Sequence-based machine learning reveals 3D genome differences between bonobos and chimpanzees.

The 3D structure of the genome is an important mediator of gene expression. As phenotypic divergence is largely driven by gene regulatory variation, comparing genome 3D contacts across species can further understanding of the molecular basis of species differences. However, while experimental data on genome 3D contacts in humans is increasingly abundant, only a handful of 3D genome contact maps exist for other species. Here, we demonstrate that human experimental data can be used to close this data gap. We apply a machine learning model that predicts 3D genome contacts from DNA sequence to the genomes from 56 bonobos and chimpanzees and identify species-specific patterns of genome folding. We estimated 3D divergence between individuals from the resulting contact maps in 4,420 1 Mb genomic windows, of which ∼17% were substantially divergent in predicted genome contacts. Bonobos and chimpanzees diverged at 89 windows, overlapping genes associated with multiple traits implicated in Pan phenotypic divergence. We discovered 51 bonobo-specific variants that individually produce the observed bonobo contact pattern in bonobo-chimpanzee divergent windows. Our results demonstrate that machine learning methods can leverage human data to fill in data gaps across species, offering the first look at population-level 3D genome variation in non-human primates. We also identify loci where changes in 3D folding may contribute to phenotypic differences in our closest living relatives.

Sperm competition intensity shapes divergence in both sperm morphology and reproductive genes across murine rodents.

It remains unclear how variation in the intensity of sperm competition shapes phenotypic and molecular evolution across clades. Mice and rats in the subfamily Murinae are a rapid radiation exhibiting incredible diversity in sperm morphology and production. We combined phenotypic and genomic data to perform phylogenetic comparisons of male reproductive traits and genes across 78 murine species. We identified several shifts towards smaller relative testes mass, presumably reflecting reduced sperm competition. Several sperm traits were associated with relative testes mass, suggesting that mating system evolution selects for convergent suites of traits related to sperm competitive ability. We predicted that sperm competition would also drive more rapid molecular divergence in species with large testes. Contrary to this, we found that many spermatogenesis genes evolved more rapidly in species with smaller relative testes mass due to relaxed purifying selection. While some reproductive genes evolved rapidly under recurrent positive selection, relaxed selection played a greater role in underlying rapid evolution in small testes species. Our work demonstrates that postcopulatory sexual selection can impose strong purifying selection shaping the evolution of male reproduction, and that broad patterns of molecular evolution may help identify genes that contribute to male fertility.

The Role of Intention, Behavioral Regulation, and Physical Activity Behavior in the Prediction of Physical Activity Identity across Time.

Physical activity identity represents an important determinant of sustained physical activity behavior. The purpose of this investigation was to examine whether intention, behavioral regulation, and moderate-to-vigorous physical activity (MVPA) behavior explain significant variation in physical activity identity across time. Using a repeated measures observational design, lower-active adults new or returning to physical activity participation (N = 66) completed measures of study variables every three weeks over the course of a nine-week period (four assessments total). Based on the results of mixed-effects regression modelling, there was a small, non-significant increase in physical activity identity across time (b = 0.07, p = 0.13). Intention, MVPA, and behavioral regulation mostly had significant (ps < 0.05) bivariate correlations with physical activity identity at the same time point of assessment. Behavioral regulation explained significant variation in physical activity identity across time (b = 0.26, p < 0.0001), but intention and MVPA were non-significant (ps > 0.05) after including a random intercept and controlling for behavioral regulation. Identity was resistant to change among new physical activity initiates in this study and longer time frames of assessment are needed (e.g., six months). Behavioral regulation should be examined as a determinant of physical activity identity in future investigations.

Yellow fever disease severity and endothelial dysfunction are associated with elevated serum levels of viral NS1 protein and syndecan-1.

BACKGROUND: Yellow fever virus (YFV) infections are a major global disease concern with high mortality in humans, and as such it is critical to identify clinical correlates of disease severity. While nonstructural protein 1 (NS1) of the related dengue virus is implicated in contributing to vascular leak, little is known about the role of YFV NS1 in severe YF and mechanisms of vascular dysfunction in YFV infections. METHODS: Using serum samples from laboratory-confirmed YF patients with severe (n = 39) or non-severe (n = 18) disease in a well-defined hospital observational cohort in Brazil, plus samples from healthy uninfected controls (n = 11), we investigated factors associated with disease severity and endothelial dysfunction. FINDINGS: We found significantly increased levels of NS1, as well as syndecan-1, a marker of vascular leak, in serum from severe YF as compared to non-severe YF or control groups. We also showed that hyperpermeability of endothelial cell monolayers treated with serum from severe YF patients was significantly higher compared to non-severe YF and control groups, as measured by transendothelial electrical resistance (TEER). Further, we demonstrated that YFV NS1 induces shedding of syndecan-1 from the surface of human endothelial cells. Notably, YFV NS1 serum levels significantly correlated with syndecan-1 serum levels, TEER values, and signs of disease severity. Syndecan-1 levels also significantly correlated with clinical laboratory parameters of disease severity, viral load, hospitalization, and death. INTERPRETATION: This study provides further evidence for endothelial dysfunction as a mechanism of YF pathogenesis in humans and suggests serum quantification of YFV NS1 and syndecan-1 as valuable tools for disease diagnosis and/or prognosis. FUNDING: This work was supported by the US NIH and FAPESP.

Kinetics and Mechanism of PPh3/Ni-Catalyzed, Zn-Mediated, Aryl Chloride Homocoupling: Antagonistic Effects of ZnCl2/Cl.

The Ni/PPh3-catalyzed homocoupling of aryl chlorides in DMF using Zn as the stochiometric reducing agent is one of a general class of Ni-catalyzed processes, where the mechanism has been a matter of long-standing debate. This study re-evaluates prior conclusions and insights. NMR spectroscopy is used to identify [(PPh3)2NiII(Ar)Cl] as a key intermediate and to explore the indirect roles of using Zn as the reductant. The [ZnCl2] coproduct is responsible for several features, including a sequential transmetalation pathway involving [ArZnCl]. [ZnCl2] also abstracts halide from [(PPh3)2NiCl2] to generate [NiIICl(DMF)5]+[ZnCl3(DMF)]-, and in doing so, affects the NiII + Ni0 ↔ 2 NiI speciation. [ZnCl2] thus acts as an accelerator and inhibitor, resulting in mildly sigmoidal reaction profiles. When the [ZnCl2] concentration becomes too high or the phosphine ligand concentration too low, catalysis stalls. Turnover is restored by the addition of further phosphine ligand, or chloride ion. In the presence of an exogenous chloride ion, turnover is rapid, again proceeding via [(PPh3)2NiII(Ar)Cl] but via dinuclear metathesis. The generation of [ZnCl3(DMF)]- results in mutually antagonistic effects between [ZnCl2] and [Cl]- such that turnover proceeds via one mechanism or the other, depending on which species is in excess. The intermediacy of [ArZnCl] suggests a solution to the long-standing anomaly that many other reductants were found to be much less effective than Zn in inducing turnover of Ni/PPh3 catalyzed aryl chloride homocoupling in DMF. The use of DMAc as a solvent in place of DMF inhibits stalling through the steric inhibition of mixed metalate generation.

DNA methylation clocks struggle to distinguish inflammaging from healthy aging, but feature rectification improves coherence and enhances detection of inflammaging.

Biological age estimation from DNA methylation and determination of relevant biomarkers is an active research problem which has predominantly been tackled with black-box penalized regression. Machine learning is used to select a small subset of features from hundreds of thousands CpG probes and to increase generalizability typically lacking with ordinary least-squares regression. Here, we show that such feature selection lacks biological interpretability and relevance in the clocks of the first- and next-generations, and clarify the logic by which these clocks systematically exclude biomarkers of aging and disease. Moreover, in contrast to the assumption that regularized linear regression is needed to prevent overfitting, we demonstrate that hypothesis-driven selection of biologically relevant features in conjunction with ordinary least squares regression yields accurate, well-calibrated, generalizable clocks with high interpretability. We further demonstrate that the interplay of disease-related shifts of predictor values and their corresponding weights, which we term feature shifts, contributes to the lack of resolution between health and disease in conventional linear models. Lastly, we introduce a method of feature rectification, which aligns these shifts to improve the distinction of age predictions for healthy people vs. patients with various diseases. Key Findings: There is no apparent biological significance of the CpGs selected by first- and next-generation clocksThe range of residuals for first- and next-generation clock predications on healthy samples is very large; for all models tested, a prediction error of +/-10-20 years is within the 95% range of variation for healthy controls and does not signify age accelerationThere is no significant shift in the mean of residuals for patient populations relative to healthy populations for most studied first- and next-generation clocks. For those with significance, the effect size is very small.Hypothesis-driven feature pre-selection, coupled with modified forward step-wise selection yields age predictors on par with first and next-generation clocks. EN/ML is not needed.Disease-related shifts at different CpG probes, along with learned model weights, can be either positive or negative; their combination leads to de-coherence effect in linear models.Model coherence can be induced by rectifying features to have only positive shifts in patient samples; this provides a better resolution between health and disease in DNAm age models, and expectedly, introduces more non-linearity to the input data.

Machine learning reveals the diversity of human 3D chromatin contact patterns.

Understanding variation in chromatin contact patterns across diverse humans is critical for interpreting non-coding variants and their effects on gene expression and phenotypes. However, experimental determination of chromatin contact patterns across large samples is prohibitively expensive. To overcome this challenge, we develop and validate a machine learning method to quantify the variation in 3D chromatin contacts at 2 kilobase resolution from genome sequence alone. We apply this approach to thousands of human genomes from the 1000 Genomes Project and the inferred hominin ancestral genome. While patterns of 3D contact divergence genome-wide are qualitatively similar to patterns of sequence divergence, we find substantial differences in 3D divergence and sequence divergence in local 1 megabase genomic windows. In particular, we identify 392 windows with significantly greater 3D divergence than expected from sequence. Moreover, for 31\% of genomic windows, a single individual has a rare divergent 3D contact map pattern. Using in silico mutagenesis we find that most single nucleotide sequence changes do not result in changes to 3D chromatin contacts. However, in windows with substantial 3D divergence just one or a few variants can lead to divergent 3D chromatin contacts without the individuals carrying those variants having high sequence divergence. In summary, inferring 3D chromatin contact maps across human populations reveals variable contact patterns. We anticipate that these genetically diverse maps of 3D chromatin contact will provide a reference for future work on the function and evolution of 3D chromatin contact variation across human populations.

Perspective: Food Access at Dollar Stores and its Implications for Public Health: Report of a Workshop on Identifying Research Priorities.

The rapid growth of dollar stores as retail sources of food in the United States is a phenomenon with implications for diets, nutrition, and well-being. We convened a broadly interdisciplinary group of researchers and experts from government and academia at the 2-day Food Access at Dollar Stores (FADS) workshop, held in Boston, MA in 2022. The event brought together economists, social scientists, public health researchers and advocates to discuss the concerns and research questions raised by the growth of dollar stores, and their increased role in food retail and access. In-person, moderated discussions on day two of the workshop generated a range of topics considered important for future research. A subsequent survey, using a modified Delphi approach, identified priority research areas. Nine research area categories emerged as a result of discussion at the FADS workshop and received prioritization from the experts: Local Community Impacts; Health and Nutrition Impacts; Policy and Programs; Systemic Issues - Racism, Poverty, and Food Access; Store Offerings and Locations; Shoppers and Customers; Employees and Employment; Corporate Distribution, Strategy, and Marketing; and Dollar Stores vs. Other Food Sources. The growth of dollar stores as food retailers remains an under-researched area of study for food access and nutrition that requires interdisciplinary expertise and collaboration to understand. STATEMENT OF SIGNIFICANCE: Dollar stores have grown rapidly as food retailers in the United States over the past decade. This work reports the findings of a research workshop and provides a roadmap for prioritizing research topics and tools related to understanding the public health, equity and economic impacts of this important change in how many consumers are accessing food.

Clinical outcomes of three follitropin alfa preparations for ovarian stimulation using an oral micronized progesterone-primed protocol in an oocyte donation program.

Introduction: This large multicenter study aimed to evaluate clinical outcomes using three follitropin alfa preparations within a progestin-primed ovarian stimulation (PPOS) protocol, while identifying contributing factors to cycle success. Methods: A retrospective, anonymized cohort analysis was conducted on donor-recipient cycles from 12 clinics during 2019 to 2021. 7389 oocyte donors underwent ovarian stimulation (OS) with three follitropin alfa preparations (Ovaleap® [n=3231], Bemfola® [n=3542], Gonal-F® [n=616]) were included. Stimulation began on cycle days 2 or 3 with daily administration of 150-225 IU follitropin alfa. 10 mg medroxyprogesterone acetate (MPA) was administered daily until GnRH agonist trigger using a single dose of 0.2mg GnRH agonist for final follicular maturation. Statistical analysis included ANOVA, Chi-squared, and logistic regression. Results: Whilst there were some differences in patient and stimulation characteristics, including donor age and number of retrieved oocytes, clinical variables did not significantly differ among the three study groups. Linear regression revealed donor age [0.986 (0.974-0.999)] and number of mature oocytes [1.027 (1.007-1.047)] significantly impacted ongoing pregnancy rates, while the type of follitropin alfa [1.048 (0.956-1.149)] used did not. No significant differences were observed in the cumulative live birth rate (CLBR) among oocytes obtained from stimulation with Bemfola (64.9%), Gonal-F (64.1%) and Ovaleap (66.1%), p= 0.385. Discussion: This study demonstrated comparable clinical outcomes and CLBR between biosimilars and the reference product of follitropin alfa within PPOS protocols, hence they are interchangeable in a real-world patient setting.

Herbivore kairomones affect germination speed, seedling growth, and herbivory.

Seeds and seedlings are particularly vulnerable to herbivory. Unlike mature plants, which can wait until herbivory is experienced to induce defense, seeds and seedlings face mortality if they wait. Slug mucus functions as a kairomone, a non-attack-related substance emitted by consumers that is detected by a prey species (in this case, plants). While snail mucus has been shown to induce defense in seedlings, it is not widely confirmed whether slugs have the same effect and whether seeds can also detect and react to such herbivore cues. We investigated how exposure to Arion subfuscus mucus affected growth and defense in Brassica nigra seeds and seedlings. Seeds exposed to slug mucus germinated 5% faster than control (water only) seeds, but the resulting seedlings weighed 16% less than control seedlings. To test whether this difference results from herbivore-exposed plants allocating energy from growth to defense, we conducted choice bioassays assessing slug preference for control seedlings versus seedlings that were either (A) exposed to mucus only as a seed; or (B) exposed to mucus as a seed and seedling. While slugs did not differentiate between control seedlings and ones exposed to herbivore cues only as a seed, they ate 88% less biomass of seedlings exposed to mucus as both seeds and seedlings. These results suggest that slug mucus induces changes in plant traits related to defense and growth/competitive ability. Future research should determine the chemical mechanisms of this induced defense.

Evaluation of Pericardial Effusions in Alopecia Patients on Low-Dose Oral Minoxidil Therapy.

BACKGROUND: Minoxidil is an anti-hypertensive vasodilator increasingly used off-label for the treatment of alopecia. It is associated with an increased risk of pericardial effusions, with recent reports even in patients on low-dose oral minoxidil (LDOM) therapy. OBJECTIVE: To evaluate whether LDOM is associated with increased prevalence of pericardial effusions in patients with alopecia. METHODS: In this cross-sectional study, point-of-care ultrasound was used to screen alopecia patients at dermatology appointments. Scans were evaluated by two independent cardiologists for the presence and size of effusions. The prevalence of effusions was compared between patients on LDOM therapy and patients not on minoxidil therapy. RESULTS: A total of 100 patients were evaluated for pericardial effusion: 51 LDOM patients and 49 control patients. The two groups were similar in terms of age (53.7 vs 54.1; P=0.91), sex (86% vs 73% female; P=0.14), and race. Small pericardial effusions (<1 cm) were identified in 5.8% of LDOM patients and 6% of control patients (P=1), none of which were symptomatic. LIMITATIONS: This is a small, cross-sectional study with limitations on speculation of causality in confirmed cases. CONCLUSION: We did not find evidence of increased prevalence of pericardial effusions in a small group of alopecia patients on LDOM. J Drugs Dermatol. 2024;23(9):725-728. doi:10.36849/JDD.8029.

Pharmacological Management of Pediatric Critical Asthma.

Pediatric critical asthma, or formerly known as status asthmaticus, is a common pediatric condition encountered in emergency departments, hospital wards, and pediatric intensive care units. Systemic corticosteroids and inhaled bronchodilators are evidence-based, initial treatments for patients with pediatric critical asthma. If clinical symptoms do not improve, pediatric practitioners often prescribe adjunctive medications including inhaled anticholinergics, intravenous ketamine, intravenous magnesium, intravenous short acting beta 2 agonists, and intravenous methylxanthines (such as aminophylline). In this narrative review, we will summarize the current evidence and present the research gaps related to these therapies in the pediatric population.

Estimating the distribution of reedbed in Britain demonstrates challenges of remotely sensing rare land cover types at large spatial scales.

Common Reed Phragmites australis, globally one of the mostly widely distributed wetland plants, is important for biodiversity and for humans. However, like most wetland plant communities, reedbed has rarely been mapped at large geographical scales, restricting the information available to study reed's range dynamics or inform its management. Using Sentinel-2 data and machine learning, we aimed to produce the first published remotely-sensed reedbed map of Britain; however, accuracy as assessed by field validation was relatively low (AUC = 0.671), with many false positives (commission error of 93.4%). A similar workflow carried out in Google Earth Engine, using nearly an order of magnitude more images, gave a lower commission error but a disproportionately higher omission error. Using the known commission and omission error, we estimate that in 2015-2017 ~ 7800 ha of Britain was reedbed. Our study highlights the enduring barriers to accurate land cover classification at large spatial scales. Even with a 'big data' approach, reflectance error and ecological factors such as confusion land cover types and geographical variation in temporal reflectance function will probably continue to limit the size of area for which land cover can be classified accurately, therefore limiting the utility of remote sensing for ecologists.

Modeling Cortical Versus Hippocampal Network Dysfunction in a Human Brain Assembloid Model of Epilepsy and Intellectual Disability.

Neurodevelopmental disorders often impair multiple cognitive domains. For instance, a genetic epilepsy syndrome might cause seizures due to cortical hyperexcitability and present with memory impairments arising from hippocampal dysfunction. This study examines how a single disorder differentially affects distinct brain regions by using human patient iPSC-derived cortical- and hippocampal-ganglionic eminence assembloids to model Developmental and Epileptic Encephalopathy 13 (DEE-13), a condition arising from gain-of-function mutations in the SCN8A gene. While cortical assembloids showed network hyperexcitability akin to epileptogenic tissue, hippocampal assembloids did not, and instead displayed network dysregulation patterns similar to in vivo hippocampal recordings from epilepsy patients. Predictive computational modeling, immunohistochemistry, and single-nucleus RNA sequencing revealed changes in excitatory and inhibitory neuron organization that were specific to hippocampal assembloids. These findings highlight the unique impacts of a single pathogenic variant across brain regions and establish hippocampal assembloids as a platform for studying neurodevelopmental disorders.

Barriers to Offering Organ Preservation for Rectal Cancer in a Predominantly Hispanic Safety Net Hospital.

BACKGROUND: Total neoadjuvant therapy (TNT) for locally advanced rectal cancer (LARC) has shown promise in achieving pathologic complete response (pCR) and enabling organ preservation through watch-and-wait (WW) strategies. However, implementation of WW protocols in diverse patient populations and safety-net hospitals faces unique challenges. The objective of this study is to evaluate TNT outcomes and identify barriers to WW implementation in a predominantly Hispanic safety-net hospital in South Texas. METHODS: A retrospective review was conducted of 40 LARC patients treated with TNT at an academic tertiary referral center in South Texas between 2018 and 2023. Patient demographics, disease characteristics, and pCR rates were analyzed. A survey of multidisciplinary providers assessed perceived institutional and patient-related barriers to WW implementation. RESULTS: The cohort was 70% Hispanic, with a median age of 54 years. Most patients had advanced disease at diagnosis (57.5% T4, 65% N2). The pCR rate was 18.5% (5/27) among patients undergoing surgery. Re-review of MRIs for pCR patients revealed that 2/5 had minimal residual disease. The provider survey identified MRI quality variability, lack of dedicated treatment coordinators, and concerns about patient compliance and financial barriers as key obstacles to WW implementation. CONCLUSIONS: Despite advanced disease presentation in a predominantly Hispanic population, TNT achieved pCR rates comparable to international trials. Institutional and patient-level barriers to WW were identified, informing the development of a tailored WW protocol for this unique patient population.

An online delivered running and walking group program to support low-active post-secondary students' well-being and exercise behavior during the COVID-19 pandemic: a pilot randomized controlled trial.

OBJECTIVE: Examine the feasibility and acceptability of a social identity-informed, online delivered, running and walking group program to support low-active post-secondary students' exercise behavior and well-being during the COVID-19 pandemic. METHODS: A two-arm, non-blinded, parallel pilot randomized controlled trial was conducted whereby low-active post-secondary students at a Canadian university were equally randomized to an online delivered running/walking group program or an attention control condition. Primary feasibility and acceptability outcomes included program interest, study enrolment and retention, questionnaire completion, program attendance, program satisfaction, and affective exercise attitudes. Post-program interviews were conducted to ascertain participants' experiences with the program. Secondary outcomes included well-being, exercise behavior, social identity, social support, and exercise identity. RESULTS: Ninety-two individuals were screened for eligibility, and 72 were equally randomized to the online group program or attention control condition. Recruitment exceeded the target sample size (60), study adherence and questionnaire completion were above 90%, program attendance was moderate (M = 5.03/8), self-report program satisfaction was moderate-to-high (M = 4.13/5), and there was no condition effect for affective attitudes. During interviews, participants expressed satisfaction with the program. They also discussed challenges with developing a shared sense of identity and social connection with group members via online platforms. There were small condition effects for exercise-related well-being and exercise identity and no condition effects for the remaining secondary outcomes. Social identity scores were moderate (M = 4.63/7). CONCLUSIONS: The STRIDE program was feasible and acceptable but should be delivered and piloted in-person before a full-scale efficacy trial is conducted. TRIAL REGISTRATION: ClinicalTrials.gov NCT04857918; 2021-04-20.

Skill progress during a dedicated societal robotic surgery training curriculum including several robotic surgery platforms.

BACKGROUND: Robot-assisted procedures are increasingly common, and several systems are available for thoraco-abdominal surgery. Specific structured training is necessary, while access to these systems is still limited. This study aimed to assess surgeons' skill progress during consecutive training days of a curriculum with exposure to different robotic systems. METHODS: This prospective observational study enrolled 47 surgeons with anonymized analysis of SimNow™ simulator performance scores and dedicated questionnaires after written consent. The primary outcome was the overall score, based on economy of motion, time to complete the exercise, and penalty for errors. Course participants in 2022-2023 had chosen 2 full hands-on days on Da Vinci® consoles with either virtual reality (VR) simulation training using the SimNow (n = 21, 44.7%) or digestive surgery procedures with a live animal model (n = 26, 55.3%). In all participants, training on Da Vinci® systems included console functions and principles of docking, camera, and instrument use for console and procedural training. They additionally had access to introductory dry-lab and VR simulator exercises on the Versius, HugoTMRAS, and Dexter systems and to VR exercises on the ROBOTiS simulator. RESULTS: The participants (16F/31M, median age 40 years, range 29-58) from various surgical specialties (general/visceral/vascular) had no (n = 35, 74.5%) or little (n = 12, 25.5%) robotic experience including bedside assistance only and 20 (42.6%) had robotic simulator experience. The demographic variables fully completed by 44/47 participants (93.6%) and choice of module had no significant impact on the primary outcome. The considerable performance improvement from days 1 to 2 was exemplified by a significantly increased economy of motion and decreased amount of excessive force. CONCLUSION: Robotic surgical training is increasingly complex with several systems on the market. Within a dedicated robotic surgery curriculum and based on integrated performance metrics, a significant improvement of skill levels was observed in a relatively short period of time.

Electric buses as an air pollution and meteorological observation network: Methodology and preliminary results.

Many local agencies in the United States and other countries are tasked to install air pollution monitoring systems of highly accurate sensors that have high acquisition, operating, and maintenance costs. The need for expanded coverage of air quality measurements across Salt Lake County (SLCO), Utah is being met by mounting air quality and temperature sensors on an expanding fleet of battery electric buses (BEBs). Monitoring air quality from a mobile sensor network provides real-time insights into air pollution patterns at high temporal and spatial resolution. Mobile measurements contribute to assessing residents' exposure to air pollution, facilitating the implementation of cost-effective public health policies and highlighting disparities. The Electric Bus Air Quality Observation Project was launched in SLCO during July 2021 and has collected millions of observations to date. A BEB traveling at typical traffic speeds (~10 m s-1) can provide multiple measurements along city block lengths of up to ~200 m. With careful analysis that factors in the time response of the differing sensors, variability from block-to-block may be attributed to fine-scale factors (e.g., pollution and heat sources, tree shading and urban vegetation, etc.). Preliminary findings showcase the value of increased coverage and resolution. During an extreme heat event in July 2023, both the morning and afternoon temperature readings showed differences of over 6.5 °C (12 °F), primarily as an east-west gradient with similar gradients in ozone. We conclude that temperature and pollutant concentration readings, at fine spatial and temporal resolutions, will facilitate future health studies and equitable policy and mitigation strategies. Our study demonstrates that our partnerships established with governmental, non-profit, and transit agencies facilitate the successful transfer of research and development to operational real-time mobile air quality monitoring.

Introducing Casbah, Kronus, and MmasiCarm, Members of the Mycobacteriophage Subcluster B3.

Background: As part of a large science education effort, bacteriophages that lyse Mycobacterium smegmatis mc2155 continue to be discovered. Materials and Methods: Phages were isolated from soil samples from urban sites in the Northeastern United States. Their genomes were sequenced, assembled, and bioinformatically compared. Results: Three lytic siphoviruses belonging to subcluster B3 with high similarity to each other and other B3 mycobacteriophages were isolated. These phages contain double-stranded DNA genomes (68,754 to 69,495 bp) with high GC content (67.4-67.5%) and 102-104 putative protein coding genes. Notable features include a HicA-like toxin and 33 genes exclusive to subcluster B3. One phage had an intein in its terminase sequence. Conclusions: Genomic analyses of these phages provide insights into genome evolution and horizontal gene transfer (HGT). The networks for HGT are apparently vast and gene specific. Interestingly, a number of genes are found in both B3 and Gordonia DR phages.