO1 or strain PA14 samples with each aligned to their cognate reference genome. We confirmed strain annotations and identified other samples for inclusion by assessing each sample’s median expression of PAO1-only or PA14-only accessory genes. We then compared the patterns of core gene expression in each strain. To do so, we developed a method by which we analyzed genes in terms of which genes showed similar expression patterns across strain types. We found that some core genes had consistent correlated expression patterns across both compendia, while others were less stable in an interstrain comparison. For each accessory gene, we also determined core genes with correlated expression patterns. We found that stable core genes had fewer coexpressed neighbors that were accessory genes. Overall, this approach for analyzing expression patterns across strain types can be extended to other groups of genes, like phage genes, or applied for analyzing patterns beyond groups of strains, such as samples with different traits, to reveal a deeper understanding of regulation. IMPORTANCE Pseudomonas aeruginosa is a ubiquitous pathogen. There is much diversity among P. aeruginosa strains, including two divergent but well-studied strains, PAO1 and PA14. Understanding how these different strain-level traits manifest is important for identifying targets that regulate different traits of interest. With the availability of thousands of PAO1 and PA14 samples, we created two strain-specific RNA-seq compendia where each one contains hundreds of samples from PAO1 or PA14 strains and used them to compare the expression patterns of core genes that are conserved in both strain types and to determine which core genes have expression patterns that are similar to those of accessory genes that are unique to one strain or the other using an approach that we developed. We found a subset of core genes with different transcriptional patterns across PAO1 and PA14 strains and identified those core genes with expression patterns similar to those of strain-specific accessory genes.

Summary: The emergence of recombinant viruses is a threat to public health, as recombination may integrate variant-specific features that together result in escape from treatment or immunity. The selective advantages of recombinant SARS-CoV-2 isolates over their parental lineages remain unknown. We identified a Delta-Omicron (AY.45-BA.1) recombinant in an immunosuppressed transplant recipient treated with monoclonal antibody Sotrovimab. The single recombination breakpoint is located in the spike N-terminal domain adjacent to the Sotrovimab binding site. While Delta and BA.1 are sensitive to Sotrovimab neutralization, the Delta-Omicron recombinant is highly resistant. To our knowledge, this is the first described instance of recombination between circulating SARS-CoV-2 variants as a functional mechanism of resistance to treatment and immune escape.

Background and aimsHigh quality clinical research that addresses important questions requires significant resources. In resource-constrained environments, projects will therefore need to be prioritized. The Australia and New Zealand Musculoskeletal (ANZMUSC) Clinical Trials Network aimed to develop a stakeholder-based, transparent, easily implementable tool that provides a score for the 'importance' of a research question which could be used to rank research projects in order of importance.MethodsUsing a mixed-methods, multi-stage approach that included a Delphi survey, consensus workshop, inter-rater reliability testing, validity testing and calibration using a discrete-choice methodology, the Research Question Importance Tool (ANZMUSC-RQIT) was developed. The tool incorporated broad stakeholder opinion, including consumers, at each stage and is designed for scoring by committee consensus.ResultsThe ANZMUSC-RQIT tool consists of 5 dimensions (compared to 6 dimensions for an earlier version of RQIT): (1) extent of stakeholder consensus, (2) social burden of health condition, (3) patient burden of health condition, (4) anticipated effectiveness of proposed intervention, and (5) extent to which health equity is addressed by the research. Each dimension is assessed by defining ordered levels of a relevant attribute and by assigning a score to each level. The scores for the dimensions are then summed to obtain an overall ANZMUSC-RQIT score, which represents the importance of the research question. The result is a score on an interval scale with an arbitrary unit, ranging from 0 (minimal importance) to 1000. The ANZMUSC-RQIT dimensions can be reliably ordered by committee consensus (ICC 0.73-0.93) and the overall score is positively associated with citation count (standardised regression coefficient 0.33, pConclusionWe propose that the ANZMUSC-RQIT is a useful tool for prioritising the importance of a research question.

Much is known about environmental influences on metabolism and systemic insulin levels. Less is known about how those influences are translated into molecular mechanisms regulating insulin production. To better understand the molecular mechanisms we generated marked cells homozygous for a null mutation in the Drosophila TGF-β signal transducer dSmad2 in unmated adult females. We then conducted side-by-side single cell comparisons of the pixel intensity of two Drosophila insulin-like peptides (dILP2 and dILP5) in dSmad2- mutant and wild type insulin producing cells (IPCs). The analysis revealed multiple features of dSmad2 regulation of dILPs. In addition, we discovered that dILP5 is expressed and regulated by dSmad2 in circadian pacemaker cells (CPCs). Outcomes of regulation by dSmad2 differ between dILP2 and dILP5 within IPCs and differ for dILP5 between IPCs and CPCs. Modes of dSmad2 regulation differ between dILP2 and dILP5. dSmad2 antagonism of dILP2 in IPCs is robust but dSmad2 regulation of dILP5 in IPCs and CPCs toggles between antagonism and agonism depending upon dSmad2 dosage. Companion studies of dILP2 and dILP5 in the IPCs of dCORL mutant (fussel in Flybase and SKOR in mammals) and upd2 mutant unmated adult females showed no significant difference from wild type. Taken together, the data suggest that dSmad2 regulates dILP2 and dILP5 via distinct mechanisms in IPCs (antagonist) and CPCs (agonist) and in unmated adult females that dSmad2 acts independently of dCORL and upd2.

Large outdoor fires have become commonplace all over the world. The International Organization for Standardization (ISO) defines large outdoor fires as an urban fire, tsunami-generated fire, volcano-generated fire, wildland-urban interface (WUI) fire, wildland fire, or informal settlement fire, where the total burnout area is significant. Perhaps of all the large outdoor fires, it is wildland fires that spread into urban areas, simply called WUI fires that attract the most attention. A glance at the recent headlines in the summer of 2022 reveals numerous catastrophic WUI fires all over Europe. Across the Atlantic Ocean in the USA, there is yet another destructive WUI fire raging in the USA state of California. With the increasing risks from a changing climate, these large outdoor fire disasters are only going to become more and more commonplace all over the world. More homes will be lost and more lives will be lost. It is the authors opinion that a targeted, multi-disciplinary approach is needed to address the large outdoor fire problem. In this short, invited paper to Horizons in Mechanical Engineering, it is argued that large outdoor fire problem is a fascinating and challenging research area and that engineers have the necessary skills and training to impact a problem that influences millions upon millions of people all over the world. An important danger, present in all large outdoor fires, are firebrands. Firebrands are introduced for non-specialist readers, and the most recent literature is reviewed. Several challenges are discussed, in particular, areas where engineers may help move the needle forward on this globally important topic.

Elaborate behaviours are produced by tightly controlled flexor-extensor motor neuron activation patterns. Motor neurons are regulated by a network of interneurons within the spinal cord, but the computational processes involved in motor control are not fully understood. The neuroanatomical arrangement of motor and premotor neurons into topographic patterns related to their controlled muscles is thought to facilitate how information is processed by spinal circuits. Rabies retrograde monosynaptic tracing has been used to label premotor interneurons innervating specific motor neuron pools, with previous studies reporting topographic mediolateral positional biases in flexor and extensor premotor interneurons. To more precisely define how premotor interneurons contacting specific motor pools are organized, we used multiple complementary viral-tracing approaches in mice to minimize systematic biases associated with each method. Contrary to expectations, we found that premotor interneurons contacting motor pools controlling flexion and extension of the ankle are highly intermingled rather than segregated into specific domains like motor neurons. Thus, premotor spinal neurons controlling different muscles process motor instructions in the absence of clear spatial patterns among the flexor-extensor circuit components.

ABSTRACT The last 20 years have witnessed an explosion in publicly available gene expression and proteomic data and new tools to help researchers analyze these data. Tools typically include statistical approaches to identify differential expression, integrate prior knowledge, visualize results, and suggest how differential expression relates to changes in phenotype. Here, we provide a simple web-based tool that bridges some of the gaps between the functionality available to those studying eukaryotes and those studying prokaryotes. Specifically, our Shiny web application ESKAPE Act PLUS allows researchers to upload results of high-throughput bacterial gene or protein expression experiments from 13 species, including the six ESKAPE pathogens, to our system and receive (i) an analysis of which KEGG pathways or GO terms are significantly activated or repressed, (ii) visual representations of the magnitude of activation or repression in each category, and (iii) detailed diagrams showing known relationships between genes in each regulated KEGG pathway and fold changes of individual genes. Importantly, our statistical approach does not require users to identify which genes or proteins are differentially expressed. ESKAPE Act PLUS provides high-quality statistics and graphical representations not available using other web-based systems to assess whether prokaryotic biological functions are activated or repressed by experimental conditions. To our knowledge, ESKAPE Act PLUS is the first application that provides pathway activation analysis and pathway-level visualization of gene or protein expression for prokaryotes. IMPORTANCE ESKAPE pathogens are bacteria of concern because they develop antibiotic resistance and can cause life-threatening infections, particularly in more susceptible immunocompromised people. ESKAPE Act PLUS is a user-friendly web application that will advance research on ESKAPE and other pathogens commonly studied by the biomedical community by allowing scientists to infer biological phenotypes from the results from high-throughput bacterial gene or protein expression experiments. ESKAPE Act PLUS currently supports analysis of 23 strains of bacteria from 13 species and can also be used to re-analyze publicly available data to generate new findings and hypotheses for follow-up experiments.

Abstract The millennial-scale variability of the Atlantic Meridional Overturning Circulation (AMOC) is well documented for the last glacial termination and beyond. Despite its importance for the climate system, the evolution of the South Pacific overturning circulation (SPOC) is by far less well understood. A recently published study highlights the potential applicability of the 231Pa/230Th-proxy in the Pacific. Here, we present five sedimentary down-core profiles of 231Pa/230Th-ratios measured on a depth transect from the Pacific sector of the Southern Ocean to test this hypothesis using downcore records. Our data are consistent with an increase in SPOC as early as 20 ka that peaked during Heinrich Stadial 1. The timing indicates that the SPOC did not simply react to AMOC changes via the bipolar seesaw but were triggered via Southern Hemisphere processes.

Here, the authors describe the emergence and spread of a new potential SARS-CoV-2 variant of interest, B.1.620. They show that this lineage, first identified in Lithuania, has established local transmission in Europe on multiple occasions and likely emerged in Central Africa.

Abstract At the end of 2020, several new variants of SARS-CoV-2—designated variants of concern—were detected and quickly suspected to be associated with a higher transmissibility and possible escape of vaccine-induced immunity. In Belgium, this discovery has motivated the initiation of a more ambitious genomic surveillance program, which is drastically increasing the number of SARS-CoV-2 genomes to analyse for monitoring the circulation of viral lineages and variants of concern. In order to efficiently analyse the massive collection of genomic data that are the result of such increased sequencing efforts, streamlined analytical strategies are crucial. In this study, we illustrate how to efficiently map the spatio-temporal dispersal of target mutations at a regional level. As a proof of concept, we focus on the Belgian province of Liège that has been consistently sampled throughout 2020, but was also one of the main epicenters of the second European epidemic wave. Specifically, we employ a recently developed phylogeographic workflow to infer the regional dispersal history of viral lineages associated with three specific mutations on the spike protein (S98F, A222V and S477N) and to quantify their relative importance through time. Our analytical pipeline enables analysing large data sets and has the potential to be quickly applied and updated to track target mutations in space and time throughout the course of an epidemic.

Summary: Background: A comparison of pneumonias due to SARS-CoV-2 and influenza, in terms of clinical course and predictors of outcomes, might inform prognosis and resource management. We aimed to compare clinical course and outcome predictors in SARS-CoV-2 and influenza pneumonia using multi-state modelling and supervised machine learning on clinical data among hospitalised patients. Methods: This multicenter retrospective cohort study of patients hospitalised with SARS-CoV-2 (March-December 2020) or influenza (Jan 2015-March 2020) pneumonia had the composite of hospital mortality and hospice discharge as the primary outcome. Multi-state models compared differences in oxygenation/ventilatory utilisation between pneumonias longitudinally throughout hospitalisation. Differences in predictors of outcome were modelled using supervised machine learning classifiers. Findings: Among 2,529 hospitalisations with SARS-CoV-2 and 2,256 with influenza pneumonia, the primary outcome occurred in 21% and 9%, respectively. Multi-state models differentiated oxygen requirement progression between viruses, with SARS-CoV-2 manifesting rapidly-escalating early hypoxemia. Highly contributory classifier variables for the primary outcome differed substantially between viruses. Interpretation: SARS-CoV-2 and influenza pneumonia differ in presentation, hospital course, and outcome predictors. These pathogen-specific differential responses in viral pneumonias suggest distinct management approaches should be investigated. Funding: This project was supported by NIH/NCATS UL1 TR002345, NIH/NCATS KL2 TR002346 (PGL), the Doris Duke Charitable Foundation grant 2015215 (PGL), NIH/NHLBI R35 HL140026 (CSC), and a Big Ideas Award from the BJC HealthCare and Washington University School of Medicine Healthcare Innovation Lab and NIH/NIGMS R35 GM142992 (PS).

Introduction: In response to the ongoing opioid overdose crisis, US officials urged the expansion of access to naloxone for opioid overdose reversal. Since then, emergency medical services’ (EMS) dispensing of naloxone kits has become an emerging harm reduction strategy. Methods: We created a naloxone training and low-barrier distribution program in San Francisco: Project FRIEND (First Responder Increased Education and Naloxone Distribution). The team assembled an advisory committee of stakeholders and subject-matter experts, worked with local and state EMS agencies to augment existing protocols, created training curricula, and developed a naloxone-distribution data collection system. Naloxone kits were labeled for registration and data tracking. Emergency medical technicians and paramedics were asked to distribute naloxone kits to any individuals (patient or bystander) they deemed at risk of experiencing or witnessing an opioid overdose, and to voluntarily register those kits. Results: Training modalities included a video module (distributed to over 700 EMS personnel) and voluntary, in-person training sessions, attended by 224 EMS personnel. From September 25, 2019–September 24, 2020, 1,200 naloxone kits were distributed to EMS companies. Of these, 232 kits (19%) were registered by EMS personnel. Among registered kits, 146 (63%) were distributed during encounters for suspected overdose, and 103 (44%) were distributed to patients themselves. Most patients were male (n = 153, 66%) and of White race (n = 124, 53%); median age was 37.5 years (interquartile range 31–47). Conclusion: We describe a successful implementation and highlight the feasibility of a low-threshold, leave-behind naloxone program. Collaboration with multiple entities was a key component of the program’s success.

Objectives: Venous thrombosis has been widely described in the setting of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection; however, arterial thrombosis has rarely been reported. This study aims to assess the incidence, risk factors, interventions, and outcomes of acute aortoiliac arterial thrombosis in patients with active SARS-CoV-2 infections. Methods: We present seven SARS-CoV-2-positive patients from our institution who acutely developed thrombi in the aortoiliac arterial system (7/2020-1/2021). A systematic review of the literature on aortoiliac arterial thrombosis in patients with SARS-CoV-2 infections in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines was also performed. The available data from all reported cases in the literature and at our institution were analyzed. Results: Thirty published articles and journal correspondences, including 52 patients, were reviewed and analyzed in addition to our institution's 7 cases. In total, 59 SARS-CoV-2-positive patients were found to have acute aortoiliac thrombosis. The abdominal aorta was the most frequent location for the development of a thrombus. Baseline demographics and medical comorbidities were not significantly different between the symptomatic and asymptomatic cohorts. Seventy-one percent of patients were symptomatic (lower limb ischemia: 75.0%, renal infarction: 20.0%, stroke: 12.5%, mesenteric ischemia: 10.0%). All patients with thrombus involving the ascending aorta, aortic bifurcation, or iliac artery developed thromboembolic or ischemic complications. All patients received systemic anticoagulation. Fifty-three percent of all patients were managed medically. Ninety-four percent of the asymptomatic patients were managed medically. One asymptomatic patient underwent endovascular aspiration of a mobile thrombus. Three (23.1%) deaths occurred in the asymptomatic cohort from hypoxic respiratory failure. Fourteen (36.8%) deaths occurred in the symptomatic cohort. The in-hospital mortality rate was 33.3% overall and 43.8% for patients with thrombi involving more than one aortoiliac segment. Conclusions: The presence of thrombi in the aortoiliac arterial system appears to be a poor prognostic indicator for patients with active SARS-CoV-2 infections. Medical management of patients with asymptomatic aortoiliac thrombi may be considered. The presence of thrombi involving the ascending aorta, aortic bifurcation, or iliac artery may warrant consideration for operative intervention due to the risk for thromboembolic or ischemic complications. Further study is needed to fully delineate the risk factors, optimal treatment, and outcomes of arterial thrombosis in the setting of SARS-CoV-2 infection.

Opposing evidence exists for the source of the hydrogen ions (H+) during ketoacidosis. Organic and computational chemistry using dissociation constants and alpha equations for all pertinent ionizable metabolites were used to (1) document the atomic changes in the chemical reactions of ketogenesis and ketolysis and (2) identify the sources and quantify added fractional (~) H+ exchange (~H+e). All computations were performed for pH conditions spanning from 6.0 to 7.6. Summation of the ~H+e for given pH conditions for all substrates and products of each reaction of ketogenesis and ketolysis resulted in net reaction and pathway ~H+e coefficients, where negative revealed ~H+ release and positive revealed ~H+ uptake. Results revealed that for the liver (pH = 7.0), the net ~H+e for the reactions of ketogenesis ending in each of acetoacetate (AcAc), β-hydroxybutyrate (β-HB), and acetone were −0.9990, 0.0026, and 0.0000, respectively. During ketogenesis, ~H+ release was only evident for HMG CoA production, which is caused by hydrolysis and not ~H+ dissociation. Nevertheless, there is a net ~H+ release during ketogenesis, though this diminishes with greater proportionality of acetone production. For reactions of ketolysis in muscle (pH = 7.1) and brain (pH = 7.2), net ~H+ coefficients for β-HB and AcAc oxidation were −0.9649 and 0.0363 (muscle), and −0.9719 and 0.0291 (brain), respectively. The larger ~H+ release values for β-HB oxidation result from covalent ~H+ release during the oxidation–reduction. For combined ketogenesis and ketolysis, which would be the metabolic condition in vivo, the net ~H+ coefficient depends once again on the proportionality of the final ketone body product. For ketone body production in the liver, transference to blood, and oxidation in the brain and muscle for a ratio of 0.6:0.2:0.2 for β-HB:AcAc:acetone, the net ~H+e coefficients for liver ketogenesis, blood transfer, brain ketolysis, and net total (ketosis) equate to −0.1983, −0.0003, −0.2872, and −0.4858, respectively. The traditional theory of ketone bodies being metabolic acids causing systemic acidosis is incorrect. Summation of ketogenesis and ketolysis yield H+ coefficients that differ depending on the proportionality of ketone body production, though, in general, there is a small net H+ release during ketosis. Products formed during ketogenesis (HMG-CoA, acetoacetate, β-hydroxybutyrate) are created as negatively charged bases, not acids, and the final ketone body, acetone, does not have pH-dependent ionizable groups. Proton release or uptake during ketogenesis and ketolysis are predominantly caused by covalent modification, not acid dissociation/association. Ketosis (ketogenesis and ketolysis) results in a net fractional H+ release. The extent of this release is dependent on the final proportionality between acetoacetate, β-hydroxybutyrate, and acetone.

Summary The ability to directly modify native and established biofilms has enormous potential in understanding microbial ecology and application of biofilm in 'real‐world' systems. However, efficient genetic transformation of established biofilms at any scale remains challenging. In this study, we applied an ultrasound‐mediated DNA delivery (UDD) technique to introduce plasmid to established non‐competent biofilms in situ. Two different plasmids containing genes coding for superfolder green fluorescent protein (sfGFP) and the flavin synthesis pathway were introduced into established bacterial biofilms in microfluidic flow (transformation efficiency of 3.9 ± 0.3 × 10‐7 cells in biofilm) and microbial fuel cells (MFCs), respectively, both employing UDD. Gene expression and functional effects of genetically modified bacterial biofilms were observed, where some cells in UDD‐treated Pseudomonas putida UWC1 biofilms expressed sfGFP in flow cells and UDD‐treated Shewanella oneidensis MR‐1 biofilms generated significantly (P

Abstract Background Despite cumulative socioeconomic disadvantage and risk factors, Black Americans have a lower prevalence of depression than whites. Given the emerging focus of depression as a public mental health crisis, culturally informed depression measures and scale development techniques are needed to better alleviate the mental health burden of socially marginalized populations. Yet, for Black men, race- and gender-related factors that position emotional vulnerability as a sign of weakness, may potentially mask the timely identification of mental health needs in this population. Thus, we address these gaps by employing a stakeholder-driven, community-engaged process for understanding Black men’s depression experience. Methods We use concept mapping, a structured mixed methods approach, to determine how stakeholders of Black men’s health conceptualize their depressive symptoms. Thirty-six stakeholders participated in a three-phase concept mapping study conducted in 2018. Three separate stakeholder groups were engaged for this study, including Black men, Black women, and primary care providers. Results Participants generated 68 characteristics of Black men’s depression which were reflected within five conceptual clusters: (1) physical states; (2) emotional states; (3) diminished drive; (4) internal conflicts; (5) communication with others; and (6) social pressures. Using a content analysis approach, we found that items comprising the “social pressures” cluster were not reflected in any common depression scales. Conclusions Findings from this study illustrate the similar and divergent pathways in which Black men express depressed mood. Furthermore, concept mapping results also yield a novel opportunity for culturally informed scale development in future research.

MDM2 and MDM4 proteins are key negative regulators of tumor suppressor p53. MDM2 and MDM4 interact via their RING domains and form a heterodimer polyubiquitin E3 ligase essential for p53 degradation. MDM4 also forms heterodimer E3 ligases with MDM2 isoforms that lack p53-binding domains, which regulate p53 and MDM4 stability. We are working to identify small-molecule inhibitors targeting the RING domain of MDM2-MDM4 (MMRi) that can inactivate the total oncogenic activity of MDM2-MDM4 heterodimers. Here, we describe the identification and characterization of MMRi62 as an MDM4-degrader and apoptosis inducer in leukemia cells. Biochemically, in our experiments, MMRi62 bound to preformed RING domain heterodimers altered the substrate preference toward MDM4 ubiquitination and promoted MDM2-dependent MDM4 degradation in cells. This MDM4-degrader activity of MMRi62 was found to be associated with potent apoptosis induction in leukemia cells. Interestingly, MMRi62 effectively induced apoptosis in p53 mutant, multidrug-resistant leukemia cells and patient samples in addition to p53 wild-type cells. In contrast, MMRi67 as a RING heterodimer disruptor and an enzymatic inhibitor of the MDM2-MDM4 E3 complex lacked MDM4-degrader activity and failed to induce apoptosis in these cells. In summary, this study identifies MMRi62 as a novel MDM2-MDM4-targeting agent and suggests that small molecules capable of promoting MDM4 degradation may be a viable new approach to killing leukemia cells bearing non-functional p53 by apoptosis.

This multiple case study investigated a peer-based intervention and instruction (PBII) for social play, Play Time/Social Time (PT/ST), in four inclusive Swedish preschools. PT/ST contains 28 learning activities where children playfully practice six social skills with significance for social play and friendships. One teacher in each preschool was trained and instructed to implement PT/ST, two with coaching early in the implementation, and two without. At each preschool, one child with special educational needs (SEN) in social play (n = 4) and one or two socially skilled peers (n = 6) participated. The study aimed to explore how the teachers perceived the influence of PT/ST on social engagement and social play skills in the children with SEN, with/without coaching, and if PT/ST supported social play between the children with and without SEN. It also aimed to examine the feasibility of PT/ST and the influence on preschool inclusion quality in the preschools, with/without coaching. Observational assessments and video observations were used. The results indicate that PT/ST was beneficial for the children with SEN to engage in social play with peers and practice social skills, and for the preschool’s inclusion quality regarding involvement in peer interactions and guidance in play, both with/without coaching for the teachers. However, the coaching strengthened the intervention fidelity. Social play occurred between the children with and without SEN in activities where they seemed similarly attracted by the toys and play materials and when they all could engage in the play goals, tasks, and roles. For this, they sometimes needed instructions and encouragement from the teachers.

Although US tobacco use trends show overall improvement, social disadvantage continues to drive significant disparities. Traditional tobacco cessation interventions and public policy initiatives have failed to equitably benefit socially-disadvantaged populations. Advancements in mobile digital technologies have created new opportunities to develop resource-efficient mobile health (mHealth) interventions that, relative to traditional approaches, have greater reach while still maintaining comparable or greater efficacy. Their potential for affordability, scalability, and efficiency gives mHealth tobacco cessation interventions potential as tools to help redress tobacco use disparities. We discuss our perspectives on the state of the science surrounding mHealth tobacco cessation interventions for use by socially-disadvantaged populations. In doing so, we outline existing models of health disparities and social determinants of health (SDOH) and discuss potential ways that mHealth interventions might be optimized to offset or address the impact of social determinants of tobacco use. Because smokers from socially-disadvantaged backgrounds face multi-level barriers that can dynamically heighten the risks of tobacco use, we discuss cutting-edge mHealth interventions that adapt dynamically based on context. We also consider complications and pitfalls that could emerge when designing, evaluating, and implementing mHealth tobacco cessation interventions for socially-disadvantaged populations. Altogether, this perspective article provides a conceptual foundation for optimizing mHealth tobacco cessation interventions for the socially-disadvantaged populations in greatest need.

Neutrophils play a major role in many equine conditions, including equine asthma, laminitis, and intestinal ischemia and reperfusion injury, and therefore represent an attractive target for innovative therapeutic approaches. Novel strategies for reducing neutrophilic inflammation include modulation of neutrophil functions and lifespan. Withaferin A (WFA) is a phytochemical with well-established in vitro and in vivo anti-inflammatory properties, but its direct effects on neutrophils are largely unknown. We hypothesized that WFA would inhibit adhesion, migration, and respiratory burst by equine neutrophils and promote timely apoptosis of primed equine neutrophils. Consistent with this hypothesis, our data show that WFA causes a significant, concentration-dependent inhibition of equine neutrophil adhesion, migration, and respiratory burst in response to diverse stimuli. Further, WFA treatment increased apoptosis of equine neutrophils exposed to GM-CSF for 24 h. This pro-apoptotic effect of WFA was not observed in unprimed neutrophils, nor at the 2-h time point relevant to our functional neutrophil experiments. Our data demonstrate that WFA may reduce neutrophil-mediated inflammation through multiple mechanisms, including suppression of inflammatory responses and promotion of apoptosis. Additional research is needed to elucidate the molecular mechanisms for these effects and evaluate the potential clinical use of WFA in veterinary and human patients.

Objectives: The effect of lockdown periods on the number of residential fires was investigated based on three factors: the weekly change in the number of residential fires, the time of the day of residential fires, and the notional cost associated with residential fires. Study design: observational study. Methods: Analysis from Open Data Source. A new index was introduced and the weekly change during the lockdown periods was investigated to accommodate the seasonal differences in the number of residential fires. Results: From the index change, the number of residential fires increased at the beginning of each lockdown period. The timing of residential fires shifted during the day. Conclusions: These changes were associated with meal preparation or mealtimes. Adjustment to lockdowns as the global pandemic dragged on, such as changes to mealtimes, and getting used to lockdown life, are believed to be responsible for these changes.

Habitat loss and degradation represent a major threat to Nearctic-neotropical migratory birds in the tropics. Managed agroecosystems have the potential to mitigate some impacts of land conversion, however, we know little regarding the quality of expanding oil palm plantation habitat for migratory birds in the neotropics. In this study, we used sex and age ratios, body condition, fat deposition, and muscle mass to assess oil palm habitat quality for seven species of migratory songbirds. Specifically, we captured individuals in native forest fragments and oil palm plantations in the state of Tabasco, Mexico, during two winter seasons (2017–2018, 2018–2019), and compared differences in age and sex ratios, and condition indices between habitats. We found that, when differences occurred, most species exhibited indicators of better habitat quality in native forest (older males with higher body condition indices) when compared to oil palm. Our results suggest that age and sex ratios combined with measures of physiological condition can be used to assess habitat quality for Nearctic-neotropical migratory birds overwintering in modified landscapes. Importantly, determining a species’ territorial behavior is key when selecting a given indicator of habitat quality for each species, and in certain cases, more intensive approaches such as estimates of survival, territory size, and food availability may be needed. Our results suggest that management strategies that promote forest-like conditions in oil palm plantations will improve habitat quality for declining populations of Nearctic-neotropical migratory birds.

Abstract Background Past studies examining the health outcomes of diabetes mellitus (DM) patients found that social determinants of health disparities were associated with variabilities in health outcomes. However, improving access to healthcare, such as health insurance, should mitigate negative health outcomes. The aim of the study was to explore the association between four types of health insurance, namely, Medicare Fee-For-Service (FFS), Medicare Managed Care (MC), Private FFS, and Private MC plans, and the health outcomes of DM patients, controlling for patients’ social determinants of health. Methods This is a retrospective cross-sectional archival record study to explore the relationships between types of health insurance and health outcomes of DM patients who were at least 65 years old, or the elderly. Data was drawn from the 2012 Maryland Clinical Public Use Data and received an exempt status from our Institutional Review Board. Elderly Maryland residents with chronic DM were included in the study, resulting in a sample size of 43,519 individuals. Predictor variables were four types of insurance and health outcome variables were length of hospital stay (LOS), 30-day readmission, and end-stage renal disease (ESRD). Control variables included hospital characteristics, patient characteristics, and social determinants of health. Student’s t-tests determined the statistical differences for the control variables between the types of insurance. Multiple hierarchical regression analysis was applied to test the association between insurance plans and LOS, while logistic regression analyses were applied to test the association between insurance plans with 30-day readmission and ESRD. Statistical significance was set at p

Abstract We consider a quantum relay that is used by two parties to perform several continuous-variable protocols of quantum communication, from entanglement distribution (swapping and distillation) to quantum teleportation, and quantum key distribution. The theory of these protocols is suitably extended to a non-Markovian model of decoherence characterized by correlated Gaussian noise in the bosonic environment. In the worst-case scenario where bipartite entanglement is completely lost at the relay, we show that the various protocols can be reactivated by the assistance of classical (separable) correlations in the environment. In fact, above a critical amount, these correlations are able to guarantee the distribution of a weaker form of entanglement (quadripartite), which can be localized by the relay into a stronger form (bipartite) that is exploitable by the parties. Our findings are confirmed by a proof-of-principle experiment where we show, for the first time, that memory effects in the environment can drastically enhance the performance of a quantum relay, well beyond the single-repeater bound for quantum and private communications.

Objective Prednisolone is an effective oral glucocorticoid for managing symptoms of rheumatoid arthritis (RA) but has predictable and common adverse effects. We explored patient perspectives of prednisolone use in RA. Methods Patients with RA registered with the Australian Rheumatology Association Database (ARAD) who had completed an ARAD questionnaire in the preceding 12 months were invited to participate in an online survey. Responses were linked to already collected respondent demographics, medication use, and patient‐reported outcome measures. The Beliefs about Medicine Questionnaire (BMQ) measured patient beliefs on medication necessity and concerns. Free‐text responses outlining reasons for stopping or declining prednisolone underwent thematic analysis using NVivo 12. Results The survey response rate was 79.6% (804/1010), including 251 (31.2%) reporting current prednisolone use and 432 (53.7%) reporting previous use. Compared with previous users, current users were older (P = 0.0002) and had worse self‐reported pain, disease activity, health‐related quality of life, and function (all P < 0.001). Current users had higher BMQ scores for prednisolone‐specific necessity (3.6 versus 1.7; P

Abstract Background Malaria is one of the most serious infectious diseases in the world. The malaria burden is greatly affected by human immunity, and immune responses vary between populations. Genetic diversity in KIR and HLA-C genes, which are important in immunity to infectious diseases, is likely to play a role in this heterogeneity. Several studies have shown that KIR and HLA-C genes influence the immune response to viral infections, but few studies have examined the role of KIR and HLA-C in malaria infection, and these have used low-resolution genotyping. The aim of this study was to determine whether genetic variation in KIR and their HLA-C ligands differ in Ugandan populations with historically varied malaria transmission intensity using more comprehensive genotyping approaches. Methods High throughput multiplex quantitative real-time PCR method was used to genotype KIR genetic variants and copy number variation and a high-throughput real-time PCR method was developed to genotype HLA-C1 and C2 allotypes for 1344 participants, aged 6 months to 10 years, enrolled from Ugandan populations with historically high (Tororo District), medium (Jinja District) and low (Kanungu District) malaria transmission intensity. Results The prevalence of KIR3DS1, KIR2DL5, KIR2DS5, and KIR2DS1 genes was significantly lower in populations from Kanungu compared to Tororo (7.6 vs 13.2%: p = 0.006, 57.2 vs 66.4%: p = 0.005, 33.2 vs 46.6%: p

Palayam, Ganapathy, Guercio et al. determine the crystal structure of the photosensory domain of Arabidopsis Cryptochrome-2 (CRY2) in a tetrameric active state, identifying critical residues that participate in photo-induced oligomerization of CRY2. This study offers an updated model of CRY’s photoactivation mechanism.

Abstract Background Many point-of-care ultrasound devices are now “pocket-sized” or handheld, allowing easy transport during travel and facilitating use in crowded spaces or in austere low-resource settings. Concerns remain about their durability, image quality, and clinical utility in those environments. Method Five emergency physicians with training in point-of-care ultrasound employed the Butterfly iQ, a novel handheld ultrasound device, in routine clinical care in a busy, high-acuity African emergency department over a period of 10 weeks. We retrospectively evaluated the performance of the Butterfly iQ from the perspectives of both the clinicians using the device and expert ultrasound faculty reviewing the images. Results We found advantages of the Butterfly iQ in a high-acuity African emergency department include its use of a single probe for multiple functions, small size, ease of transport, relatively low cost, and good image quality in most functions. Disadvantages include large probe footprint, lower, though still adequate, cardiac imaging quality, frequent overheating, and reliance on internet-based cloud storage, but these were surmountable. We also report a wide variety of patient presentations, pathology, and procedures to which the device was used. Conclusion We conclude the Butterfly iQ is an effective, though imperfect, point-of-care ultrasound device in a low-resource emergency setting. We will continue to employ the device in clinical emergency care and teaching in this setting.

A Southern Ocean influences on the carbon cycle is considered a key component of deglacial changes. Here, the authors show spatial differences in glacial Southern Ocean carbon storage that dissipated rapidly 14.6 kyr ago, revealing a South Indian Ocean contribution to rapid deglacial atmospheric CO2 increases.

Multidrug-resistant Salmonella enterica subspecies enterica 4,[5],12:i:- sequence type 34 represents a worldwide public health risk. To determine its origin in the United States, we reconstructed a time-scaled phylogeny with a discrete trait geospatial model. The clone in the United States was introduced from Europe on multiple occasions in the early 2000s.

Abstract Considering the BSSF steelmaking slag generated in a Brazilian steelwork, it would be worth to separate iron and calcium from it, with the objective of increasing its iron content, or producing Fe2O3 and CaO by selective precipitation from cations in aqueous solution. In this way, materials could be produced and used in-house, e.g., sintering plant. This possibility was explored through acid leaching for an industrial sample. A possibility to increase concentration of iron of the slag is to leach it with a 2 mol.L-1 HCl solution; in this condition, 63.6% of the CaO is extracted from the slag to the aqueous solution, and Fe content of the slag increases from 27.4 to 37.1 wt%. Another possibility is to use HCl 5 mol.L-1; in this condition, 86.8% of the Fe and 90.7% of the CaO are transferred to the liquid solution. Then separation of iron and calcium can be achieved by selective precipitation: firstly, adding ammonia to precipitate Fe(OH)3, and then calcinating it to produce Fe2O3 (~ 200 °C); in the following, adding sodium carbonate to precipitate CaCO3, which in turn can be calcinated to produce CaO (~ 900 °C). In this way, Fe2O3 and CaO could be produced.

During late spring 2020, when states were issuing stay-at-home orders, the majority of congregations and Americans followed protocols and avoided in-person worship. Yet a vocal minority of Americans defied protocols and gathered in worship. The authors use national panel data collected in mid-May and August 2020 to assess whether Americans who attended worship more frequently during lockdown restrictions were more likely to report testing positive for coronavirus disease 2019 (COVID-19) three months later. Accounting for relevant correlates including mask use, general attendance at large gatherings, and knowing others who had tested positive, the likelihood that Americans tested positive for COVID-19 between May and August 2020 grew almost linearly as Americans attended in-person worship more frequently during lockdown. However, interactions indicate that this increase was limited primarily to those who were not regular attenders previously. The results suggest that worship attendance during lockdown substantially increased COVID-19 infections for the minority who attended possibly as a form of protest.

Summary: microRNAs (miRNAs) have unique gene regulatory effects in different neuronal subpopulations. Here, we describe a protocol to identify neuronal subtype-specific effects of a miRNA in murine motor neuron subpopulations. We detail the preparation of primary mouse spinal tissue for single cell RNA sequencing and bioinformatics analyses of pseudobulk expression data. This protocol applies differential gene expression testing approaches to identify miRNA target networks in heterogeneous neuronal subpopulations that cannot otherwise be captured by bulk RNA sequencing approaches.For complete details on the use and execution of this protocol, please refer to Amin et al. (2021).

Failure to maintain segregation of oral and gut microbial communities has been linked to several diseases. We sought to characterize oral-fecal microbiome community coalescence, ectopic extension of oral bacteria, clinical variables contributing to this phenomenon, and associated infectious consequences by analyzing the 16S rRNA V4 sequences of longitudinal fecal (n=551) and oral (n=737) samples from 97 patients with acute myeloid leukemia (AML) receiving induction chemotherapy (IC). Clustering observed in permutation based multivariate analysis of variance (PERMANOVA) of Bray-Curtis dissimilarity and PCoA plot of UniFrac distances between intra-patient longitudinal oral-stool sample pairs suggested potential oral-stool microbial community coalescence. Bray-Curtis dissimilarities and UniFrac distances were used to create an objective definition of microbial community coalescence. We determined that only 23 of the 92 patients exhibited oral-stool community coalescence. This was validated through a linear mixed model which determined that patients who experienced coalescence had an increased proportion of shared to unique OTUs between their oral-stool sample pairs over time compared to non-coalesced patients. Evaluation of longitudinal microbial characteristics revealed that patients who experienced coalescence had increased stool abundance of Streptococcus and Stenotrophomonas compared to non-coalesced patients. When treated as a time-varying covariate, each additional day of linezolid (HR 1.15, 95% CI 1.06 – 1.24, P

PURPOSEThe global pediatric oncology clinical research landscape, particularly in Central and South America, Africa, and Asia, which bear the highest burden of global childhood cancer cases, is less characterized in the literature. Review of how existing pediatric cancer clinical trial groups internationally have been formed and how their research goals have been pursued is critical for building global collaborative research and data-sharing efforts, in line with the WHO Global Initiative for Childhood Cancer.METHODSA narrative literature review of collaborative groups performing pediatric cancer clinical research in each continent was conducted. An inventory of research groups was assembled and reviewed by current pediatric cancer regional and continental leaders. Each group was narratively described with identification of common structural and research themes among consortia.RESULTSThere is wide variability in the structure, history, and goals of pediatric cancer clinical trial collaborative groups internationally. Several continental regions have longstanding endogenously-formed clinical trial groups that have developed and published numerous adapted treatment regimens to improve outcomes, whereas other regions have consortia focused on developing foundational database registry infrastructure supported by large multinational organizations or twinning relationships.CONCLUSIONThere cannot be a one-size-fits-all approach to increasing collaboration between international pediatric cancer clinical trial groups, as this requires a nuanced understanding of local stakeholders and resources necessary to form partnerships. Needs assessments, performed either by local consortia or in conjunction with international partners, have generated productive clinical trial infrastructure. To achieve the goals of the Global Initiative for Childhood Cancer, global partnerships must be sufficiently granular to account for the distinct needs of each collaborating group and should incorporate grassroots approaches, robust twinning relationships, and implementation science.

Abstract Background Black individuals with muscle‐invasive bladder cancer (MIBC) experienced 21% lower odds of guideline‐based treatment (GBT) and differences in treatment explain 35% of observed Black‐White differences in survival. Yet little is known of how interactions between race/ethnicity and receipt of GBT drive within‐ and between‐race survival differences. Methods Black, White, and Latino individuals diagnosed with nonmetastatic, locally advanced MIBC from 2004 to 2013 within the National Cancer Database were included. Guideline‐based treatment was defined as the receipt including one or more of the following treatment modalities: radical cystectomy (RC), neoadjuvant chemotherapy with RC, RC with adjuvant chemotherapy, and/or chemoradiation based on American Urological Association guidelines. Cox proportional hazards model of mortality estimated effects of GBT status, race/ethnicity, and the GBT‐by‐race/ethnicity interaction, adjusting for covariates. Results Of the 54 910 MIBC individuals with 125 821 person‐years of posttreatment observation (max = 11 years), 6.9% were Black, and 3.0% were Latino. Overall, 51.4%, 45.3%, and 48.5% of White, Black, and Latino individuals received GBT. Latino individuals had lower hazard of death compared to Black (HR 0.81, 95% CI 0.75‐0.87) and White individuals (HR 0.92, 95% 0.86‐0.98). With GBT, Latino and White individuals had similar outcomes (HR = 1.00, 95% 0.91‐1.10) and both fared better than Black individuals (HR = 0.88, 95% 0.79‐0.99 and HR = 0.88, 95% 0.83‐0.94, respectively). Without GBT, Latino individuals fared better than White (HR = 0.85, 95% 0.77‐0.93) and Black individuals (HR = 0.74, 95% 0.67‐0.82) while White individuals fared better than Black individuals (HR = 0.87, 95% 0.83‐0.92). Black individuals with GBT fared worse than Latinos without GBT (HR = 1.02, 95% 0.92‐1.14), although not statistically significant. Conclusion Low GBT levels demonstrated an “under‐allocation” of GBT to those who needed it most—Black individuals. Interventions to improve GBT allocation may mitigate race‐based survival differences observed in MIBC.

Most data-independent acquisition (DIA) methods depend on mass spectral libraries for peptide identification but tools to assess library quality are lacking. Here, the authors develop DIALib- QC for the systematic evaluation and correction of spectral libraries.

Spatiotemporal sampling gaps in existing pathogen genomic data limits their use in understanding epidemiological patterns. Here, the authors apply a phylogeographic approach with SARS-CoV-2 genomes to accurately reproduce pathogen spread by accounting for spatial biases and travel history of the individual.

Abstract Background Cancer survivors experience compromised quality of life due to impaired cognitive function as a result of cancer diagnosis and treatment. Although exercise has proven to be effective in improving cognitive function across the lifespan, interventions comprehensively testing the effectiveness for cancer survivors are limited. The STAY Fit Trial is a three-armed pilot randomized controlled trial designed to compare the effects of a 12-week yoga, aerobic walking, and stretch and tone intervention on cognitive function among adult cancer survivors. Methods This pilot study aims to recruit 75 adult cancer survivors who will complete assessments of cognitive function, cardiovascular fitness, physical activity, and psychosocial measures at baseline and after the 12-week intervention. The aims of STAY Fit are (1) to assess the efficacy of yoga to improve cognitive function among cancer survivors, compared to aerobic exercise and an active control group; (2) to examine changes in cardiovascular fitness as a result of the interventions; and (3) to assess changes in quality of life among our population as a result of the exercise interventions. Discussion The STAY Fit Trial will test the effectiveness of yoga, aerobic exercise, and stretching and toning exercises in improving cognitive function and fitness among adult cancer survivors. The results of this pilot study will enable us to understand the most effective physical activity modality to improve cognitive function in this population and potentially combat cancer-related cognitive impairment. Trial registration ClinicalTrials.gov NCT03650322 . Registered on 28 August 2018.