A novel cellular pathway of antigen presentation and CD4 T cell activation in vivo

Dendritic cell activation of CD4 T cells in the lymph node draining a site of infection or vaccination is widely considered the central event in initiating adaptive immunity. The accepted dogma is that this occurs by stimulating local activation and antigen acquisition by dendritic cells, with subsequent lymph node migration, however the generalizability of this mechanism is unclear. Here we show that in some circumstances antigen can bypass the injection site inflammatory response, draining freely and rapidly to the lymph nodes where it interacts with subcapsular sinus (SCS) macrophages resulting in their death. Debris from these dying SCS macrophages is internalized by monocytes recruited from the circulation. This coordinated response leads to antigen presentation by monocytes and interactions with naïve CD4 T cells that can drive the initiation of T cell and B cell responses. These studies demonstrate an entirely novel pathway leading to initiation of adaptive immune responses in vivo

The pH dependency of the boron isotopic composition of diatom opal (Thalassiosira weissflogii)

The high-latitude oceans are key areas of carbon and heat exchange between the atmosphere and the ocean. As such, they are a focus of both modern oceanographic and palaeoclimate research. However, most palaeoclimate proxies that could provide a long-term perspective are based on calcareous organisms, such as foraminifera, that are scarce or entirely absent in deep-sea sediments south of 50∘ S in the Southern Ocean and north of 40∘ N in the North Pacific. As a result, proxies need to be developed for the opal-based organisms (e.g. diatoms) found at these high latitudes, which dominate the biogenic sediments recovered from these regions. Here we present a method for the analysis of the boron (B) content and isotopic composition (δ11B) of diatom opal. We apply it for the first time to evaluate the relationship between seawater pH, δ11B and B concentration ([B]) in the frustules of the diatom Thalassiosira weissflogii, cultured across a range of carbon dioxide partial pressure (pCO2) and pH values. In agreement with existing data, we find that the [B] of the cultured diatom frustules increases with increasing pH (Mejía et al., 2013). δ11B shows a relatively well defined negative trend with increasing pH, completely distinct from any other biomineral previously measured. This relationship not only has implications for the magnitude of the isotopic fractionation that occurs during boron incorporation into opal, but also allows us to explore the potential of the boron-based proxies for palaeo-pH and palaeo-CO2 reconstruction in high-latitude marine sediments that have, up until now, eluded study due to the lack of suitable carbonate material

Developing a xenograft model of human vasculature in the mouse ear pinna

Humanised xenograft models allow for the analysis of human tissue within a physiological environment in vivo. However, current models often rely on the angiogenesis and ingrowth of recipient vasculature to perfuse tissues, preventing analysis of biological processes and diseases involving human blood vessels. This limits the effectiveness of xenografts in replicating human physiology and may lead to issues with translating findings into human research. We have designed a xenograft model of human vasculature to address this issue. Human subcutaneous fat was cultured in vitro to promote blood vessel outgrowth prior to implantation into immunocompromised mice. We demonstrate that implants survived, retained human vasculature and anastomosed with the circulatory system of the recipient mouse. Significantly, by performing transplants into the ear pinna, this system enabled intravital observation of xenografts by multiphoton microscopy, allowing us to visualise the steps leading to vascular cytoadherence of erythrocytes infected with the human parasite Plasmodium falciparum. This model represents a useful tool for imaging the interactions that occur within human tissues in vivo and permits visualization of blood flow and cellular recruitment in a system which is amenable to intervention for various studies in basic biology together with drug evaluation and mechanism of action studies

Stories of self, us, and now: narrative and power for health equity in grassroots community organizing

IntroductionCommunity organizing initiatives, which build power through cycles of listening, participatory research, collective action, and reflection, have demonstrated the capacity to intervene on, complicate, and resist dominant societal narratives while promoting alternative public narratives focused on shared values and hope for a better future.MethodsTo explore processes of public narrative change and their relationship to community and organizational empowerment, we interviewed 35 key leaders in community organizing initiatives in Detroit, MI and Cincinnati, OH about how narrative change takes place within community organizing practices.ResultsLeaders’ perspectives revealed crucial roles for narrative and storytelling in guiding individual and collective behavior, supporting the development of relationships of trust and accountability, and linking personal and collective experiences to pressing social issues.DiscussionFindings from this study indicate that systemic change is a labor-intensive process and one that requires the development of leaders (stories of self) and the cultivation of collective structures (stories of us) capable of enacting power to effect change with urgency (stories of now). We conclude by discussing implications of these findings for public narrative interventions and related health equity promotion efforts

The clinical and cost-effectiveness of rehabilitation of memory in brain injury: the ReMemBrIn RCT

Background People with traumatic brain injuries (TBIs) commonly report memory impairments. These are persistent, debilitating, and reduce quality of life, but patients do not routinely receive memory rehabilitation after discharge from hospital. Objectives To assess the clinical and cost-effectiveness of a group memory rehabilitation programme for people with TBI. Design Multi-centre, pragmatic, cluster randomised controlled trial. Qualitative and health economic evaluations were also undertaken. Setting Community settings in nine sites in England. Participants Participants were aged 18-69 years, with TBI more than 3 months prior to recruitment, reported memory problems, who were able to travel to a site to attend group sessions, communicate in English, and gave informed consent. Randomisation and blinding Clusters of 4 to 6 participants were randomised to intervention or control on a 1:1 ratio. Randomisation was based on a computer generated pseudo-random code using random permuted blocks of randomly varying size, stratified by study site. Participants and therapists were aware of the treatment allocation; outcome assessors were blinded. Interventions Ten weekly sessions of a manualised memory rehabilitation programme were provided in addition to usual care. Participants were taught restitution strategies to retrain impaired memory functions and compensation strategies to enable them to cope with memory problems. The control arm received usual care only. Outcomes Outcomes were assessed at 6 and 12 months after randomisation. Primary: Patient-completed Everyday Memory Questionnaire (EMQ-p) at 6-month follow-up. Secondary: Rivermead Behavioural Memory Test-3, General Health Questionnaire-30, European Brain Injury Questionnaire, Everyday Memory Questionnaire-relative version, individual goal attainment. Costs (based on a UK NHS and PSS perspective) were collected using a service use questionnaire, with the EQ-5D 5L used to derive Quality Adjusted Life Years. A Markov model was developed to explore cost-effectiveness at 5 and 10 years, with 3.5% discount applied. Results We randomised 328 participants (intervention: n=171; control: n=157), with 129 in the intervention arm and 122 in the control arm included in the primary analysis. We found no clinically important difference on the EMQ-p between the two arms at 6-month follow-up (adjusted difference in means -2.1, 95% CI -6.7 to 2.5, p=0.37). For secondary outcomes, differences favouring the intervention arm were observed at 6-month follow-up for RBMT and goal attainment, but remained only for goal attainment at 12-month follow-up. There were no differences between arms in mood or quality of life. Qualitative results suggested positive experiences of participating in the trial and of attending the groups. Participants reported that memory rehabilitation was not routinely accessible in usual care. The primary health economics outcome at 12-months found memory rehabilitation to be £26.89 cheaper than usual care but less effective with an incremental QALY loss of 0.007. Differences in costs and effects were not statistically significant and non-parametric bootstrapping demonstrated considerable uncertainty in these findings. No safety concerns were raised and no deaths reported. Limitations As a pragmatic trial, we had broad inclusion criteria, therefore there was considerable heterogeneity within the sample. The study was not powered to perform further sub-group analyses. Participants and therapists could not be blinded to treatment allocation. Conclusions The group memory rehabilitation delivered in this trial is very unlikely to lead to clinical benefits or to be a cost-effective treatment for people with TBI in the community. Future work Future studies should examine the inclusion and selection of participants who may benefit most from memory rehabilitation. Registration ISRCTN65792154 Funding National Institute for Health Research, Health Technology Assessmen

Covariation in urban birds providing cultural services or disservices and people

This is the author accepted manuscript. The final version is available from Wiley via the DOI in this record.1. The spatial distributions of biodiversity and people vary across landscapes, and are critical to the delivery of ecosystem services and disservices. The high densities of people, and often of birds, in urban areas lead to frequent human-avian interactions, which can be positive or negative for people’s well-being. The identities of the bird species providing these services or disservices tend to be quite different, however it is unclear how their abundance and richness covary with human population density, and hence with potential recipients of these services and disservices. 2. We surveyed bird populations in 106 tiles (500x500 m) across the 174 km2 of an extended urban area in southern England. From the literature, we identified two groups of species: those associated with positive interactions for human well-being, and those that display behaviours that are negative for human well-being. We estimated the abundance (adjusted for detection probability) and richness of each group, and modelled how they covary with human population density. 3. Aggregation of population estimates for the 35 service and nine disservice species observed revealed 593,128 (95% confidence interval: 541,817-657,046) and 225,491 (200,134-235,066) birds, respectively. Across the surveyed tiles there were 1.09 service, and 0.42 disservice birds per person. 4. There was a peaking quadratic relationship between service abundance and human population density, but a negative linear relationship between richness and human density. Conversely, there were positive linear relationships for both abundance and richness of disservice species with human density. The ratio of service to disservice birds shifted from 3.5 to 1 at intermediate human densities to 1 to 1 in more densely populated areas. 5. Synthesis and applications. Differences in the distributions of service and disservice species, and the extremely low ratios of birds to people particularly in socioeconomically deprived areas, mean that people there have few opportunities for contact with birds, and the contact that they do have is equally likely to be negative as positive for human well-being. We recommend spatial targeting of improvements in green infrastructure, combined with the targeted provisioning of food and nesting places for service species, to promote positive interactions between birds and people.We thank M. Evans and M. Gregory for their fieldwork, and J. Harris and R. Corstanje for their advice and logistical support. All authors were supported by the Fragments, Functions, Flows and Urban Ecosystem Services project, NERC grant NE/J015237/1, funded under the NERC Biodiversity and Ecosystem Service Sustainability programme. The authors declare no conflict of interest

Methods for the extraction, storage, amplification and sequencing of DNA from environmental samples

Advances in the sequencing of DNA extracted from media such as soil and water offer huge opportunities for biodiversity monitoring and assessment, particularly where the collection or identification of whole organisms is impractical. However, there are myriad methods for the extraction, storage, amplification and sequencing of DNA from environmental samples. To help overcome potential biases that may impede the effective comparison of biodiversity data collected by different researchers, we propose a standardised set of procedures for use on different taxa and sample media, largely based on recent trends in their use. Our recommendations describe important steps for sample pre-processing and include the use of (a) Qiagen DNeasy PowerSoil® and PowerMax® kits for extraction of DNA from soil, sediment, faeces and leaf litter; (b) DNeasy PowerSoil® for extraction of DNA from plant tissue; (c) DNeasy Blood and Tissue kits for extraction of DNA from animal tissue; (d) DNeasy Blood and Tissue kits for extraction of DNA from macroorganisms in water and ice; and (e) DNeasy PowerWater® kits for extraction of DNA from microorganisms in water and ice. Based on key parameters, including the specificity and inclusivity of the primers for the target sequence, we recommend the use of the following primer pairs to amplify DNA for analysis by Illumina MiSeq DNA sequencing: (a) 515f and 806RB to target bacterial 16S rRNA genes (including regions V3 and V4); (b) #3 and #5RC to target eukaryote 18S rRNA genes (including regions V7 and V8); (c) #3 and #5RC are also recommended for the routine analysis of protist community DNA; (d) ITS6F and ITS7R to target the chromistan ITS1 internal transcribed spacer region; (e) S2F and S3R to target the ITS2 internal transcribed spacer in terrestrial plants; (f) fITS7 or gITS7, and ITS4 to target the fungal ITS2 region; (g) NS31 and AML2 to target glomeromycota 18S rRNA genes; and (h) mICOIintF and jgHCO2198 to target cytochrome c oxidase subunit I (COI) genes in animals. More research is currently required to confirm primers suitable for the selective amplification of DNA from specific vertebrate taxa such as fish. Combined, these recommendations represent a framework for efficient, comprehensive and robust DNA-based investigations of biodiversity, applicable to most taxa and ecosystems. The adoption of standardised protocols for biodiversity assessment and monitoring using DNA extracted from environmental samples will enable more informative comparisons among datasets, generating significant benefits for ecological science and biosecurity applications

Pan-viral serology implicates enteroviruses in acute flaccid myelitis.

Since 2012, the United States of America has experienced a biennial spike in pediatric acute flaccid myelitis (AFM)1-6. Epidemiologic evidence suggests non-polio enteroviruses (EVs) are a potential etiology, yet EV RNA is rarely detected in cerebrospinal fluid (CSF)2. CSF from children with AFM (n = 42) and other pediatric neurologic disease controls (n = 58) were investigated for intrathecal antiviral antibodies, using a phage display library expressing 481,966 overlapping peptides derived from all known vertebrate and arboviruses (VirScan). Metagenomic next-generation sequencing (mNGS) of AFM CSF RNA (n = 20 cases) was also performed, both unbiased sequencing and with targeted enrichment for EVs. Using VirScan, the viral family significantly enriched by the CSF of AFM cases relative to controls was Picornaviridae, with the most enriched Picornaviridae peptides belonging to the genus Enterovirus (n = 29/42 cases versus 4/58 controls). EV VP1 ELISA confirmed this finding (n = 22/26 cases versus 7/50 controls). mNGS did not detect additional EV RNA. Despite rare detection of EV RNA, pan-viral serology frequently identified high levels of CSF EV-specific antibodies in AFM compared with controls, providing further evidence for a causal role of non-polio EVs in AFM

A group memory rehabilitation programme for people with traumatic brain injuries: the ReMemBrIn RCT

Main outcome measures: Outcomes were assessed at 6 and 12 months after randomisation. Primary outcome: patient-completed Everyday Memory Questionnaire – patient version (EMQ-p) at 6 months’ follow-up. Secondary outcomes: Rivermead Behavioural Memory Test – third edition (RBMT-3), General Health Questionnaire 30-item version, European Brain Injury Questionnaire, Everyday Memory Questionnaire – relative version and individual goal attainment. Costs (based on a UK NHS and Personal Social Services perspective) were collected using a service use questionnaire, with the EuroQol-5 Dimensions, five-level version, used to derive quality-adjusted life-years (QALYs). A Markov model was developed to explore cost-effectiveness at 5 and 10 years, with a 3.5% discount applied.Results: We randomised 328 participants (memory rehabilitation, n = 171; usual care, n = 157), with 129 in the memory rehabilitation arm and 122 in the usual-care arm included in the primary analysis. We found no clinically important difference on the EMQ-p between the two arms at 6 months’ follow-up (adjusted difference in mean scores –2.1, 95% confidence interval –6.7 to 2.5; p = 0.37). For secondary outcomes, differences favouring the memory rehabilitation arm were observed at 6 months’ follow-up for the RBMT-3 and goal attainment, but remained only for goal attainment at 12 months’ follow-up. There were no differences between arms in mood or quality of life. The qualitative results suggested positive experiences of participating in the trial and of attending the groups. Participants reported that memory rehabilitation was not routinely accessible in usual care. The primary health economics outcome at 12 months found memoryrehabilitation to be £26.89 cheaper than usual care but less effective, with an incremental QALY loss of 0.007. Differences in costs and effects were not statistically significant and non-parametric bootstrapping demonstrated considerable uncertainty in these findings. No safety concerns were raised and no deaths were reported.Limitations: As a pragmatic trial, we had broad inclusion criteria and, therefore, there was considerable heterogeneity within the sample. The study was not powered to perform further subgroup analyses.Participants and therapists could not be blinded to treatment allocation.Conclusions: The group memory rehabilitation delivered in this trial is very unlikely to lead to clinical benefits or to be a cost-effective treatment for people with TBI in the community. Future studies should examine the selection of participants who may benefit most from memory rehabilitation