The smallest worthwhile effect on pain intensity of exercise therapy for people with chronic low back pain: a discrete choice experiment study.

OBJECTIVE: To identify the smallest worthwhile effect (SWE) of exercise therapy for people with non-specific chronic low back pain (CLBP). DESIGN: Discrete choice experiment. METHODS: The SWE was estimated as the lowest reduction in pain that participants would consider exercising worthwhile, compared to not exercising i.e., effects due to natural history and other components (e.g., regression to the mean). We recruited English-speaking adults in Australia with non-specific CLBP to our online survey via email obtained from a registry of previous participants and advertisements on social media. We used discrete choice experiment to estimate the SWE of exercise compared to no exercise for pain intensity. We analysed the discrete choice experiment using a mixed logit model, and mitigated hypothetical bias through certainty calibration, with sensitivity analyses performed with different certainty calibration thresholds. RESULTS: Two-hundred and thirteen participants completed the survey. The mean age (±SD) was 50.7±16.5, median (IQR) pain duration 10 years (5-20), and mean pain intensity (±SD) was 5.8±2.3 on a 0-10 numerical rating scale. For people with CLBP the SWE of exercise was a between-group reduction in pain of 20%, compared to no exercise. In the sensitivity analyses, the SWE varied with different levels of certainty calibration; from 0% without certainty calibration to 60% with more extreme certainty calibration. CONCLUSION: This patient-informed threshold of clinical importance could guide the interpretation of findings from randomised trials and meta-analyses of exercise therapy compared to no exercise.

A Rare Case of Complete Inguinoscrotal Bladder Herniation With Ureteric Involvement: Assessing Diagnostic Challenges and Complex Surgical Management.

Inguinoscrotal hernias involving the urinary bladder are exceedingly rare, constituting a small subset of inguinal hernias. We present a case of a 47-year-old male with long-standing scrotal enlargement and obstructive uropathy due to complete herniation of the bladder with ureteric involvement. Diagnostic imaging confirmed the condition. Following an open laparotomy, the bladder was reduced, and a modified Bassini technique with orchiopexy was used for repair. Recurrence of the inguinoscrotal hernia with evidence of the bladder in the scrotal sac required additional surgery. This case underscores the rarity, diagnostic complexity, and potential complications of inguinoscrotal bladder hernias. Specialized surgical techniques and a multidisciplinary approach are crucial for successful management, especially in cases of complete bladder herniation. Future considerations should include innovative approaches to enhance primary repair outcomes for extensive hernias involving the bladder.

Investigative fatigue: how sleep-circadian factors shape criminal investigations.

Investigating criminal complaints and identifying culprits to be prosecuted in the court of law is an essential process for law-enforcement and public safety. However, law-enforcement investigators operate under very challenging conditions due to stressful environments, understaffing, and public scrutiny, which factors into investigative errors (e.g. uncleared cases). This paper argues that one contributing factor to investigative failures involves sleep and circadian disruption of investigators themselves, known to be prevalent among law-enforcement. By focusing on investigative interviewing, this analysis illustrates how sleep and circadian disruption could impact investigations by considering three broad phases of (1) preparation, (2) information elicitation, and (3) assessment and corroboration. These phases are organized in a framework that outlines theory-informed pathways in need of empirical attention, with special focus on effort and decision-making processes critical to investigations. While existing evidence is limited, preliminary findings support some elements of investigative fatigue. The paper concludes by placing investigative fatigue in a broader context of investigative work while providing recommendations for future research throughout. This paper is part of the Sleep and Circadian Health in the Justice System Collection.

Spatial transcriptomics reveals discrete tumour microenvironments and autocrine loops within ovarian cancer subclones.

High-grade serous ovarian carcinoma (HGSOC) is genetically unstable and characterised by the presence of subclones with distinct genotypes. Intratumoural heterogeneity is linked to recurrence, chemotherapy resistance, and poor prognosis. Here, we use spatial transcriptomics to identify HGSOC subclones and study their association with infiltrating cell populations. Visium spatial transcriptomics reveals multiple tumour subclones with different copy number alterations present within individual tumour sections. These subclones differentially express various ligands and receptors and are predicted to differentially associate with different stromal and immune cell populations. In one sample, CosMx single molecule imaging reveals subclones differentially associating with immune cell populations, fibroblasts, and endothelial cells. Cell-to-cell communication analysis identifies subclone-specific signalling to stromal and immune cells and multiple subclone-specific autocrine loops. Our study highlights the high degree of subclonal heterogeneity in HGSOC and suggests that subclone-specific ligand and receptor expression patterns likely modulate how HGSOC cells interact with their local microenvironment.

PERCEPTION predicts patient response and resistance to treatment using single-cell transcriptomics of their tumors.

Tailoring optimal treatment for individual cancer patients remains a significant challenge. To address this issue, we developed PERCEPTION (PERsonalized Single-Cell Expression-Based Planning for Treatments In ONcology), a precision oncology computational pipeline. Our approach uses publicly available matched bulk and single-cell (sc) expression profiles from large-scale cell-line drug screens. These profiles help build treatment response models based on patients' sc-tumor transcriptomics. PERCEPTION demonstrates success in predicting responses to targeted therapies in cultured and patient-tumor-derived primary cells, as well as in two clinical trials for multiple myeloma and breast cancer. It also captures the resistance development in patients with lung cancer treated with tyrosine kinase inhibitors. PERCEPTION outperforms published state-of-the-art sc-based and bulk-based predictors in all clinical cohorts. PERCEPTION is accessible at https://github.com/ruppinlab/PERCEPTION . Our work, showcasing patient stratification using sc-expression profiles of their tumors, will encourage the adoption of sc-omics profiling in clinical settings, enhancing precision oncology tools based on sc-omics.

Barriers and enablers to exercise adherence in people with nonspecific chronic low back pain: a systematic review of qualitative evidence.

ABSTRACT: Exercise is a first-line treatment for chronic low back pain (CLBP), reducing pain and disability in the short term. However, exercise benefits decrease over time, with a lack of long-term exercise adherence a potential reason for this. This study aimed to synthesize the perceptions and beliefs of individuals with CLBP and identify their barriers and enablers to exercise adherence. We searched CENTRAL, Embase, CINAHL, SPORTDiscus, PubMed, PsycINFO, and Scopus databases from inception to February 28, 2023, for qualitative studies that explored the factors influencing exercise adherence for people with CLBP. A hybrid approach combining thematic synthesis with the Theoretical Domains Framework was used to analyze data. We assessed methodological quality using the Critical Appraisal Skills Programme checklist and the level of confidence of the themes generated using the Confidence in the Evidence from Reviews of Qualitative Studies. Twenty-three papers (n = 21 studies) were included (n = 677 participants). Four main themes affected exercise adherence: (1) exercise, pain, and the body, (2) psychological factors, (3) social factors, and (4) external factors. These themes contained 16 subthemes that were predominantly both barriers and enablers to exercise adherence. The individual's experiences of barriers and enablers were most appropriately represented across a spectrum, where influencing factors could be a barrier or enabler to exercise adherence, and these could be specific to pre-exercise, during-exercise, and post-exercise situations. These findings may be used to improve exercise adherence and ultimately treatment outcomes in people with CLBP.

Influenza Induces Lung Lymphangiogenesis Independent of YAP/TAZ Activity in Lymphatic Endothelial Cells.

The lymphatic system consists of a vessel network lined by specialized lymphatic endothelial cells (LECs) that are responsible for tissue fluid homeostasis and immune cell trafficking. The mechanisms for organ-specific LEC responses to environmental cues are not well understood. We found robust lymphangiogenesis during influenza A virus infection in the adult mouse lung. We show that the number of LECs increases 2-fold at 7 days post-influenza infection (dpi) and 3-fold at 21 dpi, and that lymphangiogenesis is preceded by lymphatic dilation. We also show that the expanded lymphatic network enhances fluid drainage to mediastinal lymph nodes. Using EdU labeling, we found that a significantly higher number of pulmonary LECs are proliferating at 7 dpi compared to LECs in homeostatic conditions. Lineage tracing during influenza indicates that new pulmonary LECs are derived from preexisting LECs rather than non-LEC progenitors. Lastly, using a conditional LEC-specific YAP/TAZ knockout model, we established that lymphangiogenesis, fluid transport and the immune response to influenza are independent of YAP/TAZ activity in LECs. These findings were unexpected, as they indicate that YAP/TAZ signaling is not crucial for these processes.

Alpha-mannosidase-2 modulates arbovirus infection in a pathogen- and Wolbachia-specific manner in Aedes aegypti mosquitoes.

Multiple Wolbachia strains can block pathogen infection, replication and/or transmission in Aedes aegypti mosquitoes under both laboratory and field conditions. However, Wolbachia effects on pathogens can be highly variable across systems and the factors governing this variability are not well understood. It is increasingly clear that the mosquito host is not a passive player in which Wolbachia governs pathogen transmission phenotypes; rather, the genetics of the host can significantly modulate Wolbachia-mediated pathogen blocking. Specifically, previous work linked variation in Wolbachia pathogen blocking to polymorphisms in the mosquito alpha-mannosidase-2 (αMan2) gene. Here we use CRISPR-Cas9 mutagenesis to functionally test this association. We developed αMan2 knockouts and examined effects on both Wolbachia and virus levels, using dengue virus (DENV; Flaviviridae) and Mayaro virus (MAYV; Togaviridae). Wolbachia titres were significantly elevated in αMan2 knockout (KO) mosquitoes, but there were complex interactions with virus infection and replication. In Wolbachia-uninfected mosquitoes, the αMan2 KO mutation was associated with decreased DENV titres, but in a Wolbachia-infected background, the αMan2 KO mutation significantly increased virus titres. In contrast, the αMan2 KO mutation significantly increased MAYV replication in Wolbachia-uninfected mosquitoes and did not affect Wolbachia-mediated virus blocking. These results demonstrate that αMan2 modulates arbovirus infection in A. aegypti mosquitoes in a pathogen- and Wolbachia-specific manner, and that Wolbachia-mediated pathogen blocking is a complex phenotype dependent on the mosquito host genotype and the pathogen. These results have a significant impact for the design and use of Wolbachia-based strategies to control vector-borne pathogens.

Containing misinformation: Modeling spatial games of fake news.

The spread of fake news on social media is a pressing issue. Here, we develop a mathematical model on social networks in which news sharing is modeled as a coordination game. We use this model to study the effect of adding designated individuals who sanction fake news sharers (representing, for example, correction of false claims or public shaming of those who share such claims). By simulating our model on synthetic square lattices and small-world networks, we demonstrate that social network structure allows fake news spreaders to form echo chambers and more than doubles fake news' resistance to distributed sanctioning efforts. We confirm our results are robust to a wide range of coordination and sanctioning payoff parameters as well as initial conditions. Using a Twitter network dataset, we show that sanctioners can help contain fake news when placed strategically. Furthermore, we analytically determine the conditions required for peer sanctioning to be effective, including prevalence and enforcement levels. Our findings have implications for developing mitigation strategies to control misinformation and preserve the integrity of public discourse.

Dermal absorption of high molecular weight parent and alkylated polycyclic aromatic hydrocarbons from manufactured gas plant soils using in vitro assessment.

An enhanced in vitro human dermal bioavailability method was developed to measure the release of twenty parent and seven alkylated high molecular weight (HMW) polycyclic aromatic hydrocarbons (PAHs) from contaminated soils collected from five former manufactured Gas Plants (MGP) in England. GC-MS/MS was used to quantify HMW PAHs in soil, Strat-M artificial membrane representing skin, and synthetic receptor solution (RS) representing systemic circulation at 1-h, 10-h, and 24-h timesteps. Fluoranthene and pyrene exhibited the highest fluxes from soils to membrane (ranging from 9.5 - 281 ng/cm2/h) and soil to RS (

Research Note: Clostridium perfringens NetB and CnaA neutralizing nanobodies in feed reduce the incidence of poultry necrotic enteritis.

Necrotic enteritis is a devastating disease to poultry caused by the bacterium Clostridium perfringens. As a novel approach to combating poultry necrotic enteritis, we identified and characterized several hundred single domain antibody fragments (or nanobodies) capable of binding either the NetB toxin or the collagen-binding adhesin (CnaA) of C. perfringens. Many of the nanobodies could neutralize the in vitro functions of NetB or CnaA with inhibitory concentrations in the nanomolar range. The nanobodies were also screened for proteolytic stability in an extract derived from gastrointestinal tract fluids of chickens. A collection of 6 nanobodies (4 targeting NetB and 2 targeting CnaA) with high neutralizing activity and high gastrointestinal tract extract stability were expressed and secreted by Pichia pastoris or Bacillus subtilis. Chickens were given a feed with 1 of the 2 nanobody-containing groups: 1) nanobody-containing P. pastoris supernatants that were semi-purified, lyophilized, and enterically coated, or 2) B. subtilis spores from strains containing the nanobody genes. Compared to untreated chickens (23.75% mortality), mortality of chickens receiving feed modified with the P. pastoris and B. subtilis products decreased to 11.25 and 7.5%, respectively. These results offer a new opportunity to improve the control of poultry necrotic enteritis by incorporating highly specific nanobodies or bacteria expressing these nanobodies directly into chicken feed.

Variation in multimorbidity by sociodemographics and social drivers of health among patients seen at community-based health centers.

Purpose: Understanding variation in multimorbidity across sociodemographics and social drivers of health is critical to reducing health inequities. Methods: From the multi-state OCHIN network of community-based health centers (CBHCs), we identified a cross-sectional cohort of adult (> 25 years old) patients who had a visit between 2019-2021. We used generalized linear models to examine the relationship between the Multimorbidity Weighted Index (MWI) and sociodemographics and social drivers of health (Area Deprivation Index [ADI] and social risks [e.g., food insecurity]). Each model included an interaction term between the primary predictor and age to examine if certain groups had a higher MWI at younger ages. Results: Among 642,730 patients, 28.2% were Hispanic/Latino, 42.8% were male, and the median age was 48. The median MWI was 2.05 (IQR: 0.34, 4.87) and was higher for adults over the age of 40 and American Indians and Alaska Natives. The regression model revealed a higher MWI at younger ages for patients living in areas of higher deprivation. Additionally, patients with social risks had a higher MWI (3.16; IQR: 1.33, 6.65) than those without (2.13; IQR: 0.34, 4.89) and the interaction between age and social risk suggested a higher MWI at younger ages. Conclusions: Greater multimorbidity at younger ages and among those with social risks and living in areas of deprivation shows possible mechanisms for the premature aging and disability often seen in community-based health centers and highlights the need for comprehensive approaches to improving the health of vulnerable populations.

A Qualitative Study Identifying Barriers and Enablers to Exercise Adherence in People with Chronic Low Back Pain. "It's a personal journey".

Exercise leads to clinically meaningful pain reductions in people with chronic low back pain and is recommended as a first line treatment. The benefits of exercise for chronic low back pain decrease over time with a lack of long-term exercise adherence as a potential reason for this decreasing effect. We aimed to identify the barriers and enablers to exercise adherence from the perspective of people with chronic low back pain. This qualitative study was underpinned by a constructivist epistemology and used a critical realist ontological perspective. Adults (18-65 years) with chronic low back pain who had exercised since the onset of their back pain were recruited to participate in focus groups and individual interviews. Audio data were transcribed and then analysed in 2 stages 1) inductive coding using reflexive thematic analysis, followed by 2) deductive analysis through mapping codes onto the Theoretical Domains Framework. Five enablers and 3 barriers were identified across 6 of the 14 Theoretical Domain Framework domains. Exercise identity and confidence in deciding to self-manage pain were enablers, whereas beliefs about the consequences of exercise, exercise context, and relationships could function as either barriers or enablers. These barriers and enablers were complex and fluid, with participants reporting conflicting barriers and enablers that varied, depending on context. These findings improve our understanding of the barriers and enablers to exercise adherence from the individual perspective of people with chronic low back pain and can be utilised for more effective exercise treatment in this population. PERSPECTIVE: This article presents the barriers and enablers to exercise adherence from the perspective of people with chronic low back pain. These perspectives may aid to individualise and optimise exercise treatment, improve its long-term adherence and therefore its effectiveness for chronic low back pain.

Exploring the Role of Guidelines in Contributing to Medication Errors: A Descriptive Analysis of National Patient Safety Incident Data.

INTRODUCTION: Clinical guidelines can contribute to medication errors but there is no overall understanding of how and where these occur. OBJECTIVES: We aimed to identify guideline-related medication errors reported via a national incident reporting system, and describe types of error, stages of medication use, guidelines, drugs, specialties and clinical locations most commonly associated with such errors. METHODS: Retrospective analysis of reports to the National Reporting and Learning System for England and Wales. A hierarchical task analysis (HTA) was developed, describing expected practice when using guidelines. A free-text search was conducted of medication incident reports (2016-2021) using search terms related to common guidelines. All identified reports linked to moderate-severe harm or death, and a random sample of 5100 no/low-harm reports were coded to describe deviations from the HTA. A random sample of 500 cases were independently double-coded. RESULTS: In total, 28,217 reports were identified, with 608 relating to moderate-severe harm or death. Fleiss' kappa for interrater reliability was 0.46. Of the 5708 reports coded, 642 described an HTA step discrepancy (including four linked to a death), suggesting over 3200 discrepancies in the entire dataset of 28,217 reports. Discrepancies related to finding guidelines (n = 300 reports), finding information within guidelines (n = 166) and using information (n = 176). Discrepancies were most frequently identified for guidelines produced by a local organisation (n = 405), and most occurred during prescribing (n = 277) or medication administration (n = 241). CONCLUSION: Difficulties finding and using information from clinical guidelines contribute to thousands of prescribing and medication administration incidents, some of which are associated with substantial patient harm.

Investigations into Increased Incidence of Severe Gizzard Erosions and Ulcerations in U.S. Commercial Broilers.

During a series of pathology surveys in four production complexes of a U.S. broiler integrator, the technical services veterinarians of an animal health company noted a high incidence of severe gizzard erosions and ulcerations (GEU), prompting further clinical investigation and a battery trial. No growth-promoting antibiotics or ionophore coccidiostats were used during the period of these surveys. All used tribasic copper chloride (TBCC) at ≤120 ppm added copper in broiler rations. Clostridium perfringens was isolated from 83% and 67% of gizzard lesions cultured in two complexes, and cecal C. perfringens most probable number determinations were higher in severely affected than in mildly affected or unaffected birds. Histopathology revealed both acellular koilin fusion defects characteristic of copper toxicity, as well as inflammatory cell infiltrates. Intralesional bacilli suggestive of C. perfringens were noted in 78% of affected flocks examined. Species E Aviadenovirus was isolated from one bird in one complex, and that bird had a single intranuclear inclusion body; no other flocks had Adenoviruses isolated or detected on PCR, nor any inclusion bodies. Other viruses detected were thought to be incidental. A pilot study using feed with supplemental copper from TBCC or copper sulfate and challenge with one of the isolated C. perfringens strains reproduced the lesions. A battery study was conducted with an unchallenged negative control group fed a diet with 16 ppm added copper, a group fed the control diet and orally challenged with 108 organisms of a field strain of C. perfringens at 21 and 22 days, and a group treated with the same diet containing 250 ppm added copper from TBCC and orally challenged with C. perfringens. Birds were necropsied at 23 and 28 days. All challenged groups developed lesions, with those receiving both TBCC and C. perfringens having significantly higher gross and histopathological lesion scores than the unchallenged negative controls. Lesions were qualitatively similar to those in the field and contained suspected C. perfringens bacilli. Because the levels of TBCC used in the commercial birds and in the battery trial generally have been considered safe, and because C. perfringens is usually regarded as a pathogen of the lower GI tract, the possible association of these two agents with GEU is a novel observation and warrants further investigation.

Investigaciones sobre el aumento de la incidencia de erosiones y ulceraciones severas en la molleja en pollos de engorde comerciales en los Estados Unidos. Durante una serie de estudios de patología en cuatro complejos de producción de un integrador de pollos de engorde de los Estados Unidos, veterinarios de servicio técnico de una empresa de salud animal observaron una alta incidencia de erosiones y ulceraciones severas de la molleja (GEU), lo que motivó una mayor investigación clínica y un estudio en batería. Durante el período de estas encuestas no se utilizaron antibióticos promotores del crecimiento ni coccidiostáticos ionóforos. Todos utilizaron cloruro de cobre tribásico (TBCC) con un nivel de ≤120 ppm de cobre agregado en raciones para pollos de engorde. Se aisló Clostridium perfringens del 83% y el 67% de las lesiones de molleja cultivadas en dos complejos, y las determinaciones del número más probable de C. perfringens en los sacos ciegos fueron mayores en aves severamente afectadas que en aves levemente afectadas o no afectadas. La histopatología reveló defectos de fusión de la capa córnea acelular característicos de la toxicidad por cobre, así como infiltrados de células inflamatorias. Se observaron bacilos intralesionales sugestivos de C. perfringens en el 78% de las parvadas afectadas examinadas. La especie Aviadenovirus E se aisló de un ave en un complejo, y esa ave tenía un único cuerpo de inclusión intranuclear; en ninguna otra parvada se aislaron o detectaron adenovirus mediante PCR, ni se observaron cuerpos de inclusión. Se pensó que otros virus detectados fueron incidentales. Un estudio piloto que utilizó alimento con cobre suplementario de cloruro de cobre tribásico o sulfato de cobre y con desafío con una de las cepas aisladas de C. perfringens reprodujo las lesiones. Se realizó un estudio de batería con un grupo de control negativo no desafiado alimentado con una dieta con 16 ppm de cobre agregado, un grupo alimentado con la dieta de control y desafiado por vía oral con 108 organismos de una cepa de campo de C. perfringens a los 21 y 22 días, y un grupo tratado con la misma dieta que contenía 250 ppm de cobre agregado de cloruro de cobre tribásico y desafiados por vía oral con C. perfringens. A las aves se les realizó la necropsia a los 23 y 28 días. Todos los grupos desafiados desarrollaron lesiones, y aquellos que recibieron cloruro de cobre tribásico y C. perfringens tuvieron puntuaciones de lesiones macroscópicas e histopatológicas significativamente más altas que los controles negativos no desafiados. Las lesiones eran cualitativamente similares a las del campo y contenían bacilos sospechosos de C. perfringens. Debido a que los niveles de cloruro de cobre tribásico utilizados en las aves comerciales y en el ensayo en batería generalmente se han considerado seguros, y debido a que C. perfringens generalmente se considera un patógeno del tracto gastrointestinal inferior, la posible asociación de estos dos agentes con erosiones y ulceraciones severas de la molleja es una observación reciente y justifica una mayor investigación.

Precordial electrocardiographic recording and QT measurement from a novel wearable ring device.

Background: The availability of portable and wearable electrocardiographic (ECG) devices has increased secondary to technological development. Single-lead ECG recordings have been shown to reliably detect and characterize cardiac rhythms such as atrial fibrillation. Acquisition of precordial electrodes for full 12-lead ECG reconstruction from bipolar recordings is complicated by the absence of a body ground/Wilson central terminal electrode. The extent of difference between standard precordial leads and those from a wearable bipolar ECG recorder has not been characterized. Objective: The purpose of this study was to characterize the precordial ECG lead set from sequential bipolar recordings from an ECG ring wearable device. Methods: In 70 patients who wore an ECG device on a right-hand finger, sequential precordial leads (CR1-CR6) were obtained along with chest electrodes (V1-V6). During acquisition of the modified precordial lead CR6, a full standardized 12-lead ECG capture was obtained. Signal quality was assessed using automated analysis software, and correlation values between the ring-derived ECG precordial leads and standard ECG leads were compared with regard to QRS duration, QT width, and RR interval. Results: High concordance in the morphologies of precordial ECG leads obtained in a standard fashion and those recorded through an ECG ring was observed. Morphologic alignment improved with increasing laterality of the precordial lead with chest to right arm ring recording (CR5, CR6) compared with anterior chest leads to right arm (CR1, CR2). Segmental measurements of QRS duration and QT segment were well aligned and of high correlation. Conclusion: Wearable ring-based ECG technology is capable of high-fidelity recordings of precordial leads for nonsimultaneous reconstruction of complete ECG sets. These recordings correlate highly with surface-obtained QRS and QT duration measurements and have significant implications for clinical applications. Uninterpretable tracings were primarily due to electrode noise from poor electrode contact.

CoRAL accurately resolves extrachromosomal DNA genome structures with long-read sequencing.

Extrachromosomal DNA (ecDNA) is a central mechanism for focal oncogene amplification in cancer, occurring in approximately 15% of early stage cancers and 30% of late-stage cancers. EcDNAs drive tumor formation, evolution, and drug resistance by dynamically modulating oncogene copy-number and rewiring gene-regulatory networks. Elucidating the genomic architecture of ecDNA amplifications is critical for understanding tumor pathology and developing more effective therapies. Paired-end short-read (Illumina) sequencing and mapping have been utilized to represent ecDNA amplifications using a breakpoint graph, where the inferred architecture of ecDNA is encoded as a cycle in the graph. Traversals of breakpoint graph have been used to successfully predict ecDNA presence in cancer samples. However, short-read technologies are intrinsically limited in the identification of breakpoints, phasing together of complex rearrangements and internal duplications, and deconvolution of cell-to-cell heterogeneity of ecDNA structures. Long-read technologies, such as from Oxford Nanopore Technologies, have the potential to improve inference as the longer reads are better at mapping structural variants and are more likely to span rearranged or duplicated regions. Here, we propose CoRAL (Complete Reconstruction of Amplifications with Long reads), for reconstructing ecDNA architectures using long-read data. CoRAL reconstructs likely cyclic architectures using quadratic programming that simultaneously optimizes parsimony of reconstruction, explained copy number, and consistency of long-read mapping. CoRAL substantially improves reconstructions in extensive simulations and 9 datasets from previously-characterized cell-lines as compared to previous short-read-based tools. As long-read usage becomes wide-spread, we anticipate that CoRAL will be a valuable tool for profiling the landscape and evolution of focal amplifications in tumors. Availability: https://github.com/AmpliconSuite/CoRAL.

The sleep-circadian interface: A window into mental disorders.

Sleep, circadian rhythms, and mental health are reciprocally interlinked. Disruption to the quality, continuity, and timing of sleep can precipitate or exacerbate psychiatric symptoms in susceptible individuals, while treatments that target sleep-circadian disturbances can alleviate psychopathology. Conversely, psychiatric symptoms can reciprocally exacerbate poor sleep and disrupt clock-controlled processes. Despite progress in elucidating underlying mechanisms, a cohesive approach that integrates the dynamic interactions between psychiatric disorder with both sleep and circadian processes is lacking. This review synthesizes recent evidence for sleep-circadian dysfunction as a transdiagnostic contributor to a range of psychiatric disorders, with an emphasis on biological mechanisms. We highlight observations from adolescent and young adults, who are at greatest risk of developing mental disorders, and for whom early detection and intervention promise the greatest benefit. In particular, we aim to a) integrate sleep and circadian factors implicated in the pathophysiology and treatment of mood, anxiety, and psychosis spectrum disorders, with a transdiagnostic perspective; b) highlight the need to reframe existing knowledge and adopt an integrated approach which recognizes the interaction between sleep and circadian factors; and c) identify important gaps and opportunities for further research.

Deciphering cell states and genealogies of human haematopoiesis.

The human blood system is maintained through the differentiation and massive amplification of a limited number of long-lived haematopoietic stem cells (HSCs)1. Perturbations to this process underlie diverse diseases, but the clonal contributions to human haematopoiesis and how this changes with age remain incompletely understood. Although recent insights have emerged from barcoding studies in model systems2-5, simultaneous detection of cell states and phylogenies from natural barcodes in humans remains challenging. Here we introduce an improved, single-cell lineage-tracing system based on deep detection of naturally occurring mitochondrial DNA mutations with simultaneous readout of transcriptional states and chromatin accessibility. We use this system to define the clonal architecture of HSCs and map the physiological state and output of clones. We uncover functional heterogeneity in HSC clones, which is stable over months and manifests as both differences in total HSC output and biases towards the production of different mature cell types. We also find that the diversity of HSC clones decreases markedly with age, leading to an oligoclonal structure with multiple distinct clonal expansions. Our study thus provides a clonally resolved and cell-state-aware atlas of human haematopoiesis at single-cell resolution, showing an unappreciated functional diversity of human HSC clones and, more broadly, paving the way for refined studies of clonal dynamics across a range of tissues in human health and disease.