Information processing at the foxa node of the sea urchin endomesoderm specification network

The foxa regulatory gene is of central importance for endoderm specification across Bilateria, and this gene lies at an essential node of the well-characterized sea urchin endomesoderm gene regulatory network (GRN). Here we experimentally dissect the cis-regulatory system that controls the complex pattern of foxa expression in these embryos. Four separate cis-regulatory modules (CRMs) cooperate to control foxa expression in different spatial domains of the endomesoderm, and at different times. A detailed mutational analysis revealed the inputs to each of these cis-regulatory modules. The complex and dynamic expression of foxa is regulated by a combination of repressors, a permissive switch, and multiple activators. A mathematical kinetic model was applied to study the dynamic response of foxa cis-regulatory modules to transient inputs. This study shed light on the mesoderm–endoderm fate decision and provides a functional explanation, in terms of the genomic regulatory code, for the spatial and temporal expression of a key developmental control gene

Integrating Flux Balance Analysis into Kinetic Models to Decipher the Dynamic Metabolism of Shewanella oneidensis MR-1

Shewanella oneidensis MR-1 sequentially utilizes lactate and its waste products (pyruvate and acetate) during batch culture. To decipher MR-1 metabolism, we integrated genome-scale flux balance analysis (FBA) into a multiple-substrate Monod model to perform the dynamic flux balance analysis (dFBA). The dFBA employed a static optimization approach (SOA) by dividing the batch time into small intervals (i.e., ∼400 mini-FBAs), then the Monod model provided time-dependent inflow/outflow fluxes to constrain the mini-FBAs to profile the pseudo-steady-state fluxes in each time interval. The mini-FBAs used a dual-objective function (a weighted combination of “maximizing growth rate” and “minimizing overall flux”) to capture trade-offs between optimal growth and minimal enzyme usage. By fitting the experimental data, a bi-level optimization of dFBA revealed that the optimal weight in the dual-objective function was time-dependent: the objective function was constant in the early growth stage, while the functional weight of minimal enzyme usage increased significantly when lactate became scarce. The dFBA profiled biologically meaningful dynamic MR-1 metabolisms: 1. the oxidative TCA cycle fluxes increased initially and then decreased in the late growth stage; 2. fluxes in the pentose phosphate pathway and gluconeogenesis were stable in the exponential growth period; and 3. the glyoxylate shunt was up-regulated when acetate became the main carbon source for MR-1 growth

User-Centered Development of a Patient Decision Aid for Choice of Early Abortion Method: Multi-Cycle Mixed Methods Study.

BACKGROUND: People seeking abortion in early pregnancy have the choice between medication and procedural options for care. The choice is preference-sensitive-there is no clinically superior option and the choice depends on what matters most to the individual patient. Patient decision aids (PtDAs) are shared decision-making tools that support people in making informed, values-aligned health care choices. OBJECTIVE: We aimed to develop and evaluate the usability of a web-based PtDA for the Canadian context, where abortion care is publicly funded and available without legal restriction. METHODS: We used a systematic, user-centered design approach guided by principles of integrated knowledge translation. We first developed a prototype using available evidence for abortion seekers' decisional needs and the risks, benefits, and consequences of each option. We then refined the prototype through think-aloud interviews with participants at risk of unintended pregnancy ("patient" participants). Interviews were audio-recorded and documented through field notes. Finally, we conducted a web-based survey of patients and health care professionals involved with abortion care, which included the System Usability Scale. We used content analysis to identify usability issues described in the field notes and open-ended survey questions, and descriptive statistics to summarize participant characteristics and close-ended survey responses. RESULTS: A total of 61 individuals participated in this study. Further, 11 patients participated in think-aloud interviews. Overall, the response to the PtDA was positive; however, the content analysis identified issues related to the design, language, and information about the process and experience of obtaining abortion care. In response, we adapted the PtDA into an interactive website and revised it to include consistent and plain language, additional information (eg, pain experience narratives), and links to additional resources on how to find an abortion health care professional. In total, 25 patients and 25 health care professionals completed the survey. The mean System Usability Scale score met the threshold for good usability among both patient and health care professional participants. Most participants felt that the PtDA was user-friendly (patients: n=25, 100%; health care professionals: n=22, 88%), was not missing information (patients: n=21, 84%; health care professionals: n=18, 72%), and that it was appropriate for patients to complete the PtDA before a consultation (patients: n=23, 92%; health care professionals: n=23, 92%). Open-ended responses focused on improving usability by reducing the length of the PtDA and making the website more mobile-friendly. CONCLUSIONS: We systematically designed the PtDA to address an unmet need to support informed, values-aligned decision-making about the method of abortion. The design process responded to a need identified by potential users and addressed unique sensitivities related to reproductive health decision-making

Barcoded DNA-Tag Reporters for Multiplex Cis-Regulatory Analysis

Cis-regulatory DNA sequences causally mediate patterns of gene expression, but efficient experimental analysis of these control systems has remained challenging. Here we develop a new version of “barcoded" DNA-tag reporters, “Nanotags" that permit simultaneous quantitative analysis of up to 130 distinct cis-regulatory modules (CRMs). The activities of these reporters are measured in single experiments by the NanoString RNA counting method and other quantitative procedures. We demonstrate the efficiency of the Nanotag method by simultaneously measuring hourly temporal activities of 126 CRMs from 46 genes in the developing sea urchin embryo, otherwise a virtually impossible task. Nanotags are also used in gene perturbation experiments to reveal cis-regulatory responses of many CRMs at once. Nanotag methodology can be applied to many research areas, ranging from gene regulatory networks to functional and evolutionary genomics

Influence of GluN2 subunit identity on NMDA receptor function

AbstractN-methyl-d-aspartate receptors (NMDARs) are ligand-gated ion channels (‘ionotropic’ receptors) activated by the major excitatory neurotransmitter, l-glutamate. While the term ‘the NMDAR’ is often used it obscures the fact that this class of receptor contains within it members whose properties are as different as they are similar. This heterogeneity was evident from early electrophysiological, pharmacological and biochemical assessments of the functional properties of NMDARs and while the molecular basis of this heterogeneity has taken many years to elucidate, it indicated from the outset that the diversity of NMDAR phenotypes could allow this receptor family to subserve a variety of functions in the mammalian central nervous system. In this review we highlight some recent studies that have identified structural elements within GluN2 subunits that contribute to the heterogeneous biophysical properties of NMDARs, consider why some recently described novel pharmacological tools may permit better identification of native NMDAR subtypes, examine the evidence that NMDAR subtypes differentially contribute to the induction of long-term potentiation and long-term depression and discuss how through the use of chimeric proteins additional insights have been obtained that account for NMDAR subtype-dependency of physiological and pathophysiological signalling.This article is part of the Special Issue entitled ‘Glutamate Receptor-Dependent Synaptic Plasticity’

Advancing Research on Racial–Ethnic Health Disparities: Improving Measurement Equivalence in Studies with Diverse Samples

To conduct meaningful, epidemiologic research on racial–ethnic health disparities, racial–ethnic samples must be rendered equivalent on other social status and contextual variables via statistical controls of those extraneous factors. The racial–ethnic groups must also be equally familiar with and have similar responses to the methods and measures used to collect health data, must have equal opportunity to participate in the research, and must be equally representative of their respective populations. In the absence of such measurement equivalence, studies of racial–ethnic health disparities are confounded by a plethora of unmeasured, uncontrolled correlates of race–ethnicity. Those correlates render the samples, methods, and measures incomparable across racial–ethnic groups, and diminish the ability to attribute health differences discovered to race–ethnicity vs. to its correlates. This paper reviews the non-equivalent yet normative samples, methodologies and measures used in epidemiologic studies of racial–ethnic health disparities, and provides concrete suggestions for improving sample, method, and scalar measurement equivalence

Effect of angiotensin-converting enzyme inhibitor and angiotensin receptor blocker initiation on organ support-free days in patients hospitalized with COVID-19

IMPORTANCE Overactivation of the renin-angiotensin system (RAS) may contribute to poor clinical outcomes in patients with COVID-19. Objective To determine whether angiotensin-converting enzyme (ACE) inhibitor or angiotensin receptor blocker (ARB) initiation improves outcomes in patients hospitalized for COVID-19. DESIGN, SETTING, AND PARTICIPANTS In an ongoing, adaptive platform randomized clinical trial, 721 critically ill and 58 non–critically ill hospitalized adults were randomized to receive an RAS inhibitor or control between March 16, 2021, and February 25, 2022, at 69 sites in 7 countries (final follow-up on June 1, 2022). INTERVENTIONS Patients were randomized to receive open-label initiation of an ACE inhibitor (n = 257), ARB (n = 248), ARB in combination with DMX-200 (a chemokine receptor-2 inhibitor; n = 10), or no RAS inhibitor (control; n = 264) for up to 10 days. MAIN OUTCOMES AND MEASURES The primary outcome was organ support–free days, a composite of hospital survival and days alive without cardiovascular or respiratory organ support through 21 days. The primary analysis was a bayesian cumulative logistic model. Odds ratios (ORs) greater than 1 represent improved outcomes. RESULTS On February 25, 2022, enrollment was discontinued due to safety concerns. Among 679 critically ill patients with available primary outcome data, the median age was 56 years and 239 participants (35.2%) were women. Median (IQR) organ support–free days among critically ill patients was 10 (–1 to 16) in the ACE inhibitor group (n = 231), 8 (–1 to 17) in the ARB group (n = 217), and 12 (0 to 17) in the control group (n = 231) (median adjusted odds ratios of 0.77 [95% bayesian credible interval, 0.58-1.06] for improvement for ACE inhibitor and 0.76 [95% credible interval, 0.56-1.05] for ARB compared with control). The posterior probabilities that ACE inhibitors and ARBs worsened organ support–free days compared with control were 94.9% and 95.4%, respectively. Hospital survival occurred in 166 of 231 critically ill participants (71.9%) in the ACE inhibitor group, 152 of 217 (70.0%) in the ARB group, and 182 of 231 (78.8%) in the control group (posterior probabilities that ACE inhibitor and ARB worsened hospital survival compared with control were 95.3% and 98.1%, respectively). CONCLUSIONS AND RELEVANCE In this trial, among critically ill adults with COVID-19, initiation of an ACE inhibitor or ARB did not improve, and likely worsened, clinical outcomes. TRIAL REGISTRATION ClinicalTrials.gov Identifier: NCT0273570

Access experiences and attitudes toward abortion among youth experiencing homelessness in the United States: A systematic review

Objectives: We sought to review the literature on the access experiences and attitudes toward abortion among youth experiencing homelessness in the United States. Methods: We conducted a systematic review of peer‐reviewed literature published from 2001 to 2019. We included qualitative studies involving US participants that focused on access experiences, views, or accounts of unintended pregnancy and/or abortion among youth experiencing homelessness. We excluded studies published before 2001 as that was the year mifepristone medication abortion was made available in the US and we aimed to investigate experiences of access to both medical and surgical abortion options. Results: Our thematic analysis of the data resulted in five key themes that characterize the abortion attitudes and access experiences of youth experiencing homelessness: (1) engaging in survival sex and forced sex, (2) balancing relationships and autonomy, (3) availability does not equal access, (4) attempting self-induced abortions using harmful methods, and (5) feeling resilient despite traumatic unplanned pregnancy experiences. Conclusions: Youth experiencing homelessness experience barriers to abortion access across the US, including in states with a supportive policy context and publicly funded abortion services. In the absence of accessible services, youth may consider harmful methods of self-induced abortion. Improved services should be designed to offer low-barrier abortion care with the qualities that youth identified as important to them, including privacy and autonomy.SM is supported by a Michael Smith Foundation for Health Research Scholar Award (18270) www.msfhr.or