A risk-reward examination of sample multiplexing reagents for single cell RNA-Seq.

Single-cell RNA sequencing (scRNA-Seq) has emerged as a powerful tool for understanding cellular heterogeneity and function. However the choice of sample multiplexing reagents can impact data quality and experimental outcomes. In this study, we compared various multiplexing reagents, including MULTI-Seq, Hashtag antibody, and CellPlex, across diverse sample types such as human peripheral blood mononuclear cells (PBMCs), mouse embryonic brain and patient-derived xenografts (PDXs). We found that all multiplexing reagents worked well in cell types robust to ex vivo manipulation but suffered from signal-to-noise issues in more delicate sample types. We compared multiple demultiplexing algorithms which differed in performance depending on data quality. We find that minor improvements to laboratory workflows such as titration and rapid processing are critical to optimal performance. We also compared the performance of fixed scRNA-Seq kits and highlight the advantages of the Parse Biosciences kit for fragile samples. Highly multiplexed scRNA-Seq experiments require more sequencing resources, therefore we evaluated CRISPR-based destruction of non-informative genes to enhance sequencing value. Our comprehensive analysis provides insights into the selection of appropriate sample multiplexing reagents and protocols for scRNA-Seq experiments, facilitating more accurate and cost-effective studies.

Apgar Score and Neurodevelopmental Outcomes at Age 5 Years in Infants Born Extremely Preterm.

Importance: The Apgar score is used worldwide as an assessment tool to estimate the vitality of newborns in their first minutes of life. Its applicability to estimate neurodevelopmental outcomes in infants born extremely preterm (EPT; <28 weeks' gestation) is not well established. Objective: To investigate the association between the Apgar score and neurodevelopmental outcomes in infants born EPT. Design, Setting, and Participants: This cohort study was conducted using data from the Effective Perinatal Intensive Care in Europe-Screening to Improve Health in Very Preterm Infants in Europe (EPICE-SHIPS) study, a population-based cohort in 19 regions of 11 European countries in 2011 to 2012. Clinical assessments of cognition and motor function at age 5 years were performed in infants born EPT and analyzed in January to July 2023. Exposures: Apgar score at 5 minutes of life categorized into 4 groups (0-3, 4-6, 7-8, and 9-10 points). Main Outcomes and Measures: Cognitive and motor outcomes were assessed using the Wechsler Preschool and Primary Scale of Intelligence test of IQ derived from locally normed versions by country and the Movement Assessment Battery for Children-Second Edition. Parents additionally provided information on communication and problem-solving skills using the Ages and Stages Questionnaire, third edition (ASQ-3). All outcomes were measured as continuous variables. Results: From the total cohort of 4395 infants born EPT, 2522 infants were live born, 1654 infants survived to age 5 years, and 996 infants (478 females [48.0%]) followed up had at least 1 of 3 outcome measures. After adjusting for sociodemographic variables, perinatal factors, and severe neonatal morbidities, there was no association of Apgar score with IQ, even for scores of 3 or less (ß = -3.3; 95% CI, -10.5 to 3.8) compared with the score 9 to 10 category. Similarly, no association was found for ASQ-3 (ß = -2.1; 95% CI, -24.6 to 20.4). Congruent results for Apgar scores of 3 or less were obtained for motor function scores for all children (ß = -4.0; 95% CI, -20.1 to 12.1) and excluding children with a diagnosis of cerebral palsy (ß = 0.8, 95% CI -11.7 to 13.3). Conclusions and Relevance: This study found that low Apgar scores were not associated with longer-term outcomes in infants born EPT. This finding may be associated with high interobserver variability in Apgar scoring, reduced vitality signs and poorer responses to resuscitation after birth among infants born EPT, and the association of more deleterious exposures in the neonatal intensive care unit or of socioeconomic factors with greater changes in outcomes during the first 5 years of life.

Experimental and spontaneous metastasis assays can result in divergence in clonal architecture.

Intratumoural heterogeneity is associated with poor outcomes in breast cancer. To understand how malignant clones survive and grow in metastatic niches, in vivo models using cell lines and patient-derived xenografts (PDX) have become the gold standard. Injections of cancer cells in orthotopic sites (spontaneous metastasis assays) or into the vasculature (experimental metastasis assays) have been used interchangeably to study the metastatic cascade from early events or post-intravasation, respectively. However, less is known about how these different routes of injection impact heterogeneity. Herein we directly compared the clonality of spontaneous and experimental metastatic assays using the human cell line MDA-MB-231 and a PDX model. Genetic barcoding was used to study the fitness of the subclones in primary and metastatic sites. Using spontaneous assays, we found that intraductal injections resulted in less diverse tumours compared to other routes of injections. Using experimental metastasis assays via tail vein injection of barcoded MDA-MB-231 cells, we also observed an asymmetry in metastatic heterogeneity between lung and liver that was not observed using spontaneous metastasis assays. These results demonstrate that these assays can result in divergent clonal outputs in terms of metastatic heterogeneity and provide a better understanding of the biases inherent to each technique.

Map-based experience replay: a memory-efficient solution to catastrophic forgetting in reinforcement learning.

Deep reinforcement learning (RL) agents often suffer from catastrophic forgetting, forgetting previously found solutions in parts of the input space when training new data. Replay memories are a common solution to the problem by decorrelating and shuffling old and new training samples. They naively store state transitions as they arrive, without regard for redundancy. We introduce a novel cognitive-inspired replay memory approach based on the Grow-When-Required (GWR) self-organizing network, which resembles a map-based mental model of the world. Our approach organizes stored transitions into a concise environment-model-like network of state nodes and transition edges, merging similar samples to reduce the memory size and increase pair-wise distance among samples, which increases the relevancy of each sample. Overall, our study shows that map-based experience replay allows for significant memory reduction with only small decreases in performance.

Cardiotocography combined with ST analysis versus cardiotocography combined with fetal blood sampling in deliveries with abnormal CTG: a randomized trial.

PURPOSE: The aim was to investigate if intrapartum monitoring with cardiotocography (CTG) in combination with ST analysis (STAN) results in an improved perinatal outcome. METHODS: We performed a two-center randomized trial. 1013 women with term fetuses in cephalic presentation entered the trial. If a CTG showed intermediate or pathological abnormalities, they were offered fetal blood sampling (FBS) and inclusion if the pH value was above 7.25. They were randomized to either CTG + FBS or CTG + STAN. The primary outcome was neonatal metabolic acidosis, defined as umbilical cord arterial blood pH below 7.05, and base excess equal to or below -10. The secondary outcomes included operative vaginal delivery for fetal distress. RESULTS: The rate of metabolic acidosis was 0.8% in the CTG + FBS group and 1.5% in women in the CTG + STAN (P = 0.338). More women in the CTG + STAN group delivered by operative vaginal delivery (25.6% vs 33.5%, P = 0.006). Significantly fewer women in the CTG + STAN group had three to five (28.8% vs 11.0%, P = < 0.001) and six to ten fetal blood samples taken (3.4% vs 0.4%, P = < 0.001). CONCLUSION: CTG + STAN did not reduce the incidence of neonatal metabolic acidosis compared to CTG + FBS. CTG + STAN was, however, associated with an increased risk of operative vaginal delivery and a reduced use of FBS. If STAN is used for fetal surveillance, we recommend that it is combined with other methods, such as FBS, for confirmation of the need for operative delivery. CLINICALTRIALS: gov ID: NCT01699646. Date of registration: October 4, 2012 (retrospectively registered). https://clinicaltrials.gov/ct2/show/NCT01699646?id=NCT01699646&draw=2&rank=1.

Replicative history marks transcriptional and functional disparity in the CD8+ T cell memory pool.

Clonal expansion is a core aspect of T cell immunity. However, little is known with respect to the relationship between replicative history and the formation of distinct CD8+ memory T cell subgroups. To address this issue, we developed a genetic-tracing approach, termed the DivisionRecorder, that reports the extent of past proliferation of cell pools in vivo. Using this system to genetically 'record' the replicative history of different CD8+ T cell populations throughout a pathogen-specific immune response, we demonstrate that the central memory T (TCM) cell pool is marked by a higher number of prior divisions than the effector memory T cell pool, owing to the combination of strong proliferative activity during the acute immune response and selective proliferative activity after pathogen clearance. Furthermore, by combining DivisionRecorder analysis with single-cell transcriptomics and functional experiments, we show that replicative history identifies distinct cell pools within the TCM compartment. Specifically, we demonstrate that lowly divided TCM cells display enriched expression of stem-cell-associated genes, exist in a relatively quiescent state, and are superior in eliciting a proliferative recall response upon activation. These data provide the first evidence that a stem-cell-like memory T cell pool that reconstitutes the CD8+ T cell effector pool upon reinfection is marked by prior quiescence.

Non-genetic determinants of malignant clonal fitness at single-cell resolution.

All cancers emerge after a period of clonal selection and subsequent clonal expansion. Although the evolutionary principles imparted by genetic intratumour heterogeneity are becoming increasingly clear1, little is known about the non-genetic mechanisms that contribute to intratumour heterogeneity and malignant clonal fitness2. Here, using single-cell profiling and lineage tracing (SPLINTR)-an expressed barcoding strategy-we trace isogenic clones in three clinically relevant mouse models of acute myeloid leukaemia. We find that malignant clonal dominance is a cell-intrinsic and heritable property that is facilitated by the repression of antigen presentation and increased expression of the secretory leukocyte peptidase inhibitor gene (Slpi), which we genetically validate as a regulator of acute myeloid leukaemia. Increased transcriptional heterogeneity is a feature that enables clonal fitness in diverse tissues and immune microenvironments and in the context of clonal competition between genetically distinct clones. Similar to haematopoietic stem cells3, leukaemia stem cells (LSCs) display heritable clone-intrinsic properties of high, and low clonal output that contribute to the overall tumour mass. We demonstrate that LSC clonal output dictates sensitivity to chemotherapy and, although high- and low-output clones adapt differently to therapeutic pressure, they coordinately emerge from minimal residual disease with increased expression of the LSC program. Together, these data provide fundamental insights into the non-genetic transcriptional processes that underpin malignant clonal fitness and may inform future therapeutic strategies.

An audit of 70 maternal deaths.

INTRODUCTION: Although women rarely die during pregnancy and childbirth in Denmark, keeping track of the maternal mortality rate and causes of death is vital in identifying learning points for future management of critical illness among obstetric patients and in pinpointing risk factors. METHODS: We identified maternal deaths between 2002 and 2017 by linking four Danish national health registers, using death certificates and reports from hospitals. An audit group then categorised each case by cause of death before identifying any suboptimal care and learning points, which may serve as a foundation for national guidelines and educational strategies. RESULTS: Seventy women died during pregnancy or within six weeks of a pregnancy in the study period. The most frequent causes of death were cardiovascular disease (n = 14), hypertensive disorder (n = 10), suicide (n = 10) and thromboembolism (n = 7). Suboptimal care was identified in 30 of the 70 cases. CONCLUSIONS: Mortality from some of the most important causes of death decreased during the study period. No deaths from preeclampsia or thrombosis, two of the leading causes of death, were identified after 2011. In 2015-2017, suicide was the main cause of maternal death, which indicates that a stronger focus on vulnerability in pregnancy and childbirth is essential. Among the 70 deaths, 34% were potentially avoidable, indicating that it is essential continuously to focus on how to reduce severe maternal morbidity and mortality. FUNDING: none TRIAL REGISTRATION. not relevant.

Reduction in maternal mortality in Denmark over three decades.

INTRODUCTION: Women very rarely die during pregnancy and childbirth in Denmark. Although maternal deaths are registered worldwide, various studies indicate that underreporting does occur. This paper presents validated Danish register data for two periods between 1985 and 2017. METHODS: Maternal deaths were identified from 1985 to 1994 and from 2002 to 2017 by linking four national health registers, death certificates and notifications from maternity wards. A group of obstetricians categorised and assessed all medical records, classifying each case by cause of death. RESULTS: Linkage of four registers yielded valid data, leading to the identification of 143 maternal deaths in the abovementioned periods. From 1985-1994 there were 73 deaths and 618,021 live births, resulting in a maternal mortality rate of 11.8 per 100,000 live births with a non-significant 2% annual increase (95% confidence interval (CI): -6.0-11.0%). From 2002 to 2017 there were 70 maternal deaths and 999,206 live births, resulting in a maternal mortality rate of 7.0 per 100,000 live births (95% CI: 5.5-8.9) with a significant 9% annual decrease (95% CI: 4.0-14.0%). CONCLUSIONS: Overall maternal mortality decreased in the course of the two periods (n = 33 years), with a significant decrease during the last period. This is suggested to be a result of multiple clinical and organisational improvements as discussed in the paper. FUNDING: none. TRIAL REGISTRATION: not relevant.

[Impacted foetal head at emergency caesarean sections].

Impacted foetal head is common in emergency caesarean sections with consequences for mother and foetus, rarely but devastatingly resulting in cranial injuries and foetal death. In prevention, the Fetal Pillow is a simple inflatable device used to push the foetal head upwards, which can reduce complications. Evidence supports applying the reverse breech technique over other manoeuvres. In this review, we emphasise limiting uterine extensions and the push-method. An algorithm which can be integrated in obstetric training, is proposed for prophylaxis and treatment of an impacted foetal head.

Mode of delivery and adverse short- and long-term outcomes in vertex-presenting very preterm born infants: a European population-based prospective cohort study.

OBJECTIVES: To compare mortality, morbidity and neurodevelopment by mode of delivery (MOD) for very preterm births with low prelabour risk of caesarean section (CS). METHODS: The study was a population-based prospective cohort study in 19 regions in 11 European countries. Multivariable mixed effects models and weighted propensity score models were used to estimate adjusted odds ratios (aOR) by observed MOD and the unit's policy regarding MOD. Population: Singleton vertex-presenting live births at 24 + 0 to 31 + 6 weeks of gestation without serious congenital anomalies, preeclampsia, HELLP or eclampsia, antenatal detection of growth restriction and prelabour CS for fetal or maternal indications. RESULTS: Main outcome measures: A composite of in-hospital mortality and intraventricular haemorrhage (grade III/IV) or periventricular leukomalacia. Secondary outcomes were components of the primary outcome, 5 min Apgar score <7 and moderate to severe neurodevelopmental impairment at two years of corrected age. The rate of CS was 29.6% but varied greatly between countries (8.0-52.6%). MOD was not associated with the primary outcome (aOR for CS 0.99; 95% confidence interval [CI] 0.65-1.50) when comparing units with a systematic policy of CS or no policy of MOD to units with a policy of vaginal delivery (aOR 0.88; 95% CI 0.59-1.32). No association was observed for two-year neurodevelopment impairment for CS (aOR 1.15; 95% CI 0.66-2.01) or unit policies (aOR 1.04; 95% CI 0.63-1.70). CONCLUSIONS: Among singleton vertex-presenting live births without medical complications requiring a CS at 24 + 0 to 31 + 6 weeks of gestation, CS was not associated with improved neonatal or long-term outcomes.

Clonal multi-omics reveals Bcor as a negative regulator of emergency dendritic cell development.

Despite advances in single-cell multi-omics, a single stem or progenitor cell can only be tested once. We developed clonal multi-omics, in which daughters of a clone act as surrogates of the founder, thereby allowing multiple independent assays per clone. With SIS-seq, clonal siblings in parallel "sister" assays are examined either for gene expression by RNA sequencing (RNA-seq) or for fate in culture. We identified, and then validated using CRISPR, genes that controlled fate bias for different dendritic cell (DC) subtypes. This included Bcor as a suppressor of plasmacytoid DC (pDC) and conventional DC type 2 (cDC2) numbers during Flt3 ligand-mediated emergency DC development. We then developed SIS-skew to examine development of wild-type and Bcor-deficient siblings of the same clone in parallel. We found Bcor restricted clonal expansion, especially for cDC2s, and suppressed clonal fate potential, especially for pDCs. Therefore, SIS-seq and SIS-skew can reveal the molecular and cellular mechanisms governing clonal fate.

Single-cell analyses reveal the clonal and molecular aetiology of Flt3L-induced emergency dendritic cell development.

Regulation of haematopoietic stem and progenitor cell (HSPC) fate is crucial during homeostasis and under stress conditions. Here we examine the aetiology of the Flt3 ligand (Flt3L)-mediated increase of type 1 conventional dendritic cells (cDC1s). Using cellular barcoding we demonstrate this occurs through selective clonal expansion of HSPCs that are primed to produce cDC1s and not through activation of cDC1 fate by other HSPCs. In particular, multi/oligo-potent clones selectively amplify their cDC1 output, without compromising the production of other lineages, via a process we term tuning. We then develop Divi-Seq to simultaneously profile the division history, surface phenotype and transcriptome of individual HSPCs. We discover that Flt3L-responsive HSPCs maintain a proliferative 'early progenitor'-like state, leading to the selective expansion of multiple transitional cDC1-primed progenitor stages that are marked by Irf8 expression. These findings define the mechanistic action of Flt3L through clonal tuning, which has important implications for other models of 'emergency' haematopoiesis.

Unit policies regarding tocolysis after preterm premature rupture of membranes: association with latency, neonatal and 2-year outcomes (EPICE cohort).

After preterm premature rupture of membranes (PPROM), antibiotics and antenatal steroids are effective evidence-based interventions, but the use of tocolysis is controversial. We investigated whether a unit policy of tocolysis use after PPROM is associated with prolonged gestation and improved outcomes for very preterm infants in units that systematically use these other evidence-based treatments. From the prospective, observational, population-based EPICE cohort study (all very preterm births in 19 regions from 11 European countries, 2011-2012), we included 607 women with a singleton pregnancy and PPROM at 24-29 weeks' gestation, of whom 101, 195 and 311 were respectively managed in 17, 32 and 45 units with no-use, restricted and liberal tocolysis policies for PPROM. The association between unit policies and outcomes (early-onset sepsis, survival at discharge, survival at discharge without severe morbidity and survival at two years without gross motor impairment) was investigated using three-level random-intercept logistic regression models, showing no differences in neonatal or two-year outcomes by unit policy. Moreover, there was no association between unit policies and prolongation of gestation in a multilevel survival analysis. Compared to a unit policy of no-use of tocolysis after PPROM, a liberal or restricted policy is not associated with improved obstetric, neonatal or two-year outcomes.

Characteristics, management and outcomes of very preterm triplets in 19 European regions.

OBJECTIVE: To describe obstetrical care and in-hospital outcomes in very preterm triplet pregnancies in a European multiregional cohort. METHODS: Data from a prospective population-based study of very preterm births between 22 + 0 and 31 + 6 weeks of gestation in 19 regions from 11 European countries participating in the EPICE project in 2011/2012 were used to describe triplet pregnancies and compare them with twins and singletons. RESULTS: Triplets constituted 1.1% of very preterm pregnancies (97/8851) and 3.3% of very preterm live births (258/7900); these percentages varied from 0% to 2.6% and 0% to 6% respectively across the regions. In-hospital mortality after live birth was 12.4% and did not differ significantly from singletons or twins or by birth order. However, 28.9% of mothers with a triplet pregnancy experienced at least one neonatal death. Ninety percent of live-born triplets were delivered by cesarean. Vaginal delivery was associated with an Apgar score of less than 7, but not with in-hospital mortality. CONCLUSIONS: The prevalence of very preterm triplets varies across European regions. Most triplets were born by cesarean and those born vaginally had lower Apgar scores. Overall, in-hospital mortality after live birth was similar to singletons and twins.

Lesbian, Gay, Bisexual, and Transgender Older Adults' Experiences With Elder Abuse and Neglect.

BACKGROUND/OBJECTIVES: Little is known about elder abuse and neglect in the lesbian, gay, bisexual, and transgender (LGBT) community; however, this population faces a greater risk of abuse and likely experiences abuse differently and needs different resources. We conducted focus groups to investigate LGBT older adults' perspectives on and experience with elder mistreatment. METHODS: We conducted three focus groups with 26 participants recruited from senior centers dedicated to LGBT older adults. A semistructured questionnaire was developed, and focus groups were audio recorded, professionally transcribed, and analyzed using grounded theory. RESULTS: Key themes that emerged included: definitions and etiologies of abuse, intersectionality of discrimination from multiple minority identities, reluctance to report, and suggestions for improving outreach. Participants defined elder abuse in multiple ways, including abuse from systems and by law enforcement and medical providers. Commonly reported etiologies included: social isolation due to discrimination, internalization of stigma, intersection of discrimination from multiple minority identities, and an abuser's desire for power and control. Participants were somewhat hesitant to report to police; however, most felt strongly that they would not report abuse to their medical provider. Most reported that they would feel compelled to report if they knew someone was being abused; however, they did not know who to report to. Strategies participants suggested to improve outreach included: increasing awareness about available resources and researchers engaging with the LGBT community directly. CONCLUSION: LGBT older adults conceptualize elder abuse differently and have different experiences with police and medical providers. Improved outreach to this potentially vulnerable population is critical to ensuring their safety. J Am Geriatr Soc 67:2338-2345, 2019.

Benchmarking single cell RNA-sequencing analysis pipelines using mixture control experiments.

Single cell RNA-sequencing (scRNA-seq) technology has undergone rapid development in recent years, leading to an explosion in the number of tailored data analysis methods. However, the current lack of gold-standard benchmark datasets makes it difficult for researchers to systematically compare the performance of the many methods available. Here, we generated a realistic benchmark experiment that included single cells and admixtures of cells or RNA to create 'pseudo cells' from up to five distinct cancer cell lines. In total, 14 datasets were generated using both droplet and plate-based scRNA-seq protocols. We compared 3,913 combinations of data analysis methods for tasks ranging from normalization and imputation to clustering, trajectory analysis and data integration. Evaluation revealed pipelines suited to different types of data for different tasks. Our data and analysis provide a comprehensive framework for benchmarking most common scRNA-seq analysis steps.

Sample path properties of the average generation of a Bellman-Harris process.

Motivated by a recently proposed design for a DNA coded randomised algorithm that enables inference of the average generation of a collection of cells descendent from a common progenitor, here we establish strong convergence properties for the average generation of a super-critical Bellman-Harris process. We further extend those results to a two-type Bellman-Harris process where one type can give rise to the other, but not vice versa. These results further affirm the estimation method's potential utility by establishing its long run accuracy on individual sample-paths, and significantly expanding its remit to encompass cellular development that gives rise to differentiated offspring with distinct population dynamics.