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Dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) is a routine method to noninvasively quantify perfusion dynamics in tissues. The standard practice for analyzing DCE-MRI data is to fit an ordinary differential equation to each voxel. Recent advances in data science provide an opportunity to move beyond existing methods to obtain more accurate measurements of fluid properties. Here, we developed a localized convolutional function regression that enables simultaneous measurement of interstitial fluid velocity, diffusion, and perfusion in 3D. We validated the method computationally and experimentally, demonstrating accurate measurement of fluid dynamics in situ and in vivo. Applying the method to human MRIs, we observed tissue-specific differences in fluid dynamics, with an increased fluid velocity in breast cancer as compared to brain cancer. Overall, our method represents an improved strategy for studying interstitial flows and interstitial transport in tumors and patients. We expect that our method will contribute to the better understanding of cancer progression and therapeutic response.

Rates of microbial processes are fundamental to understanding the significance of microbial impacts on environmental chemical cycling. However, it is often difficult to quantify rates or to link processes to specific taxa or individual cells, especially in environments where there are few cultured representatives with known physiology. Here, we describe the use of the redox-enzyme-sensitive molecular probe RedoxSensor™ Green to measure rates of anaerobic electron transfer physiology (i.e., sulfate reduction and methanogenesis) in individual cells and link those measurements to genomic sequencing of the same single cells. We used this method to investigate microbial activity in hot, anoxic, low-biomass (~103 cells mL-1) groundwater of the Death Valley Regional Flow System, California. Combining this method with electron donor amendment experiments and metatranscriptomics confirmed that the abundant spore formers including Candidatus Desulforudis audaxviator were actively reducing sulfate in this environment, most likely with acetate and hydrogen as electron donors. Using this approach, we measured environmental sulfate reduction rates at 0.14 to 26.9 fmol cell-1 h-1. Scaled to volume, this equates to a bulk environmental rate of ~103 pmol sulfate L-1 d-1, similar to potential rates determined with radiotracer methods. Despite methane in the system, there was no evidence for active microbial methanogenesis at the time of sampling. Overall, this method is a powerful tool for estimating species-resolved, single-cell rates of anaerobic metabolism in low-biomass environments while simultaneously linking genomes to phenomes at the single-cell level. We reveal active elemental cycling conducted by several species, with a large portion attributable to Ca. Desulforudis audaxviator.

Several genetic risk factors for Alzheimers disease implicate genes involved in lipid metabolism and many of these lipid genes are highly expressed in glial cells1. However, the relationship between lipid metabolism in glia and Alzheimers disease pathology remains poorly understood. Through single-nucleus RNA sequencing of brain tissue in Alzheimers disease, we have identified a microglial state defined by the expression of the lipid droplet-associated enzyme ACSL1 with ACSL1-positive microglia being most abundant in patients with Alzheimers disease having the APOE4/4 genotype. In human induced pluripotent stem cell-derived microglia, fibrillar Aβ induces ACSL1 expression, triglyceride synthesis and lipid droplet accumulation in an APOE-dependent manner. Additionally, conditioned media from lipid droplet-containing microglia lead to Tau phosphorylation and neurotoxicity in an APOE-dependent manner. Our findings suggest a link between genetic risk factors for Alzheimers disease with microglial lipid droplet accumulation and neurotoxic microglia-derived factors, potentially providing therapeutic strategies for Alzheimers disease.

Children who receive cochlear implants develop spoken language on a protracted timescale. The home environment facilitates speech-language development, yet it is relatively unknown how the environment differs between children with cochlear implants and typical hearing. We matched eighteen preschoolers with implants (31-65 months) to two groups of children with typical hearing: by chronological age and hearing age. Each child completed a long-form, naturalistic audio recording of their home environment (appx. 16 hours/child; >730 hours of observation) to measure adult speech input, child vocal productivity, and caregiver-child interaction. Results showed that children with cochlear implants and typical hearing were exposed to and engaged in similar amounts of spoken language with caregivers. However, the home environment did not reflect developmental stages as closely for children with implants, or predict their speech outcomes as strongly. Home-based speech-language interventions should focus on the unique input-outcome relationships for this group of children with hearing loss.

Climate change is increasing the frequency and severity of short-term (~1 y) drought events-the most common duration of drought-globally. Yet the impact of this intensification of drought on ecosystem functioning remains poorly resolved. This is due in part to the widely disparate approaches ecologists have employed to study drought, variation in the severity and duration of drought studied, and differences among ecosystems in vegetation, edaphic and climatic attributes that can mediate drought impacts. To overcome these problems and better identify the factors that modulate drought responses, we used a coordinated distributed experiment to quantify the impact of short-term drought on grassland and shrubland ecosystems. With a standardized approach, we imposed ~a single year of drought at 100 sites on six continents. Here we show that loss of a foundational ecosystem function-aboveground net primary production (ANPP)-was 60% greater at sites that experienced statistically extreme drought (1-in-100-y event) vs. those sites where drought was nominal (historically more common) in magnitude (35% vs. 21%, respectively). This reduction in a key carbon cycle process with a single year of extreme drought greatly exceeds previously reported losses for grasslands and shrublands. Our global experiment also revealed high variability in drought response but that relative reductions in ANPP were greater in drier ecosystems and those with fewer plant species. Overall, our results demonstrate with unprecedented rigor that the global impacts of projected increases in drought severity have been significantly underestimated and that drier and less diverse sites are likely to be most vulnerable to extreme drought.

Contrast transport models are widely used to quantify blood flow and transport in dynamic contrast-enhanced magnetic resonance imaging. These models analyze the time course of the contrast agent concentration, providing diagnostic and prognostic value for many biological systems. Thus, ensuring accuracy and repeatability of the model parameter estimation is a fundamental concern. In this work, we analyze the structural and practical identifiability of a class of nested compartment models pervasively used in analysis of MRI data. We combine artificial and real data to study the role of noise in model parameter estimation. We observe that although all the models are structurally identifiable, practical identifiability strongly depends on the data characteristics. We analyze the impact of increasing data noise on parameter identifiability and show how the latter can be recovered with increased data quality. To complete the analysis, we show that the results do not depend on specific tissue characteristics or the type of enhancement patterns of contrast agent signal.

Few evidence-based interventions exist to improve person-centred maternity care in low-resource settings. This study aimed to understand whether a quality improvement (QI) intervention could improve person-centred maternity care (PCMC) experiences for women delivering in public health facilities in Kenya. A pre-post design was used to examine changes in PCMC scores across three intervention and matched control facilities at baseline (n = 491) and endline (n = 677). A QI intervention, using the Model for Improvement, was implemented in three public health facilities in Nairobi and Kiambu Counties in Kenya. Difference-in-difference analyses using models that included main effects of both treatment group and survey round was conducted to understand the impact of the intervention on PCMC scores. Findings suggest that intervention facilities' average total PCMC score decreased by 5.3 points post-intervention compared to baseline (95% CI: -8.8, -1.9) and relative to control facilities, holding socio-demographic and facility variables constant. Additionally, the intervention was significantly associated with a 1.8-point decrease in clinical quality index pre-post-intervention (95% CI: -2.9, -0.7), decreased odds of provider visits, and less likelihood to plan to use postpartum family planning. While improving the quality of women's experiences during childbirth is a critical component to ensure comprehensive, high-quality maternity care experiences and outcomes, further research is required to understand which intervention methods may be most appropriate to improve PCMC in resource-constrained settings.

Purpose: Typically developing children assigned male at birth (AMAB) and children assigned female at birth (AFAB) produce the fricative /s/ differently: AFAB children produce /s/ with a higher spectral peak frequency. This study examined whether implicit knowledge of these differences affects speech-language pathologists'/speech and language therapists' (SLPs'/SLTs') ratings of /s/ accuracy, by comparing ratings made in conditions where SLPs/SLTs were blind to children's sex assigned at birth (SAB) to conditions in which they were told this information. Methods: SLPs (n = 95) varying in clinical experience rated the accuracy of word-initial /s/ productions (n = 87) of eight children with speech sound disorder in one of four conditions: one in which no information about the children was revealed, one in which children's SAB was revealed, one in which children's age was revealed, and one in which both were revealed. Results: Despite there being no statistically significant differences between AFAB and AMAB children's /s/ production in researcher-determined accuracy or in one acoustic characteristic, spectral centroid, SLPs in all four conditions judged the /s/ productions of AFAB children as more accurate than AMAB children. Listeners were significantly less likely to judge the productions of AMAB children to be inaccurate in the conditions in which age or age and SAB were revealed. These effects were consistent across SLPs with greatly varying levels of clinical experience. Conclusion: Knowing or imputing children's age and SAB can affect ratings of /s/ accuracy. Clinicians should be mindful of these potential effects. Future research should understand how expectations about sociolinguistic variation in speech affect appraisals of their speech and language.

Coaches develop and use a complex system of strategies to gain access to teachers' classrooms for coaching. In the process, coaches confront micropolitical forces within the school organization that shape access, either enhancing or impeding coaches' chances of being viewed as a trusted and valued partner in teacher learning. In this qualitative interview study with 28 content-focused coaches in one school district, we used a micropolitical lens to better understand how coaches coordinate micropolitical forces and strategies to gain access to teachers' classrooms, finding that force-strategy coupling was a prevalent coaching practice. We found that coaches most frequently reported using strategies to respond to 2 micropolitical forces: (1) teacher openness to coaching and (2) structures of time and workload. Coaches responded to these forces differently depending on whether the force functioned to support or inhibit access. This research expands on the micropolitical work of coaching and coach agency.

For coaches, access to classrooms isn't straightforward and is far from guaranteed. Access is a prerequisite for coaching, yet there are many barriers beyond a coach's control, making their job difficult to impossible. In this article, the authors detail how five administrative and structural forces shaped coaches' access to teachers' classrooms. The authors include recommendations for school and district leaders for how to best support coach access and, ultimately, the efficacy of coaching programs.

Coaches develop and use strategies to gain access to teachers' classrooms to support teacher learning and instructional improvement. These strategies respond to the specific conditions in which coaches work, including organizational structures and interpersonal factors that can either facilitate or impede access. In this interview study of 28 content-focused coaches in one district, we used a micropolitical lens to explore the forces that influenced coaches' access to teachers' classrooms. Ultimately, we identified nine distinct forces that either supported or constrained coaches' access to classrooms. These forces were bound together in a micropolitical system of interpersonal and structural forces influenced by larger macropolitical forces. Interpersonal forces emanated from three kinds of actors in the school organization: administrators, teachers, and the coaches themselves. Implications for the application of micropolitical theory to future research on the negotiations inherent to coaching and the implications for school districts seeking to establish an effective coaching program are discussed.

Social work has a proliferation of online courses. Both nursing and medicine have been using online technology for years with noted success within a variety of subjects. The current scoping review examined empirical research of online learning and satisfaction outcomes in social work, while also comparing results with nursing and medicine. Results showed that most social work studies that examined learning outcomes between online and traditional courses found differences, whereas approximately half of the studies in nursing and medicine reported no differences. Satisfaction results were more varied in each discipline. Taken together, both learning and satisfaction outcomes remain inconclusive due to documented limitations related to study designs. Implications for social work education are discussed and recommendations are provided.

BACKGROUND: Globally, approximately 800 women and 6400 newborns die around the time of childbirth each day. Many of these deaths could be prevented with high-quality emergency obstetric and newborn care (EmONC). The Monitoring Emergency Obstetric Care: A handbook guides strengthening EmONC services. However, the handbook contains limited quality of care measures. Our study identified and prioritised quality of care indicators for potential inclusion in the handbook, which is undergoing revision. METHODS: We conducted a consultative scoping review, mapping, and prioritisation exercise to select a short list of indicators on facility-based maternal and newborn quality of care. Indicators were identified from literature searches and expert suggestions and organised by the categories of structure, process, and outcomes as defined in the World Health Organizations Standards for Improving Quality of Maternal and Newborn Care in Health Facilities. We focused on process indicators, encompassing the provision of care and experience of care during the intrapartum period, and developed a priority list of indicators using the selection criteria of relevance and feasibility. Experience of care indicators were also mapped against the Person-Centered Maternity Care (PCMC) scale. RESULTS: We extracted a total of 3023 quality of care indicators. After removing out-of-scope and duplicate indicators and applying our selection criteria, we identified 20 provision of care indicators for possible inclusion in the revised EmONC handbook. We recommend including a score for experience of care that could be measured with the 30-item or the 13-item PCMC scale. We also identified 29 experience of care items not covered by the PCMC scale that could be used. Provider experience, patient safety, and quality of abortion care were identified as areas for which no or few indicators were found through our scoping review. CONCLUSIONS: Through a rigorous, consultative, and multi-step process, we selected a short list of process-related, facility-based quality of care indicators for emergency obstetric and newborn care. This list could be included in the EmONC handbook or used for other monitoring purposes. Country consultations to assess the utility and feasibility of the proposed indicators and their adaptation to local contexts will support their refinement and uptake. REGISTRATION: https://osf.io/msxbd (Open Science Framework).

The organic carbon (Corg) stored in seagrass meadows is globally significant and could be relevant in strategies to mitigate increasing CO2 concentration in the atmosphere. Most of that stored Corg is in the soils that underlie the seagrasses. We explored how seagrass and soil characteristics vary among seagrass meadows across the geographic range of turtlegrass (Thalassia testudinum) with a goal of illuminating the processes controlling soil organic carbon (Corg) storage spanning 23° of latitude. Seagrass abundance (percent cover, biomass, and canopy height) varied by over an order of magnitude across sites, and we found high variability in soil characteristics, with Corg ranging from 0.08 to 12.59% dry weight. Seagrass abundance was a good predictor of the Corg stocks in surficial soils, and the relative importance of seagrass-derived soil Corg increased as abundance increased. These relationships suggest that first-order estimates of surficial soil Corg stocks can be made by measuring seagrass abundance and applying a linear transfer function. The relative availability of the nutrients N and P to support plant growth was also correlated with soil Corg stocks. Stocks were lower at N-limited sites than at P-limited ones, but the importance of seagrass-derived organic matter to soil Corg stocks was not a function of nutrient limitation status. This finding seemed at odds with our observation that labile standard substrates decomposed more slowly at N-limited than at P-limited sites, since even though decomposition rates were 55% lower at N-limited sites, less Corg was accumulating in the soils. The dependence of Corg stocks and decomposition rates on nutrient availability suggests that eutrophication is likely to exert a strong influence on carbon storage in seagrass meadows.

The plant secondary cell wall is a thickened matrix of polysaccharides and lignin deposited at the cessation of growth in some cells. It forms the majority of carbon in lignocellulosic biomass, and it is an abundant and renewable source for forage, fiber, materials, fuels, and bioproducts. The complex structure and arrangement of the cell wall polymers mean that the carbon is difficult to access in an economical and sustainable way. One solution is to alter the cell wall polymer structure so that it is more suited to downstream processing. However, it remains difficult to predict what the effects of this engineering will be on the assembly, architecture, and properties of the cell wall. Here, we make use of Arabidopsis plants expressing a suite of genes to increase pectic galactan chain length in the secondary cell wall. Using multi-dimensional solid-state nuclear magnetic resonance, we show that increasing galactan chain length enhances pectin-cellulose spatial contacts and increases cellulose crystallinity. We also found that the increased galactan content leads to fewer spatial contacts of cellulose with xyloglucan and the backbone of pectin. Hence, we propose that the elongated galactan side chains compete with xyloglucan and the pectic backbone for cellulose interactions. Due to the galactan topology, this may result in comparatively weak interactions and disrupt the cell wall architecture. Therefore, introduction of this strategy into trees or other bioenergy crops would benefit from cell-specific expression strategies to avoid negative effects on plant growth.

Single-nucleotide variants (SNVs) in segmental duplications (SDs) have not been systematically assessed because of the limitations of mapping short-read sequencing data1,2. Here we constructed 1:1 unambiguous alignments spanning high-identity SDs across 102 human haplotypes and compared the pattern of SNVs between unique and duplicated regions3,4. We find that human SNVs are elevated 60% in SDs compared to unique regions and estimate that at least 23% of this increase is due to interlocus gene conversion (IGC) with up to 4.3 megabase pairs of SD sequence converted on average per human haplotype. We develop a genome-wide map of IGC donors and acceptors, including 498 acceptor and 454 donor hotspots affecting the exons of about 800 protein-coding genes. These include 171 genes that have 'relocated' on average 1.61 megabase pairs in a subset of human haplotypes. Using a coalescent framework, we show that SD regions are slightly evolutionarily older when compared to unique sequences, probably owing to IGC. SNVs in SDs, however, show a distinct mutational spectrum: a 27.1% increase in transversions that convert cytosine to guanine or the reverse across all triplet contexts and a 7.6% reduction in the frequency of CpG-associated mutations when compared to unique DNA. We reason that these distinct mutational properties help to maintain an overall higher GC content of SD DNA compared to that of unique DNA, probably driven by GC-biased conversion between paralogous sequences5,6.

Here the Human Pangenome Reference Consortium presents a first draft of the human pangenome reference. The pangenome contains 47 phased, diploid assemblies from a cohort of genetically diverse individuals1. These assemblies cover more than 99% of the expected sequence in each genome and are more than 99% accurate at the structural and base pair levels. Based on alignments of the assemblies, we generate a draft pangenome that captures known variants and haplotypes and reveals new alleles at structurally complex loci. We also add 119 million base pairs of euchromatic polymorphic sequences and 1,115 gene duplications relative to the existing reference GRCh38. Roughly 90 million of the additional base pairs are derived from structural variation. Using our draft pangenome to analyse short-read data reduced small variant discovery errors by 34% and increased the number of structural variants detected per haplotype by 104% compared with GRCh38-based workflows, which enabled the typing of the vast majority of structural variant alleles per sample.

α-Fetoprotein (AFP) is expressed by stem-like and poor outcome hepatocellular cancer tumors and is a clinical tumor biomarker. AFP has been demonstrated to inhibit dendritic cell (DC) differentiation and maturation and to block oxidative phosphorylation. To identify the critical metabolic pathways leading to human DC functional suppression, here, we used two recently described single-cell profiling methods, scMEP (single-cell metabolic profiling) and SCENITH (single-cell energetic metabolism by profiling translation inhibition). Glycolytic capacity and glucose dependence of DCs were significantly increased by tumor-derived, but not normal cord blood-derived, AFP, leading to increased glucose uptake and lactate secretion. Key molecules in the electron transport chain in particular were regulated by tumor-derived AFP. These metabolic changes occurred at mRNA and protein levels, with negative impact on DC stimulatory capacity. Tumor-derived AFP bound significantly more polyunsaturated fatty acids (PUFA) than cord blood-derived AFP. PUFAs bound to AFP increased metabolic skewing and promoted DC functional suppression. PUFAs inhibited DC differentiation in vitro, and ω-6 PUFAs conferred potent immunoregulation when bound to tumor-derived AFP. Together, these findings provide mechanistic insights into how AFP antagonizes the innate immune response to limit antitumor immunity.Significanceα-Fetoprotein (AFP) is a secreted tumor protein and biomarker with impact on immunity. Fatty acid-bound AFP promotes immune suppression by skewing human dendritic cell metabolism toward glycolysis and reduced immune stimulation.

Cell-cycle control is accomplished by cyclin-dependent kinases (CDKs), motivating extensive research into CDK targeting small-molecule drugs as cancer therapeutics. Here we use combinatorial CRISPR/Cas9 perturbations to uncover an extensive network of functional interdependencies among CDKs and related factors, identifying 43 synthetic-lethal and 12 synergistic interactions. We dissect CDK perturbations using single-cell RNAseq, for which we develop a novel computational framework to precisely quantify cell-cycle effects and diverse cell states orchestrated by specific CDKs. While pairwise disruption of CDK4/6 is synthetic-lethal, only CDK6 is required for normal cell-cycle progression and transcriptional activation. Multiple CDKs (CDK1/7/9/12) are synthetic-lethal in combination with PRMT5, independent of cell-cycle control. In-depth analysis of mRNA expression and splicing patterns provides multiple lines of evidence that the CDK-PRMT5 dependency is due to aberrant transcriptional regulation resulting in premature termination. These inter-dependencies translate to drug-drug synergies, with therapeutic implications in cancer and other diseases.