Archiving and disseminating integrative structure models.

Limitations in the applicability, accuracy, and precision of individual structure characterization methods can sometimes be overcome via an integrative modeling approach that relies on information from all available sources, including all available experimental data and prior models. The open-source Integrative Modeling Platform (IMP) is one piece of software that implements all computational aspects of integrative modeling. To maximize the impact of integrative structures, the coordinates should be made publicly available, as is already the case for structures based on X-ray crystallography, NMR spectroscopy, and electron microscopy. Moreover, the associated experimental data and modeling protocols should also be archived, such that the original results can easily be reproduced. Finally, it is essential that the integrative structures are validated as part of their publication and deposition. A number of research groups have already developed software to implement integrative modeling and have generated a number of structures, prompting the formation of an Integrative/Hybrid Methods Task Force. Following the recommendations of this task force, the existing PDBx/mmCIF data representation used for atomic PDB structures has been extended to address the requirements for archiving integrative structural models. This IHM-dictionary adds a flexible model representation, including coarse graining, models in multiple states and/or related by time or other order, and multiple input experimental information sources. A prototype archiving system called PDB-Dev ( https://pdb-dev.wwpdb.org ) has also been created to archive integrative structural models, together with a Python library to facilitate handling of integrative models in PDBx/mmCIF format

Incorporating immunizations into routine obstetric care to facilitate Health Care Practitioners in implementing maternal immunization

Immunization against pertussis, influenza, and rubella reduces morbidity and mortality in pregnant women and their offspring. Health care professionals (HCPs) caring for women perinatally are uniquely placed to reduce maternal vaccine preventable diseases (VPDs). Despite guidelines recommending immunization during the perinatal period, maternal vaccine uptake remains low. This qualitative study explored the role of obstetricians, general practitioners, and midwives in maternal vaccine uptake. Semi-structured interviews (n = 15) were conducted with perinatal HCPs at a tertiary maternity hospital in South Australia. HCPs were asked to reflect on their knowledge, beliefs, and practice relating to immunization advice and vaccine provision. Interviews were transcribed and coded using thematic analysis. Data collection and analysis was an iterative process, with collection ceasing with theoretical saturation. Participants unanimously supported maternal vaccination as an effective way of reducing risk of disease in this vulnerable population, however only rubella immunity detection and immunization is embedded in routine care. Among these professionals, delegation of responsibility for maternal immunization was unclear and knowledge about maternal immunization was variable. Influenza and pertussis vaccine prevention measures were not included in standard pregnancy record documentation, information provision to patients was ad hoc and vaccinations not offered on-site. The key finding was that the incorporation of maternal vaccinations into standard care through a structured process is an important facilitator for immunization uptake. Incorporating vaccine preventable disease management measures into routine obstetric care including incorporation into the Pregnancy Record would facilitate HCPs in implementing recommendations. Rubella prevention provides a useful template for other vaccines. 2014 Landes Bioscience

A comparison of ocean model data and satellite observations of features affecting the growth of the North Equatorial Counter Current during the strong 1997-1998 El Nino

Descriptions of the ocean's role in the El Niño usually focus on equatorial Kelvin waves and the ability of such waves to change the mean thermocline depth and the sea surface temperature (SST) in the central and eastern Pacific. In contrast, starting from a study of the transport of water with temperatures greater than 28 ∘C, sufficient to trigger deep atmospheric convection, Webb (2018) found that, during the strong El Niños of 1983–1984 and 1997–1998, advection by the North Equatorial Counter Current (NECC) had a much greater impact on sea surface temperatures than processes occurring near the Equator. Webb's analysis, which supports the scheme proposed by Wyrtki (1973, 1974), made use of archived data from a high-resolution ocean model. Previously the model had been checked in a preliminary comparison against SST observations in the equatorial Pacific, but, given the contentious nature of the new analysis, the model's behaviour in key areas needs to be checked further against observations. In this paper this is done for the 1987–1988 El Niño, making use of satellite observations of SST and sea level. SST is used to check the movement of warm water near the Equator and at the latitudes of the NECC. Sea level is used to check the model results at the Equator and at 6∘ N in the North Equatorial Trough. Sea level differences between these latitudes affect the transport of the NECC, the increased transport at the start of each strong El Niño being associated with a drop in sea level at 6∘ N in the western Pacific. Later rises in sea level at the Equator increase the transport of the NECC in mid-ocean. The variability of sea level at 6∘ N is also used to compare the strength of tropical instability waves in the model and in the observations. The model showed that in a normal year these act to dilute the temperature in the core of the NECC. However their strength declined during the development of the strong El Niños, allowing the NECC to carry warm water much further than normal across the Pacific. The results of this paper should not be taken as providing proof of the hypotheses of Wyrtki (1973, 1974) or Webb (2018) but instead as a failure of a targeted study, using satellite observations, to disprove the hypotheses

Assessing Bias in Population Size Estimates Among Hidden Populations When Using the Service Multiplier Method Combined With Respondent-Driven Sampling Surveys: Survey Study.

BACKGROUND: Population size estimates (PSEs) for hidden populations at increased risk of HIV, including female sex workers (FSWs), are important to inform public health policy and resource allocation. The service multiplier method (SMM) is commonly used to estimate the sizes of hidden populations. We used this method to obtain PSEs for FSWs at 9 sites in Zimbabwe and explored methods for assessing potential biases that could arise in using this approach. OBJECTIVE: This study aimed to guide the assessment of biases that arise when estimating the population sizes of hidden populations using the SMM combined with respondent-driven sampling (RDS) surveys. METHODS: We conducted RDS surveys at 9 sites in late 2013, where the Sisters with a Voice program (the program), which collects program visit data of FSWs, was also present. Using the SMM, we obtained PSEs for FSWs at each site by dividing the number of FSWs who attended the program, based on program records, by the RDS-II weighted proportion of FSWs who reported attending this program in the previous 6 months in the RDS surveys. Both the RDS weighting and SMM make a number of assumptions, potentially leading to biases if the assumptions are not met. To test these assumptions, we used convergence and bottleneck plots to assess seed dependence of RDS-II proportion estimates, chi-square tests to assess if there was an association between the characteristics of FSWs and their knowledge of program existence, and logistic regression to compare the characteristics of FSWs attending the program with those recruited to RDS surveys. RESULTS: The PSEs ranged from 194 (95% CI 62-325) to 805 (95% CI 456-1142) across 9 sites from May to November 2013. The 95% CIs for the majority of sites were wide. In some sites, the RDS-II proportion of women who reported program use in the RDS surveys may have been influenced by the characteristics of selected seeds, and we also observed bottlenecks in some sites. There was no evidence of association between characteristics of FSWs and knowledge of program existence, and in the majority of sites, there was no evidence that the characteristics of the populations differed between RDS and program data. CONCLUSIONS: We used a series of rigorous methods to explore potential biases in our PSEs. We were able to identify the biases and their potential direction, but we could not determine the ultimate direction of these biases in our PSEs. We have evidence that the PSEs in most sites may be biased and a suggestion that the bias is toward underestimation, and this should be considered if the PSEs are to be used. These tests for bias should be included when undertaking population size estimation using the SMM combined with RDS surveys

An innovative in silico model of the oral mucosa reveals the impact of extracellular spaces on chemical permeation through epithelium

In pharmaceutical therapeutic design or toxicology, accurately predicting the permeation of chemicals through human epithelial tissues is crucial, where permeation is significantly influenced by the tissue's cellular architecture. Current mathematical models for multi-layered epithelium such as the oral mucosa only use simplistic 'bricks and mortar' geometries and therefore do not account for the complex cellular architecture of these tissues at the microscale level, such as the extensive plasma membrane convolutions that define the extracellular spaces between cells. Chemicals often permeate tissues via this paracellular route, meaning that permeation is underestimated. To address this, measurements of human buccal mucosal tissue were conducted to ascertain the width and tortuosity of extracellular spaces across the epithelium. Using mechanistic mathematical modelling, we show that the convoluted geometry of extracellular spaces significantly impacts chemical permeation and that this can be approximated, provided that extracellular tortuosity is accounted for. We next developed an advanced physically-relevant in silico model of oral mucosal chemical permeation using partial differential equations, fitted to chemical permeation in vitro assays on tissue-engineered human oral mucosa. Tissue geometries were measured and captured in silico, and permeation examined and predicted for chemicals with different physicochemical properties. The effect of altering the extracellular space to mimic permeation enhancers was also assessed by perturbing the in silico model. This novel in vitro-in silico approach has the potential to expedite pharmaceutical innovation for testing oromucosal chemical permeation, providing a more accurate, physiologically-relevant model which can reduce animal testing with early screening based on chemical properties

TIGIT Marks Exhausted T Cells, Correlates with Disease Progression, and Serves as a Target for Immune Restoration in HIV and SIV Infection.

HIV infection induces phenotypic and functional changes to CD8+ T cells defined by the coordinated upregulation of a series of negative checkpoint receptors that eventually result in T cell exhaustion and failure to control viral replication. We report that effector CD8+ T cells during HIV infection in blood and SIV infection in lymphoid tissue exhibit higher levels of the negative checkpoint receptor TIGIT. Increased frequencies of TIGIT+ and TIGIT+ PD-1+ CD8+ T cells correlated with parameters of HIV and SIV disease progression. TIGIT remained elevated despite viral suppression in those with either pharmacological antiretroviral control or immunologically in elite controllers. HIV and SIV-specific CD8+ T cells were dysfunctional and expressed high levels of TIGIT and PD-1. Ex-vivo single or combinational antibody blockade of TIGIT and/or PD-L1 restored viral-specific CD8+ T cell effector responses. The frequency of TIGIT+ CD4+ T cells correlated with the CD4+ T cell total HIV DNA. These findings identify TIGIT as a novel marker of dysfunctional HIV-specific T cells and suggest TIGIT along with other checkpoint receptors may be novel curative HIV targets to reverse T cell exhaustion

Prescribing paradigm shift? Applying the 2019 European Society of Cardiology-led guidelines on ‘diabetes, pre-diabetes, and cardiovascular disease’ to assess eligibility for sodium-glucose co-transporter-2 inhibitors or glucagon-like peptide-1 receptor agonists as first-line monotherapy (or add-on to metformin monotherapy) in type 2 diabetes in Scotland

Objective: In 2019, the European Society of Cardiology led and released new guidelines for diabetes cardiovascular risk management, reflecting recent evidence of cardiovascular disease (CVD) reduction with sodium–glucose cotransporter 2 inhibitors (SGLT-2is) and some glucagon-like peptide 1 receptor agonists (GLP-1RAs) in type 2 diabetes (T2D). A key recommendation is that all those with T2D who are (antihyperglycemic) drug naïve or on metformin monotherapy should be CVD risk stratified and an SGLT-2i or a GLP-1RA initiated in all those at high or very high risk, irrespective of glycated hemoglobin. We assessed the impact of these guidelines in Scotland were they introduced as is.Research design and methods: Using a nationwide diabetes register in Scotland, we did a cross-sectional analysis, using variables in our register for risk stratification at 1 January 2019. We were conservative in our definitions, assuming the absence of a risk factor where data were not available. The risk classifications were applied to people who were drug naïve or on metformin monotherapy and the anticipated prescribing change calculated.Results: Of the 265,774 people with T2D in Scotland, 53,194 (20.0% of those with T2D) were drug naïve, and56,906(21.4%) were on metformin monotherapy. Of these, 74.5%and72.4%, respectively, were estimated as at least high risk given the guideline risk definitions.Conclusions: Thus, 80,830 (30.4%) of all those with T2D (n 5 265,774) would start one of these drug classes according to table 7 and figure 3 of the guideline. The sizeable impact on drug budgets, enhanced clinical monitoring, and the trade-off with reduced CVD-related health care costs will need careful consideration.</p