A large-scale proteogenomics study of apicomplexan pathogens-Toxoplasma gondii and Neospora caninum

Proteomics data can supplement genome annotation efforts, for example being used to confirm gene models or correct gene annotation errors. Here, we present a large‐scale proteogenomics study of two important apicomplexan pathogens: Toxoplasma gondii and Neospora caninum. We queried proteomics data against a panel of official and alternate gene models generated directly from RNASeq data, using several newly generated and some previously published MS datasets for this meta‐analysis. We identified a total of 201 996 and 39 953 peptide‐spectrum matches for T. gondii and N. caninum, respectively, at a 1% peptide FDR threshold. This equated to the identification of 30 494 distinct peptide sequences and 2921 proteins (matches to official gene models) for T. gondii, and 8911 peptides/1273 proteins for N. caninum following stringent protein‐level thresholding. We have also identified 289 and 140 loci for T. gondii and N. caninum, respectively, which mapped to RNA‐Seq‐derived gene models used in our analysis and apparently absent from the official annotation (release 10 from EuPathDB) of these species. We present several examples in our study where the RNA‐Seq evidence can help in correction of the current gene model and can help in discovery of potential new genes

Transient RUNX1 Expression during Early Mesendodermal Differentiation of hESCs Promotes Epithelial to Mesenchymal Transition through TGFB2 Signaling

The transition of human embryonic stem cells (hESCs) from pluripotency to lineage commitment is not fully understood, and a role for phenotypic transcription factors in the initial stages of hESC differentiation remains to be explored. From a screen of candidate factors, we found that RUNX1 is selectively and transiently upregulated early in hESC differentiation to mesendodermal lineages. Transcriptome profiling and functional analyses upon RUNX1 depletion established a role for RUNX1 in promoting cell motility. In parallel, we discovered a loss of repression for several epithelial genes, indicating that loss of RUNX1 impaired an epithelial to mesenchymal transition during differentiation. Cell biological and biochemical approaches revealed that RUNX1 depletion specifically compromised TGFB2 signaling. Both the decrease in motility and deregulated epithelial marker expression upon RUNX1 depletion were rescued by reintroduction of TGFB2, but not TGFB1. These findings identify roles for RUNX1-TGFB2 signaling in early events of mesendodermal lineage commitment

Using implementation mapping to refine strategies to improve implementation of an evidence-based mobile market intervention: a study protocol

Objectives The Veggie Van model is a mobile market model that is efficacious in increasing fruit and vegetable consumption for lower-income participants. The model is currently being evaluated for its effectiveness in a multi-state trial. Preliminary implementation data, collected through process measures surveys and implementation interviews, indicate that there are several barriers to implementation among partner organizations and implementation fidelity to the Veggie Van model was low. Consideration and planning for implementation ought to occur early and often throughout the research process order to ensure Veggie Van model effectiveness. This paper describes the step-by-step process for creating strategies to enhance implementation of Veggie Van model components. Methods Implementation mapping is a systematic process to develop implementation strategies through engagement with key stakeholders. We conducted a series of interviews (n = 31 representatives) with partner organizations (n = 8) to identify facilitators and barriers to Veggie Van model implementation. We then applied interview findings to an Implementation Mapping process to develop theory and practice-driven strategies to be integrated into existing implementation tools and technical assistance. Results We identified implementation outcomes (e.g., staff implement the Veggie Van model component of nutrition education with fidelity) and performance objectives (e.g., offer nutrition education, in the form of food lessons and/or food demonstrations, at least bi-weekly) to achieve them. We conducted a secondary qualitative analysis of the findings from implementation interviews with partner organizations to identify behavioral determinants (e.g., attitudinal beliefs, social support) which were combined with the performance objectives to generate change objectives (e.g., view the Veggie Van model as advantageous to an organization and communities served). To achieve the change objectives, we developed implementation strategies that would be integrated into existing Veggie Van training resources including an online toolkit, webinars and trainings, an annual mobile market conference, and technical assistance. Conclusion The development of theory and practice-driven implementation strategies will enable us to improve our implementation tools, thereby improving fidelity to the Veggie Van model among organizations and increasing the likelihood of its effectiveness. Detailing the design of a multifaceted implementation strategy using Implementation Mapping also provides a model to design similar strategies for other community-based interventions

Height and timing of growth spurt during puberty in young people living with vertically acquired HIV in Europe and Thailand.

OBJECTIVE: The aim of this study was to describe growth during puberty in young people with vertically acquired HIV. DESIGN: Pooled data from 12 paediatric HIV cohorts in Europe and Thailand. METHODS: One thousand and ninety-four children initiating a nonnucleoside reverse transcriptase inhibitor or boosted protease inhibitor based regimen aged 1-10 years were included. Super Imposition by Translation And Rotation (SITAR) models described growth from age 8 years using three parameters (average height, timing and shape of the growth spurt), dependent on age and height-for-age z-score (HAZ) (WHO references) at antiretroviral therapy (ART) initiation. Multivariate regression explored characteristics associated with these three parameters. RESULTS: At ART initiation, median age and HAZ was 6.4 [interquartile range (IQR): 2.8, 9.0] years and -1.2 (IQR: -2.3 to -0.2), respectively. Median follow-up was 9.1 (IQR: 6.9, 11.4) years. In girls, older age and lower HAZ at ART initiation were independently associated with a growth spurt which occurred 0.41 (95% confidence interval 0.20-0.62) years later in children starting ART age 6 to 10 years compared with 1 to 2 years and 1.50 (1.21-1.78) years later in those starting with HAZ less than -3 compared with HAZ at least -1. Later growth spurts in girls resulted in continued height growth into later adolescence. In boys starting ART with HAZ less than -1, growth spurts were later in children starting ART in the oldest age group, but for HAZ at least -1, there was no association with age. Girls and boys who initiated ART with HAZ at least -1 maintained a similar height to the WHO reference mean. CONCLUSION: Stunting at ART initiation was associated with later growth spurts in girls. Children with HAZ at least -1 at ART initiation grew in height at the level expected in HIV negative children of a comparable age

Using implementation mapping to refine strategies to improve implementation of an evidence-based mobile market intervention: a study protocol

ObjectivesThe Veggie Van model is a mobile market model that is efficacious in increasing fruit and vegetable consumption for lower-income participants. The model is currently being evaluated for its effectiveness in a multi-state trial. Preliminary implementation data, collected through process measures surveys and implementation interviews, indicate that there are several barriers to implementation among partner organizations and implementation fidelity to the Veggie Van model was low. Consideration and planning for implementation ought to occur early and often throughout the research process order to ensure Veggie Van model effectiveness. This paper describes the step-by-step process for creating strategies to enhance implementation of Veggie Van model components.MethodsImplementation mapping is a systematic process to develop implementation strategies through engagement with key stakeholders. We conducted a series of interviews (n = 31 representatives) with partner organizations (n = 8) to identify facilitators and barriers to Veggie Van model implementation. We then applied interview findings to an Implementation Mapping process to develop theory and practice-driven strategies to be integrated into existing implementation tools and technical assistance.ResultsWe identified implementation outcomes (e.g., staff implement the Veggie Van model component of nutrition education with fidelity) and performance objectives (e.g., offer nutrition education, in the form of food lessons and/or food demonstrations, at least bi-weekly) to achieve them. We conducted a secondary qualitative analysis of the findings from implementation interviews with partner organizations to identify behavioral determinants (e.g., attitudinal beliefs, social support) which were combined with the performance objectives to generate change objectives (e.g., view the Veggie Van model as advantageous to an organization and communities served). To achieve the change objectives, we developed implementation strategies that would be integrated into existing Veggie Van training resources including an online toolkit, webinars and trainings, an annual mobile market conference, and technical assistance.ConclusionThe development of theory and practice-driven implementation strategies will enable us to improve our implementation tools, thereby improving fidelity to the Veggie Van model among organizations and increasing the likelihood of its effectiveness. Detailing the design of a multifaceted implementation strategy using Implementation Mapping also provides a model to design similar strategies for other community-based interventions

Reconfiguration, contestation, and decline: conceptualizing mature large technical systems

Large technical systems (LTS) are integral to modern lifestyles but arduous to analyze. In this paper, we advance a conceptualization of LTS using the notion of mature “phases,” drawing from insights into innovation studies, science and technology studies, political science, the sociology of infra- structure, history of technology, and governance. We begin by defining LTS as a unit of analysis and explaining its conceptual utility and novelty, situating it among other prominent sociotechnical theories. Next, we argue that after LTS have moved through the (overlapping) phases proposed by Thomas Hughes of invention, expansion, growth, momentum, and style,mature LTS undergo the additional (overlapping) phases of reconfiguration, contestation (subject to pressures such as drift and crisis), and eventually stagnation and decline. We illustrate these analytical phases with historical case studies and the conceptual literature, and close by suggesting future research to refine and develop the LTS framework, particularly related to more refined typologies, temporal dimensions, and a broadening of system users. We aim to contribute to theoretical debates about the coevolution of LTS as well as empirical discussions about system-related use, socio- technical change, and policy-making

Impact of Zostavax Vaccination on T-Cell Accumulation and Cutaneous Gene Expression in the Skin of Older Humans After Varicella Zoster Virus Antigen-Specific Challenge

Background The live attenuated vaccine Zostavax was developed to prevent varicella zoster virus (VZV) reactivation that causes herpes zoster (shingles) in older humans. However, the impact of vaccination on the cutaneous response to VZV is not known. Methods We investigated the response to intradermal VZV antigen challenge before and after Zostavax vaccination in participants >70 years of age by immunohistological and transcriptomic analyses of skin biopsy specimens collected from the challenge site. Results Vaccination increased the proportion of VZV-specific CD4+ T cells in the blood and promoted the accumulation of both CD4+ and CD8+ T cells in the skin after VZV antigen challenge. However, Zostavax did not alter the proportion of resident memory T cells (CD4+ and CD8+) or CD4+Foxp3+ regulatory T cells in unchallenged skin. After vaccination, there was increased cutaneous T-cell proliferation at the challenge site and also increased recruitment of T cells from the blood, as indicated by an elevated T-cell migratory gene signature. CD8+ T-cell–associated functional genes were also highly induced in the skin after vaccination. Conclusion Zostavax vaccination does not alter the abundance of cutaneous resident memory T cells but instead increases the recruitment of VZV-specific T cells from the blood and enhances T-cell activation, particularly cells of the CD8+ subset, in the skin after VZV antigen challenge

Guideline adherence in febrile children below 3 months visiting European Emergency Departments: an observational multicenter study

Febrile children below 3 months have a higher risk of serious bacterial infections, which often leads to extensive diagnostics and treatment. There is practice variation in management due to differences in guidelines and their usage and adherence. We aimed to assess whether management in febrile children below 3 months attending European Emergency Departments (EDs) was according to the guidelines for fever. This study is part of the MOFICHE study, which is an observational multicenter study including routine data of febrile children (0-18 years) attending twelve EDs in eight European countries. In febrile children below 3 months (excluding bronchiolitis), we analyzed actual management compared to the guidelines for fever. Ten EDs applied the (adapted) NICE guideline, and two EDs applied local guidelines. Management included diagnostic tests, antibiotic treatment, and admission. We included 913 children with a median age of 1.7 months (IQR 1.0-2.3). Management per ED varied as follows: use of diagnostic tests 14-83%, antibiotic treatment 23-54%, admission 34-86%. Adherence to the guideline was 43% (374/868) for blood cultures, 29% (144/491) for lumbar punctures, 55% (270/492) for antibiotic prescriptions, and 67% (573/859) for admission. Full adherence to these four management components occurred in 15% (132/868, range 0-38%), partial adherence occurred in 56% (484/868, range 35-77%). CONCLUSION: There is large practice variation in management. The guideline adherence was limited, but highest for admission which implies a cautious approach. Future studies should focus on guideline revision including new biomarkers in order to optimize management in young febrile children. WHAT IS KNOWN: • Febrile children below 3 months have a higher risk of serious bacterial infections, which often leads to extensive diagnostics and treatment. • There is practice variation in management of young febrile children due to differences in guidelines and their usage and adherence. WHAT IS NEW: • Full guideline adherence is limited, whereas partial guideline adherence is moderate in febrile children below 3 months across Europe. • Guideline revision including new biomarkers is needed to improve management in young febrile children