High-resolution detection of copy number alterations in single cells with HiScanner.

Improvements in single-cell whole-genome sequencing (scWGS) assays have enabled detailed characterization of somatic copy number alterations (CNAs) at the single-cell level. Yet, current computational methods are mostly designed for detecting chromosome-scale changes in cancer samples with low sequencing coverage. Here, we introduce HiScanner (High-resolution Single-Cell Allelic copy Number callER), which combines read depth, B-allele frequency, and haplotype phasing to identify CNAs with high resolution. In simulated data, HiScanner consistently outperforms state-of-the-art methods across various CNA types and sizes. When applied to high-coverage scWGS data from human brain cells, HiScanner shows a superior ability to detect smaller CNAs, uncovering distinct CNA patterns between neurons and oligodendrocytes. For 179 cells we sequenced from longitudinal meningioma samples, integration of CNAs with point mutations revealed evolutionary trajectories of tumor cells. These findings show that HiScanner enables accurate characterization of frequency, clonality, and distribution of CNAs at the single-cell level in both non-neoplastic and neoplastic cells.

Comparison of qPCR and metabarcoding for environmental DNA surveillance of a freshwater parasite.

Analysis of environmental DNA (eDNA) has been successfully used across freshwater ecological parasitology to inform management of ecologically and economically important species. However, most studies have used species-specific quantitative polymerase chain reaction (qPCR) assays to detect target taxa. While generally effective, this approach limits the amount of community and management-supporting data that can be obtained from eDNA samples. If eDNA metabarcoding could be conducted with the same accuracy of a single species approach, researchers could simultaneously detect a target species while obtaining vast community data from eDNA samples. We sampled 38 freshwater sites on Fort McCoy, Wisconsin and compared qPCR to metabarcoding for eDNA detection of the ectoparasitic gill louse Salmincola edwardsii, an obligate parasite of Salvelinus fishes (chars). We found no evidence to suggest S. edwardsii occupancy or detection probabilities differed between qPCR and metabarcoding. Further, we found that the number of S. edwardsii reads from metabarcoding were negatively predictive of C T values from qPCR (C T value indicates cycle a significant amount of target eDNA is detected, with lower C Ts indicative of more DNA), demonstrating that our metabarcoding reads positively predicted qPCR DNA quantities. However, the number of reads was not predictive of overall qPCR score (number of positive qPCR replicates). In addition to S. edwardsii, metabarcoding led to the detection of a vast community of over 2600 invertebrate taxa. We underscore the necessity for conducting similar analyses across environments and target species, as the ecology of eDNA will vary on a per-study basis. Our results suggest that eDNA metabarcoding provides a highly sensitive and accurate method for detecting parasitic gill lice while also illuminating the broader biological community and co-occurrence of species in the environment.

CeO2 nanoparticle dose and exposure modulate soybean development and plant-mediated responses in root-associated bacterial communities.

Agricultural soils are increasingly undergoing inadvertent and purposeful exposures to engineered CeO2 nanoparticles (NPs), which can impact crops and root-associated microbial communities. However, interactions between NP concentration and exposure duration on plant-mediated responses of root-associated bacterial communities are not well understood. Soybeans seedlings were grown in soil with uncoated NPs added at concentrations of 0, 1 or 100 mg kg-1. Total soil exposure durations were either 190 days, starting 106 days before planting or 84 days with NP amendments coinciding with planting. We assessed plant development, bacterial diversity, differential abundance and inferred functional changes across rhizosphere, rhizoplane, and root tissue compartments. Plant non-monotonic dose responses were mirrored in bacterial communities. Most notably, effects were magnified in the rhizoplane under low-dose, short-exposures. Enriched metabolic pathways were primarily related to biosynthesis and degradation/utilization/assimilation, rather than responses to metals or oxidative stress. Our results indicate that plant-mediated bacterial responses were greater than direct NP impacts. Also, we identify needs for modeling non-monotonic legume stress responses that account for coinfection with mutualistic and parasitic bacteroids. Our findings provide new insights regarding effects of applications of soil amendments such as biosolids containing NPs or nano-enabled formulations used in cultivation of legumes and other crops.

A Longitudinal Assessment of Resident and New Graduate Well-Being According to Length of Training: A Report From the Length of Training Pilot in Family Medicine.

Background & Objectives: No prior studies have examined how length of training may influence wellness. As part of the Length of Training Pilot (LoTP), we explored resident and new graduate well-being according to program year and length of training in 3- and 4-year family medicine residency training programs. METHODS: Two surveys captured data included in these analyses. One was a resident survey that included the Mayo Clinic physician-expanded Well-Being Index (eWBI) administered annually during the In-Training Examination (2014-2019). The second was administered to graduates 1 year after completion of training between 2016 and 2022 and included the same well-being questions. Response rates ranged between 77.7% and 96.8%. RESULTS: The eWBI summary scores for burnout were highest in postgraduate year 1 (PGY1) and did not differ statistically according to length of training (PGY1: 2.02 in 3-year [3YR] programs vs 1.93 in 4-year [4YR] programs, P=.55; postgraduate year 2 [PGY2]: 2.42 in 3YR programs vs 2.38 in 4YR programs, P=.83; postgraduate year 3 [PGY3]: 2.18 in 3YR programs vs 2.28 in 4YR programs, P=.59; and 2.34 in postgraduate year 4 [PGY4] for those in 4YR programs), though some statistical differences were noted for three items. New graduates' eWBI summary scores before the COVID-19 pandemic were 1.77 among 3YR graduates and 1.66 among 4YR graduates (P=.59). These scores were higher during COVID-19 at 1.89 for 3YR graduates and 2.02 for 4YR graduates (P=.62). Length of training was not associated with differences in well-being before or during COVID-19. CONCLUSIONS: We found no associations between length of training and physician well-being during training or among new graduates before or during COVID-19.

Terson Syndrome Diagnosed by Ocular Point of Care Ultrasound on the Medical Floor.

In acute care environments, accurately assessing complications of intracranial pathology can be challenging. Ocular complications in acute intracranial disease are not consistently evaluated despite their high morbidity. We report on a case of monocular diplopia in a 63-year-old man with subacute traumatic brain injury with localized subarachnoid hemorrhage. Ocular point of care ultrasound (POCUS) identified features of vitreous hemorrhage in one globe, leading to a diagnosis of Terson syndrome and a timely referral to ophthalmology. This finding was made on the medical floor days after the initial presentation during rehabilitation when ophthalmoscopy was not possible, and vitreous hemorrhage had not been identified on presentation. Terson syndrome is a seldom discussed but important complication of intracranial hemorrhage generally associated with poor patient outcomes. Ocular POCUS can provide a useful alternative in assessing ocular complications of acute intracranial disease on the medical floor, particularly when the practicalities of performing ophthalmoscopy are challenged.

Perspectives on community-based system change for people living with persistent pain: insights from developing the "Rethinking Pain service".

In this perspective article we advocate community-based system change for people living with persistent pain. Our view is that greater use of the voluntary and community sector, in partnership with the clinical sector, creates the conditions for a "whole person" approach to pain management, leading to greater personalised care for adults living with long-term pain whilst having the potential to ease some of the pressures on General Practitioners and other clinical services. We advocate pain care that is socially connected, meaningful within socio-cultural contexts and aligned with the principles of salutogenesis. We provide an example of a UK National Health Service (NHS) commissioned pain service called "Rethinking Pain" that operationalises this perspective. Led by the voluntary and community sector, Rethinking Pain works in partnership with the clinical sector to provide a central holistic pathway of care for people experiencing persistent pain. This is the first time that this model of care has been commissioned for persistent pain in this area of England. The Rethinking Pain service is underpinned by core values to work with people to manage their pain holistically. The Rethinking Pain team proactively engage with people in the community, actively approaching and engaging those who experience the biggest health inequalities. In this article we provide an overview of the context of pain services in the UK, the rationale and supporting evidence for community-based system change, and the context, pathway, values, goals, and aspirations of the Rethinking Pain service.

Increasing spread rates of tropical non-native macrophytes in the Mediterranean Sea.

Warming as well as species introductions have increased over the past centuries, however a link between cause and effect of these two phenomena is still unclear. Here we use distribution records (1813-2023) to reconstruct the invasion histories of marine non-native macrophytes, macroalgae and seagrasses, in the Mediterranean Sea. We defined expansion as the maximum linear rate of spread (km year-1) and the accumulation of occupied grid cells (50 km2) over time and analyzed the relation between expansion rates and the species' thermal conditions at its native distribution range. Our database revealed a marked increase in the introductions and spread rates of non-native macrophytes in the Mediterranean Sea since the 1960s, notably intensifying after the 1990s. During the beginning of this century species velocity of invasion has increased to 26 ± 9 km2 year-1, with an acceleration in the velocity of invasion of tropical/subtropical species, exceeding those of temperate and cosmopolitan macrophytes. The highest spread rates since then were observed in macrophytes coming from native regions with minimum SSTs two to three degrees warmer than in the Mediterranean Sea. In addition, most non-native macrophytes in the Mediterranean (>80%) do not exceed the maximum temperature of their range of origin, whereas approximately half of the species are exposed to lower minimum SST in the Mediterranean than in their native range. This indicates that tropical/subtropical macrophytes might be able to expand as they are not limited by the colder Mediterranean SST due to the plasticity of their lower thermal limit. These results suggest that future warming will increase the thermal habitat available for thermophilic species in the Mediterranean Sea and continue to favor their expansion.

Nutritional interventions to prevent retinopathy of prematurity.

Very preterm infants are at high risk of growth failure. Poor weight gain is a prominent risk factor for retinopathy of prematurity (ROP) and optimizing nutrition could potentially promote growth and reduce ROP. Most infants at risk of ROP need parenteral nutrition initially and studies of enhanced parenteral provision of lipids and amino acids have suggested a beneficial effect on ROP. Higher amino acid intake was associated with lower incidence of hyperglycemia, a risk factor for ROP. For very preterm infants, providing unpasteurized fortified raw maternal breast milk appears to have a dose-dependent preventive effect on ROP. These infants become deficient in arachidonic acid (ArA) and docosahexaenoic acid (DHA) after birth when the maternal supply is lost. Earlier studies have investigated the impact of omega-3 fatty acids on ROP with mixed results. In a recent study, early enteral supplementation of ArA 100 mg/kg/d and DHA 50 mg/kg/d until term equivalent age reduced the incidence of severe ROP by 50%. IMPACT: Previous reviews of nutritional interventions to prevent morbidities in preterm infants have mainly addressed bronchopulmonary dysplasia, brain lesions and neurodevelopmental outcome. This review focusses on ROP. Neonatal enteral supplementation with arachidonic acid and docosahexaenoic acid, at levels similar to the fetal accretion rate, has been found to reduce severe ROP by 50% in randomized controlled trials.

Protocol for isolating amnion cells from human and non-human primate placenta for flow cytometry and transcriptomics.

The amnion is a thin layer of fetal origin in contact with the amniotic fluid which plays a key role at the feto-maternal interface during pregnancy. Here, we present a protocol for isolation of human and Rhesusmacaque amnion cells. We describe steps for tissue dissection, cell isolation for flow cytometry analysis, and RNA isolation for RNA sequencing library preparation and analysis. This protocol can provide insights into altered immunological pathways during intrauterine infections to develop new therapeutic strategies. For complete details on the use and execution of this protocol, please refer to Presicce et al.1.

The importance of decomposing periodic and aperiodic EEG signals for assessment of brain function in a global context.

Measures of early neuro-cognitive development that are suitable for use in low-resource settings are needed to enable studies of the effects of early adversity on the developing brain in a global context. These measures should have high acquisition rates and good face and construct validity. Here, we investigated the feasibility of a naturalistic electroencephalography (EEG) paradigm in a low-resource context during childhood. Additionally, we examined the sensitivity of periodic and aperiodic EEG metrics to social and non-social stimuli. We recorded simultaneous 20-channel EEG and eye-tracking in 72 children aged 4-12 years (45 females) while they watched videos of women singing nursery rhymes and moving toys, selected to represent familiar childhood experiences. These measures were part of a feasibility study that assessed the feasibility and acceptability of a follow-up data collection of the South African Safe Passage Study, which tracks environmental adversity and brain and cognitive development from before birth up until childhood. We examined whether data quantity and quality varied with child characteristics and the sensitivity of varying EEG metrics (canonical band power in the theta and alpha band and periodic and aperiodic features of the power spectra). We found that children who completed the EEG and eye-tracking assessment were, in general, representative of the full cohort. Data quantity was higher in children with greater visual attention to the stimuli. Out of the tested EEG metrics, periodic measures in the theta frequency range were most sensitive to condition differences, compared to alpha range measures and canonical and aperiodic EEG measures. Our results show that measuring EEG during ecologically valid social and non-social stimuli is feasible in low-resource settings, is feasible for most children, and produces robust indices of social brain function. This work provides preliminary support for testing longitudinal links between social brain function, environmental factors, and emerging behaviors.

A wave of specific transcript and protein accumulation accompanies pollen dehydration.

In flowering plants, male gametes are immotile and carried by dry pollen grains to the female organ. Dehydrated pollen is thought to withstand abiotic stress when grains are dispersed from the anther to the pistil, after which sperm cells are delivered via pollen tube growth for fertilization and seed set. Yet, the underlying molecular changes accompanying dehydration and the impact on pollen development are poorly understood. To gain a systems perspective, we analyzed published transcriptomes and proteomes of developing Arabidopsis thaliana pollen. Waves of transcripts are evident as microspores develop to bicellular, tricellular, and mature pollen. Between the 'early'- and 'late'-pollen-expressed genes, an unrecognized cluster of transcripts accumulated, including those encoding late-embryogenesis abundant (LEA), desiccation-related protein, transporters, lipid-droplet associated proteins, pectin modifiers, cysteine-rich proteins, and mRNA-binding proteins. Results suggest dehydration onset initiates after bicellular pollen is formed. Proteins accumulating in mature pollen like ribosomal proteins, initiation factors, and chaperones are likely components of mRNA-protein condensates resembling 'stress' granules. Our analysis has revealed many new transcripts and proteins that accompany dehydration in developing pollen. Together with published functional studies, our results point to multiple processes, including i) protect developing pollen from hyperosmotic stress, ii) remodel the endomembrane system and walls; iii) maintain energy metabolism, iv) stabilize pre-synthesized mRNA and proteins in condensates of dry pollen, and v) equip pollen for compatibility determination at the stigma and for recovery at rehydration. These findings offer novel models and molecular candidates to further determine the mechanistic basis of dehydration and desiccation tolerance in plants.

Efficacy of diadynamic currents as an adjunct to exercise to manage symptoms of knee osteoarthritis in adults: A randomized controlled clinical trial.

OBJECTIVE: To investigate the effect of diadynamic currents administered prior to exercises on pain and disability in patients with osteoarthritis of the knee. DESIGN: A randomized-controlled trial. SETTING: Special Rehabilitation Services in Taboão da Serra. PARTICIPANTS: Patients with bilateral knee osteoarthritis. INTERVENTION: Participants were randomly allocated to Group I (diadynamic currents and exercises; n = 30, 60 knees) or Group II (exercises alone; n = 30, 60 knees) and were treated three times a week for 8 weeks. MAIN OUTCOME MEASURES: The primary outcome measures were change in knee pain evaluated by visual analog scale and disability Index Score (Lequesne). Secondary outcomes included change in mobility (Timed Up and Go test), range of motion (goniometer), muscle strength (dynamometer), a composite score for pain and disability (Western Ontario and McMaster Universities Osteoarthritis questionnaire), and a drug diary to measure consumption of rescue pain medication (paracetamol). All measurements were collected at baseline, 8 weeks, and 6 months from baseline (follow-up). RESULTS: There were 60 participants with a mean (SD) age of 63.40 (8.20) years. Between-group differences in the follow-up (8 weeks and 6 months) were observed for pain at rest, pain during activities of daily living and disability. There was improvement in Group I that was maintained for the three variables 6 months after treatment. Mean difference for pain at rest was -3.08 points (95% confidence interval -4.13; -2.02), p < 0.01 with an effect size of 1.4; mean difference for pain during activities of daily living was -2.40 points (95% confidence interval -3.34; -1.45), p < 0.01 with an effect size of 1.24; and mean difference for disability was -4.08 points (95% confidence interval -5.89; -2.26), p < 0.01 with an effect size of 1.04. CONCLUSION: Patients with symptomatic knee osteoarthritis receiving 8 weeks of treatment with diadynamic currents as an adjunct to a program of exercises had significantly greater improvements in pain and disability than those receiving exercises alone. Beneficial effects were sustained for 6 months.

Using emerging science to inform risk characterizations for wildlife within current regulatory frameworks.

Many jurisdictions have regulatory frameworks that seek to reduce the effects of environmental exposures of anthropogenic chemicals on terrestrial wildlife (i.e., mammals, birds, reptiles, and amphibians). The frameworks apply for new and existing chemicals, including pesticides (prospective assessments), and to environmental contamination from releases (retrospective risk assessments). Relatively recently, there have been many scientific advances that could improve risk estimates for wildlife. Here, we briefly describe current regulations from North America (United States and Canada) and from Europe that include risk assessments for wildlife to ascertain whether they are conducive to the use of emerging science and new methods. We also provide examples where new and emerging science may be used to improve wildlife risk characterization and identify areas in need of future research. Integr Environ Assess Manag 2024;20:765-779. © 2024 His Majesty the King in Right of Canada and The Authors. Integrated Environmental Assessment and Management © 2024 Society of Environmental Toxicology & Chemistry (SETAC). Reproduced with the permission of the Minister of Environment and Climate Change Canada. This article has been contributed to by U.S. Government employees and their work is in the public domain in the USA.

Case report: Long-term follow-up of patients who received a FimCH vaccine for prevention of recurrent urinary tract infections caused by antibiotic resistant Enterobacteriaceae: a case report series.

Urinary tract infections (UTI) caused by carbapenem-resistant Enterobacteriaceae (CRE) are considered one of the most urgent health threats to humans according to the Centers for Disease Control (CDC), and the World Health Organization (WHO). A FimCH Vaccine expanded access study is being conducted in patients with a history of antibiotic resistant UTIs who are considered to be at risk for development of CRE UTI. This case series describes the clinical, safety and immunogenicity findings for four participants who received a FimCH four-vaccine series. Participants were followed for 12 months after administration of the fourth vaccine for safety, general health status and UTI occurrence. The study was later amended to allow additional follow-up of up to five years post vaccine administration to assess long-term health status, UTI occurrences and to obtain blood samples for anti-FimH antibody testing. In our population of 4 study participants, the number of symptomatic UTI occurrences caused by gram-negative bacteria in the 12-month period following peak anti-FimH antibody response were approximately 75% lower than the 12-month period preceding study enrollment. These results are consistent with the 30-patient cohort of a Phase 1 study with the same FimCH Vaccine. UTI occurrences increased during the long-term follow-up period for all 4 participants but did not reach the rate observed pre-vaccination. No new safety concerns related to the FimCH Vaccine were identified during long-term follow-up. This case series has clinical importance and public health relevance since it examines and reports on UTI frequency and recurrence following vaccination with the FimCH Vaccine in a high-risk population of patients with recurrent UTI. Additionally, participants described improved well-being following vaccination which was maintained in the long-term follow-up period.

Editorial Perspective: The paradox of precision health in early development - building large samples to yield individual-level measures.

Precision health refers to the use of individualised biomarkers or predictive models to provide more tailored information about an individual's likely prognosis. For child psychiatry and psychology, we argue that this approach requires a focus on neurocognitive measures collected in early life and at large scale. However, the large sample sizes necessary to uncover individual-level predictors are currently rare in studies of neurodevelopmental conditions in early childhood. We recommend two strategies going forward: first, including neurocognitive measures in new national cohort studies, and second, synergising measures and data across currently funded longitudinal studies.

Integrating emerging science to improve estimates of risk to wildlife from chemical exposure: What are the challenges?

Many jurisdictions require ecological risk assessments for terrestrial wildlife (i.e., terrestrial vertebrates) to assess potential adverse effects from exposure to anthropogenic chemicals. This occurs, for example, at contaminated sites and when new pesticides are proposed, and it occurs for chemicals that are in production and/or proposed for wide-scale use. However, guidance to evaluate such risks has not changed markedly in decades, despite the availability of new scientific tools to do so. In 2019, the Wildlife Toxicology World Interest Group of the Society of Environmental Toxicology and Chemistry (SETAC) initiated a virtual workshop that included a special session coincident with the annual SETAC North America meeting and which focused on the prospect of improving risk assessments for wildlife and improving their use in implementing chemical regulations. Work groups continued the work and investigated the utility of integrating emerging science and novel methods for improving problem formulation (WG1), exposure (WG2), toxicology (WG3), and risk characterization (WG4). Here we provide a summary of that workshop and the follow-up work, the regulations that drive risk assessment, and the key focus areas identified to advance the ability to predict risks of chemicals to wildlife. Integr Environ Assess Manag 2024;20:645-657. © 2024 The Authors. Integrated Environmental Assessment and Management published by Wiley Periodicals LLC on behalf of Society of Environmental Toxicology & Chemistry (SETAC).

Improved Disease-Free Survival With Adjuvant Chemotherapy After Nephroureterectomy for Upper Tract Urothelial Cancer: Final Results of the POUT Trial.

Clinical trials frequently include multiple end points that mature at different times. The initial report, typically based on the primary end point, may be published when key planned co-primary or secondary analyses are not yet available. Clinical Trial Updates provide an opportunity to disseminate additional results from studies, published in JCO or elsewhere, for which the primary end point has already been reported.POUT was a phase III, randomized, open-label trial, including 261 patients with muscle-invasive or lymph node-positive, nonmetastatic upper tract urothelial cancer (UTUC) randomly assigned after radical nephroureterectomy to platinum-based chemotherapy (132) or surveillance (129). Primary outcome analysis demonstrated that chemotherapy improved disease-free survival (DFS). At that time, the planned secondary outcome analysis of overall survival (OS) was immature. By February 2022, 50 and 67 DFS events had occurred in the chemotherapy and surveillance groups, respectively, at a median follow-up of 65 months. The 5-year DFS was 62% versus 45%, univariable hazard ratio (HR), 0.55 (95% CI, 0.38 to 0.80, P = .001). The restricted mean survival time (RMST) was 18 months longer (95% CI, 6 to 30) in the chemotherapy arm. There were 46 and 60 deaths in the chemotherapy and control arms, respectively. The 5-year OS was 66% versus 57%, with univariable HR, 0.68 (95% CI, 0.46 to 1.00, P = .049) and RMST difference 11 months (95% CI, 1 to 21). Treatment effects were consistent across chemotherapy regimens (carboplatin or cisplatin) and disease stage. Toxicities were similar to those previously reported, and there were no clinically relevant differences in quality of life between arms. In summary, although OS was not the primary outcome measure, the updated results add further support for the use of adjuvant chemotherapy in patients with UTUC, suggesting long-term benefits.

Acute Myocardial Infarction in Pregnancy.

Pregnancy-associated myocardial infarction is an overall uncommon event, but can be associated with significant maternal and fetal morbidity and mortality. In contrast to myocardial infarction in the general nonpregnant population, the mechanism of pregnancy-associated myocardial infarction is most commonly due to nonatherosclerotic mechanisms such as coronary dissection, vasospasm, or thromboembolism. The diagnosis of pregnancy-associated myocardial infarction can be challenging, requiring a high index of suspicion for prompt recognition and management. Furthermore, the management of pregnancy-associated myocardial infarction can be complex due to maternal and fetal considerations and may vary based on the specific underlying mechanism of the myocardial infarction. This review aims to review the recent literature on pregnancy-associated myocardial infarction and summarize the epidemiology, mechanisms, diagnosis, and treatment strategies for this uncommon entity.