The impact of inversions across 33,924 families with rare disease from a national genome sequencing project.

Detection of structural variants (SVs) is currently biased toward those that alter copy number. The relative contribution of inversions toward genetic disease is unclear. In this study, we analyzed genome sequencing data for 33,924 families with rare disease from the 100,000 Genomes Project. From a database hosting >500 million SVs, we focused on 351 genes where haploinsufficiency is a confirmed disease mechanism and identified 47 ultra-rare rearrangements that included an inversion (24 bp to 36.4 Mb, 20/47 de novo). Validation utilized a number of orthogonal approaches, including retrospective exome analysis. RNA-seq data supported the respective diagnoses for six participants. Phenotypic blending was apparent in four probands. Diagnostic odysseys were a common theme (>50 years for one individual), and targeted analysis for the specific gene had already been performed for 30% of these individuals but with no findings. We provide formal confirmation of a European founder origin for an intragenic MSH2 inversion. For two individuals with complex SVs involving the MECP2 mutational hotspot, ambiguous SV structures were resolved using long-read sequencing, influencing clinical interpretation. A de novo inversion of HOXD11-13 was uncovered in a family with Kantaputra-type mesomelic dysplasia. Lastly, a complex translocation disrupting APC and involving nine rearranged segments confirmed a clinical diagnosis for three family members and resolved a conundrum for a sibling with a single polyp. Overall, inversions play a small but notable role in rare disease, likely explaining the etiology in around 1/750 families across heterogeneous clinical cohorts.

Impacts of fire and prospects for recovery in a tropical peat forest ecosystem.

Uncontrolled fires place considerable burdens on forest ecosystems, compromising our ability to meet conservation and restoration goals. A poor understanding of the impacts of fire on ecosystems and their biodiversity exacerbates this challenge, particularly in tropical regions where few studies have applied consistent analytical techniques to examine a broad range of ecological impacts over multiyear time frames. We compiled 16 y of data on ecosystem properties (17 variables) and biodiversity (21 variables) from a tropical peatland in Indonesia to assess fire impacts and infer the potential for recovery. Burned forest experienced altered structural and microclimatic conditions, resulting in a proliferation of nonforest vegetation and erosion of forest ecosystem properties and biodiversity. Compared to unburned forest, habitat structure, tree density, and canopy cover deteriorated by 58 to 98%, while declines in species diversity and abundance were most pronounced for trees, damselflies, and butterflies, particularly for forest specialist species. Tracking ecosystem property and biodiversity datasets over time revealed most to be sensitive to recurrent high-intensity fires within the wider landscape. These megafires immediately compromised water quality and tree reproductive phenology, crashing commercially valuable fish populations within 3 mo and driving a gradual decline in threatened vertebrates over 9 mo. Burned forest remained structurally compromised long after a burn event, but vegetation showed some signs of recovery over a 12-y period. Our findings demonstrate that, if left uncontrolled, fire may be a pervasive threat to the ecological functioning of tropical forests, underscoring the importance of fire prevention and long-term restoration efforts, as exemplified in Indonesia.

TET3 is a positive regulator of mitochondrial respiration in Neuro2A cells.

Ten-Eleven-Translocase (TET) enzymes contribute to the regulation of the methylome via successive oxidation of 5-methyl cytosine (5mC) to derivatives which can be actively removed by base-excision-repair (BER) mechanisms in the absence of cell division. This is particularly important in post-mitotic neurons where changes in DNA methylation are known to associate with changes in neural function. TET3, specifically, is a critical regulator of both neuronal differentiation in development and mediates dynamic changes in the methylome of adult neurons associated with cognitive function. While DNA methylation is understood to regulate transcription, little is known of the specific targets of TET3-dependent catalytic activity in neurons. We report the results of an unbiased transcriptome analysis of the neuroblastoma-derived cell line; Neuro2A, in which Tet3 was silenced. Oxidative phosphorylation (OxPhos) was identified as the most significantly down-regulated functional canonical pathway, and these findings were confirmed by measurements of oxygen consumption rate in the Seahorse bioenergetics analyser. The mRNA levels of both nuclear- and mitochondrial-encoded OxPhos genes were reduced by Tet3-silencing, but we found no evidence for differential (hydroxy)methylation deposition at these gene loci. However, the mRNA expression of genes known to be involved in mitochondrial quality control were also shown to be significantly downregulated in the absence of TET3. One of these genes; EndoG, was identified as a direct target of TET3-catalytic activity at non-CpG methylated sites within its gene body. Accordingly, we propose that aberrant mitochondrial homeostasis may contribute to the decrease in OxPhos, observed upon Tet3-downregulation in Neuro2A cells.

Implementing supportive supervision in acute humanitarian emergencies: Lessons learned from Afghanistan and Ukraine.

Mental Health and Psychosocial Support (MHPSS) practitioners working in humanitarian contexts are at significant risk of mental health conditions, ultimately hindering the quality and sustainability of their work. Supportive supervision has shown to be effective in improving the wellbeing of MHPSS staff and volunteers and enhancing the effectiveness of MHPSS service delivery. Despite these proven benefits, there is a lack of standardised guidelines to inform supportive supervision within humanitarian contexts. To address this gap, the Trinity Centre for Global Health and the International Federation of the Red Cross Red Crescent Societies' Reference Centre for Psychocosial Support co-developed the 'Integrated Model for Supervision' (IMS) Handbook and supporting tools and led IMS trainings with four humanitarian organisations in Ukraine, Afghanistan, Jordan, and Nigeria from June-August 2021. The subsequent acute humanitarian emergencies that occurred in Afghanistan and Ukraine provided the opportunity to (i) examine the implementation of the IMS in the acute stages of two humanitarian crises and (ii) identify the challenges and lessons learned from this process. This study employed a case study design using semi-structured qualitative interviews with five MHPSS personnel (female: 4; male: 1) who had received training in the IMS and were directly involved in the implementation of supportive supervision using IMS guidelines in either Ukraine or Afghanistan. Results showed that participants identified the key steps needed for the implementation of supportive supervision and reported two significant barriers to implementation including the stress of a humanitarian crisis leading to competing responsibilities and priorities, staff shortages and time constraints as well as the challenge of creating a new supervision structure when none had existed previously. Overall, participants felt that the IMS resulted in improved knowledge, confidence, perceived support, team cohesion, staff wellbeing and was a helpful blueprint to guide the implementation of supportive supervision in humanitarian contexts.

Mapping the Postpartum Experience Through Obstetric Patient Navigation for Low-Income Individuals.

Background: Although the postpartum period is an opportunity to address long-term health, fragmented care systems, inadequate attention to social needs, and a lack of structured transition to primary care threaten patient wellbeing, particularly for low-income individuals. Postpartum patient navigation is an emerging innovation to address these disparities. Methods: This mixed-methods analysis uses data from the first year of an ongoing randomized controlled trial to understand the needs of low-income postpartum individuals through 1 year of patient navigation. We designed standardized logs for navigators to record their services, tracking mode, content, intensity, and target of interactions. Navigators also completed semistructured interviews every 3 months regarding relationships with patients and care teams, care system gaps, and navigation process. Log data were categorized, quantified, and mapped temporally through 1 year postpartum. Qualitative data were analyzed using the constant comparative method. Results: Log data from 50 participants who received navigation revealed the most frequent needs related to health care access (45.4%), health and wellness (18.2%), patient-navigator relationship building (14.8%), parenting (13.6%), and social determinants of health (8.0%). Navigation activities included supporting physical and mental recovery, accomplishing health goals, connecting patients to primary and specialty care, preparing for health system utilization beyond navigation, and referring individuals to community resources. Participant needs fluctuated, yielding a dynamic timeline of the first postpartum year. Conclusion: Postpartum needs evolved throughout the year, requiring support from various teams. Navigation beyond the typical postpartum care window may be useful in mitigating health system barriers, and tracking patient needs may be useful in optimizing postpartum care. Clinical Trial Registration: Registered April 19, 2019, enrollment beginning January 21, 2020, NCT03922334, https://clinicaltrials.gov/ct2/show/NCT03922334.

Evaluating feedback from an implementation advisory board to assess the rollout of a postpartum patient navigation program.

BACKGROUND: Patient navigation is an individualized intervention to facilitate comprehensive care which has not yet been fully implemented in obstetric or postpartum care. METHODS: We aimed to develop and evaluate a mechanism to incorporate feedback regarding implementation of postpartum patient navigation for low-income birthing individuals at an urban academic medical center. This study analyzed the role of an Implementation Advisory Board (IAB) in supporting an ongoing randomized trial of postpartum navigation. Over the first 24 months of the trial, the IAB included 11 rotating obstetricians, one clinic resource coordinator, one administrative leader, two obstetric nurses, one primary care physician, one social worker, and one medical assistant. Members completed serial surveys regarding program implementation, effects on patient care, and areas for improvement. Quarterly IAB meetings offered opportunities for additional feedback. Survey responses and meeting notes were analyzed using the constant comparative method and further interpreted within the Exploration, Preparation, Implementation, Sustainment (EPIS) Framework. RESULTS: Members of the IAB returned 37 surveys and participated in five meetings over 24 months. Survey analysis revealed four themes among the inner context: reduced clinician burden, connection of care teams, communication strategies, and clinic workflow. Bridging factors included improved patient access to care, improved follow-up, and adding social context to care. Innovation factors included availability of navigators, importance of consistent communication, and adaptation over time. Meeting notes highlighted the importance of bidirectional feedback regarding implementation, and members expressed positive opinions regarding navigators' effects on patient care, integration into clinic workflow, and responsiveness to feedback. IAB members initially suggested changes to improve implementation; later survey responses demonstrated successful program adaptations. CONCLUSIONS: Members of an implementation advisory board provided key insights into the implementation of postpartum patient navigation that may be useful to promote dissemination of navigation and establish avenues for the engagement of implementing partners in other innovations. TRIAL REGISTRATION: ClinicalTrials.gov, NCT03922334 . Registered April 19, 2019. The results here do not present the results of the primary trial, which is ongoing.

Elevated Inflammation Associated with Markers of Neutrophil Function and Gastrointestinal Disruption in Pilot Study of Plasmodium fragile Co-Infection of ART-Treated SIVmac239+ Rhesus Macaques.

Human immunodeficiency virus (HIV) and malaria, caused by infection with Plasmodium spp., are endemic in similar geographical locations. As a result, there is high potential for HIV/Plasmodium co-infection, which increases the pathology of both diseases. However, the immunological mechanisms underlying the exacerbated disease pathology observed in co-infected individuals are poorly understood. Moreover, there is limited data available on the impact of Plasmodium co-infection on antiretroviral (ART)-treated HIV infection. Here, we used the rhesus macaque (RM) model to conduct a pilot study to establish a model of Plasmodium fragile co-infection during ART-treated simian immunodeficiency virus (SIV) infection, and to begin to characterize the immunopathogenic effect of co-infection in the context of ART. We observed that P. fragile co-infection resulted in parasitemia and anemia, as well as persistently detectable viral loads (VLs) and decreased absolute CD4+ T-cell counts despite daily ART treatment. Notably, P. fragile co-infection was associated with increased levels of inflammatory cytokines, including monocyte chemoattractant protein 1 (MCP-1). P. fragile co-infection was also associated with increased levels of neutrophil elastase, a plasma marker of neutrophil extracellular trap (NET) formation, but significant decreases in markers of neutrophil degranulation, potentially indicating a shift in the neutrophil functionality during co-infection. Finally, we characterized the levels of plasma markers of gastrointestinal (GI) barrier permeability and microbial translocation and observed significant correlations between indicators of GI dysfunction, clinical markers of SIV and Plasmodium infection, and neutrophil frequency and function. Taken together, these pilot data verify the utility of using the RM model to examine ART-treated SIV/P. fragile co-infection, and indicate that neutrophil-driven inflammation and GI dysfunction may underlie heightened SIV/P. fragile co-infection pathogenesis.