Comparing genomic and epigenomic features across species using the WashU Comparative Epigenome Browser.

Genome browsers have become an intuitive and critical tool to visualize and analyze genomic features and data. Conventional genome browsers display data/annotations on a single reference genome/assembly; there are also genomic alignment viewer/browsers that help users visualize alignment, mismatch, and rearrangement between syntenic regions. However, there is a growing need for a comparative epigenome browser that can display genomic and epigenomic data sets across different species and enable users to compare them between syntenic regions. Here, we present the WashU Comparative Epigenome Browser. It allows users to load functional genomic data sets/annotations mapped to different genomes and display them over syntenic regions simultaneously. The browser also displays genetic differences between the genomes from single-nucleotide variants (SNVs) to structural variants (SVs) to visualize the association between epigenomic differences and genetic differences. Instead of anchoring all data sets to the reference genome coordinates, it creates independent coordinates of different genome assemblies to faithfully present features and data mapped to different genomes. It uses a simple, intuitive genome-align track to illustrate the syntenic relationship between different species. It extends the widely used WashU Epigenome Browser infrastructure and can be expanded to support multiple species. This new browser function will greatly facilitate comparative genomic/epigenomic research, as well as support the recent growing needs to directly compare and benchmark the T2T CHM13 assembly and other human genome assemblies.

Postpartum care for parent-infant dyads: A community midwifery model.

INTRODUCTION: Postpartum health is in crisis in the United States, with rising pregnancy-related mortality and worsening racial inequities. The World Health Organization recommends four postpartum visits during the 6 weeks after childbirth, yet standard postpartum care in the United States is generally one visit 6 weeks after birth. We present community midwifery postpartum care in the United States as a model concordant with World Health Organization guidelines, describing this model of care and its potential to improve postpartum health for birthing people and babies. METHODS: We conducted semi-structured interviews with 34 community midwives providing care in birth centers and home settings in Oregon and California. A multidisciplinary team analyzed data using reflexive thematic analysis. RESULTS: A total of 24 participants were Certified Professional Midwives; 10 were certified nurse-midwives. A total of 14 midwives identified as people of color. Most spoke multiple languages. We describe six key elements of the community midwifery model of postpartum care: (1) multiple visits, including home visits; typically five to eight over six weeks postpartum; (2) care for the parent-infant dyad; (3) continuity of personalized care; (4) relationship-centered care; (5) planning and preparation for postpartum; and (6) focus on postpartum rest. CONCLUSION: The community midwifery model of postpartum care is a guideline-concordant approach to caring for the parent-infant dyad and may address rising pregnancy-related morbidity and mortality in the United States.

WashU Epigenome Browser update 2022.

WashU Epigenome Browser (https://epigenomegateway.wustl.edu/browser/) is a web-based genomic data exploration tool that provides visualization, integration, and analysis of epigenomic datasets. The newly renovated user interface and functions have enabled researchers to engage with the browser and genomic data more efficiently and effectively since 2018. Here, we introduce a new integrated panel design in the browser that allows users to interact with 1D (genomic features), 2D (such as Hi-C), 3D (genome structure), and 4D (time series) data in a single web page. The browser can display three-dimensional chromatin structures with the 3D viewer module. The 4D tracks, called 'Dynamic' tracks, animatedly display time-series data, allowing for a more striking visual impact to identify the gene or genomic region candidates as a function of time. Genomic data, such as annotation features, numerical values, and chromatin interaction data can all be viewed in the dynamic track mode. Imaging data from microscopy experiments can also be displayed in the browser. In addition to software development, we continue to service and expand the data hubs we host for large consortia including 4DN, Roadmap Epigenomics, TaRGET and ENCODE, among others. Our growing user/developer community developed additional track types as plugins, such as qBed and dynseq tracks, which extend the utility of the browser. The browser serves as a foundation for additional genomics platforms including the WashU Virus Genome Browser (for COVID-19 research) and the Comparative Genome Browser. The WashU Epigenome Browser can also be accessed freely through Amazon Web Services at https://epigenomegateway.org/.

Serological characterization of lineage II insect-specific flaviviruses compared with pathogenic mosquito-borne flaviviruses.

The genus Flavivirus includes pathogenic tick- and mosquito-borne flaviviruses as well as non-pathogenic insect-specific flaviviruses (ISFVs). Phylogenetic analysis based on whole amino acid sequences has indicated that lineage II ISFVs have similarities to pathogenic flaviviruses. In this study, we used reactive analysis with immune serum against Psorophora flavivirus (PSFV) as a lineage IIa ISFV, and Barkeji virus (BJV) as a lineage IIb ISFV, to evaluate the antigenic similarity among lineage IIa and IIb ISFVs, and pathogenic mosquito-borne flaviviruses (MBFVs). Binding and antibody-dependent enhancement assays showed that anti-PSFV sera had broad cross-reactivity with MBFV antigens, while anti-BJV sera had low cross-reactivity. Both of the lineage II ISFV antisera were rarely observed to neutralize MBFVs. These results suggest that lineage IIa ISFV PSFV has more antigenic similarity to MBFVs than lineage IIb ISFV BJV.

Improved detection of flaviviruses in Australian mosquito populations via replicative intermediates.

Mosquito-borne flaviviruses are significant contributors to the arboviral disease burdens both in Australia and globally. While routine arbovirus surveillance remains a vital exercise to identify known flaviviruses in mosquito populations, novel or divergent and emerging species can be missed by these traditional methods. The MAVRIC (monoclonal antibodies to viral RNA intermediates in cells) system is an ELISA-based method for broad-spectrum isolation of positive-sense and double-stranded RNA (dsRNA) viruses based on detection of dsRNA in infected cells. While the MAVRIC ELISA has successfully been used to detect known and novel flaviviruses in Australian mosquitoes, we previously reported that dsRNA could not be detected in dengue virus-infected cells using this method. In this study we identified additional flaviviruses which evade detection of dsRNA by the MAVRIC ELISA. Utilising chimeric flaviviruses we demonstrated that this outcome may be dictated by the non-structural proteins and/or untranslated regions of the flaviviral genome. In addition, we report a modified fixation method that enables improved detection of flavivirus dsRNA and inactivation of non-enveloped viruses from mosquito populations using the MAVRIC system. This study demonstrates the utility of anti-dsRNA monoclonal antibodies for identifying viral replication in insect and vertebrate cell systems and highlights a unique characteristic of flavivirus replication.

Novel monoclonal antibodies against Australian strains of negeviruses and insights into virus structure, replication and host -restriction.

We report the isolation of Australian strains of Bustos virus and Ngewotan virus, two insect-specific viruses in the newly identified taxon Negevirus, originally isolated from Southeast Asian mosquitoes. Consistent with the expected insect-specific tropism of negeviruses, these isolates of Ngewotan and Bustos viruses, alongside the Australian negevirus Castlerea virus, replicated exclusively in mosquito cells but not in vertebrate cells, even when their temperature was reduced to 34 °C. Our data confirmed the existence of two structural proteins, putatively one membrane protein forming the majority of the virus particle, and one glycoprotein forming a projection on the apex of the virions. We generated and characterized 71 monoclonal antibodies to both structural proteins of the two viruses, most of which were neutralizing. Overall, these data increase our knowledge of negevirus mechanisms of infection and replication in vitro.

New genotypes of Liao ning virus (LNV) in Australia exhibit an insect-specific phenotype.

Liao ning virus (LNV) was first isolated in 1996 from mosquitoes in China, and has been shown to replicate in selected mammalian cell lines and to cause lethal haemorrhagic disease in experimentally infected mice. The first detection of LNV in Australia was by deep sequencing of mosquito homogenates. We subsequently isolated LNV from mosquitoes of four genera (Culex, Anopheles, Mansonia and Aedes) in New South Wales, Northern Territory, Queensland and Western Australia; the earliest of these Australian isolates were obtained from mosquitoes collected in 1988, predating the first Chinese isolates. Genetic analysis revealed that the Australian LNV isolates formed two new genotypes: one including isolates from eastern and northern Australia, and the second comprising isolates from the south-western corner of the continent. In contrast to findings reported for the Chinese LNV isolates, the Australian LNV isolates did not replicate in vertebrate cells in vitro or in vivo, or produce signs of disease in wild-type or immunodeficient mice. A panel of human and animal sera collected from regions where the virus was found in high prevalence also showed no evidence of LNV-specific antibodies. Furthermore, high rates of virus detection in progeny reared from infected adult female mosquitoes, coupled with visualization of the virus within the ovarian follicles by immunohistochemistry, suggest that LNV is transmitted transovarially. Thus, despite relatively minor genomic differences between Chinese and Australian LNV strains, the latter display a characteristic insect-specific phenotype.

Calcipotriene 0.005%--betamethasone dipropionate 0.064% ointment versus topical suspension in the treatment of plaque psoriasis: a randomized pilot study of patient preference.

Vehicle formulation plays a major role in patient adherence to topical psoriasis treatments. The objective of this study was to conduct a preliminary assessment of patient preference for ointment versus topical suspension formulations of calcipotriene 0.005%-betamethasone dipropionate 0.064% for treatment of plaque psoriasis. In our small cohort of 20 participants with mild to moderate plaque psoriasis, the topical suspension formulation was preferred over the ointment, though the difference was not statistically significant (P=.32). Overall, the topical suspension was rated as moderately appealing, while the ointment was rated as slightly appealing (P=.06). Subgroup analyses were limited due to the small sample size. The results of this study may provide clinicians with an alternative topical treatment of plaque psoriasis that provides the benefits of a combination product. In clinical practice, it may be best to offer patients both formulations and they can choose the product that is right for them.

Integrating Mental Health In Perinatal Care: Perspectives Of Interprofessional Clinicians.

Despite the prevalence of perinatal mental health issues in the United States, gaps in care persist. To address this, perinatal health care settings are asked to focus on patients' mental health by administering standardized screening and, increasingly, by integrating mental health teams in their clinics. Using in-depth interviews and ethnographic observations, I investigated these emerging practices, exploring the experiences of certified nurse-midwives, obstetricians, and mental health clinicians. I found that certified nurse-midwives and obstetricians lack time, resources, and expertise, restricting their ability to address patients' mental health. Integrated mental health clinicians are constrained by the stratified organization of health care and structural deprioritization of mental health. Redesigning perinatal health care and de-siloing mental health training are necessary to increase clinicians' effectiveness and to improve perinatal health outcomes.

Adherence to a five day treatment course of topical fluocinonide 0.1% cream in atopic dermatitis.

BACKGROUND: Adherence in the treatment of chronic inflammatory skin diseases such as atopic dermatitis is poor. Methods to improve adherence have proven difficult. PURPOSE: To determine whether a short course of treatment with a high-potency corticosteroid will improve adherence compared to longer treatment studies and if improvement in disease and itch continues after treatment. METHODS: 10 patients with mild to moderate atopic dermatitis were instructed to apply fluocinonide 0.1% cream twice daily for 5 days. Adherence was self-reported and electronically monitored. Treatment outcomes were assessed in terms of Visual Analog Scale of Itch (VAS), Eczema Area and Severity Index (EASI), and Investigator Global Assessment (IGA) scores. RESULTS: The median adherence rate was 40% (range of 0-100). The median percent change in VAS from baseline measures on days 7 and 14 were 90% (range -13, 100, p=0.02) and 52% (range 0, 100, p=0.004). On days 7 and 14, 20% and 70% patients achieved an EASI-75 and 40% and 60% an IGA of 0 or 1. LIMITATIONS: Small sample size limited subgroup analyses. CONCLUSIONS: Adherence rates with short-term treatment were similar to previously reported rates in longer term treatment studies. However, even non-adherent patients had significant improvement in itch and disease severity.

Modbed track: Visualization of modified bases in single-molecule sequencing.

Recent advances in long-read sequencing technologies have not only dramatically increased sequencing read length but also have improved the accuracy of detecting chemical modifications to the canonical nucleotide bases, thus opening exciting venues to investigate the epigenome. Currently, the ability to visualize modified bases from long-read sequencing data in genome browsers is still limited, preventing users from easily and fully exploring these type of data. To address this limitation, the WashU Epigenome Browser introduces the modbed track type, which provides visualization of modification details in each single read as well as aggregated modifications of individual or multiple molecules across a dynamic range of resolutions. The modbed file can be uploaded for visualization as a local track or viewed with an accessible URL freely on the WashU Epigenome Browser at https://epigenomegateway.wustl.edu/.

A chimeric vaccine protects farmed saltwater crocodiles from West Nile virus-induced skin lesions.

West Nile virus (WNV) causes skin lesions in farmed crocodiles leading to the depreciation of the value of their hides and significant economic losses. However, there is no commercially available vaccine designed for use in crocodilians against WNV. We tested chimeric virus vaccines composed of the non-structural genes of the insect-specific flavivirus Binjari virus (BinJV) and genes encoding the structural proteins of WNV. The BinJV/WNV chimera, is antigenically similar to wild-type WNV but replication-defective in vertebrates. Intramuscular injection of two doses of BinJV/WNV in hatchling saltwater crocodiles (Crocodylus porosus) elicited a robust neutralising antibody response and conferred protection against viremia and skin lesions after challenge with WNV. In contrast, mock-vaccinated crocodiles became viraemic and 22.2% exhibited WNV-induced lesions. This suggests that the BinJV/WNV chimera is a safe and efficacious vaccine for preventing WNV-induced skin lesions in farmed crocodilians.

Uropathogenic Escherichia coli infection-induced epithelial trained immunity impacts urinary tract disease outcome.

Previous urinary tract infections (UTIs) can predispose one to future infections; however, the underlying mechanisms affecting recurrence are poorly understood. We previously found that UTIs in mice cause differential bladder epithelial (urothelial) remodelling, depending on disease outcome, that impacts susceptibility to recurrent UTI. Here we compared urothelial stem cell (USC) lines isolated from mice with a history of either resolved or chronic uropathogenic Escherichia coli (UPEC) infection, elucidating evidence of molecular imprinting that involved epigenetic changes, including differences in chromatin accessibility, DNA methylation and histone modification. Epigenetic marks in USCs from chronically infected mice enhanced caspase-1-mediated cell death upon UPEC infection, promoting bacterial clearance. Increased Ptgs2os2 expression also occurred, potentially contributing to sustained cyclooxygenase-2 expression, bladder inflammation and mucosal wounding-responses associated with severe recurrent cystitis. Thus, UPEC infection acts as an epi-mutagen reprogramming the urothelial epigenome, leading to urothelial-intrinsic remodelling and training of the innate response to subsequent infection.

A multi-institutional pediatric dataset of clinical radiology MRIs by the Children's Brain Tumor Network.

Pediatric brain and spinal cancers remain the leading cause of cancer-related death in children. Advancements in clinical decision-support in pediatric neuro-oncology utilizing the wealth of radiology imaging data collected through standard care, however, has significantly lagged other domains. Such data is ripe for use with predictive analytics such as artificial intelligence (AI) methods, which require large datasets. To address this unmet need, we provide a multi-institutional, large-scale pediatric dataset of 23,101 multi-parametric MRI exams acquired through routine care for 1,526 brain tumor patients, as part of the Children's Brain Tumor Network. This includes longitudinal MRIs across various cancer diagnoses, with associated patient-level clinical information, digital pathology slides, as well as tissue genotype and omics data. To facilitate downstream analysis, treatment-naïve images for 370 subjects were processed and released through the NCI Childhood Cancer Data Initiative via the Cancer Data Service. Through ongoing efforts to continuously build these imaging repositories, our aim is to accelerate discovery and translational AI models with real-world data, to ultimately empower precision medicine for children.

Empathy Measurement in Autistic and Nonautistic Adults: A COSMIN Systematic Literature Review.

Empathy is essential for social functioning and is relevant to a host of clinical conditions. This COSMIN review evaluated the empirical support for empathy self-report measures used with autistic and nonautistic adults. Given autism is characterized by social differences, it is the subject of a substantial proportion of empathy research. Therefore, this review uses autism as a lens through which to scrutinize the psychometric quality of empathy measures. Of the 19 measures identified, five demonstrated "High-Quality" evidence for "Insufficient" properties and cannot be recommended. The remaining 14 had noteworthy gaps in evidence and require further evaluation before use with either group. Without tests of measurement invariance or differential item functioning, the extent to which observed group differences represent actual trait differences remains unknown. Using autism as a test case highlights an alarming tendency for empathy measures to be used to characterize, and potentially malign vulnerable populations before sufficient validation.

Evidence of Infection with Zoonotic Mosquito-Borne Flaviviruses in Saltwater Crocodiles (Crocodylus porosus) in Northern Australia.

The risk of flavivirus infections among the crocodilian species was not recognised until West Nile virus (WNV) was introduced into the Americas. The first outbreaks caused death and substantial economic losses in the alligator farming industry. Several other WNV disease episodes have been reported in crocodilians in other parts of the world, including Australia and Africa. Considering that WNV shares vectors with other flaviviruses, crocodilians are highly likely to also be exposed to flaviviruses other than WNV. A serological survey for flaviviral infections was conducted on saltwater crocodiles (Crocodylus porosus) at farms in the Northern Territory, Australia. Five hundred serum samples, collected from three crocodile farms, were screened using a pan-flavivirus-specific blocking ELISA. The screening revealed that 26% (n = 130/500) of the animals had antibodies to flaviviruses. Of these, 31.5% had neutralising antibodies to WNVKUN (Kunjin strain), while 1.5% had neutralising antibodies to another important flavivirus pathogen, Murray Valley encephalitis virus (MVEV). Of the other flaviviruses tested for, Fitzroy River virus (FRV) was the most frequent (58.5%) in which virus neutralising antibodies were detected. Our data indicate that farmed crocodiles in the Northern Territory are exposed to a range of potentially zoonotic flaviviruses, in addition to WNVKUN. While these flaviviruses do not cause any known diseases in crocodiles, there is a need to investigate whether infected saltwater crocodiles can develop a viremia to sustain the transmission cycle or farmed crocodilians can be used as sentinels to monitor the dynamics of arboviral infections in tropical areas.

The Chimeric Binjari-Zika Vaccine Provides Long-Term Protection against ZIKA Virus Challenge.

We recently developed a chimeric flavivirus vaccine technology based on the novel insect-specific Binjari virus (BinJV) and used this to generate a chimeric ZIKV vaccine (BinJ/ZIKA-prME) that protected IFNAR-/- dams and fetuses from infection. Herein, we show that a single vaccination of IFNAR-/- mice with unadjuvanted BinJ/ZIKA-prME generated neutralizing antibody responses that were retained for 14 months. At 15 months post vaccination, mice were also completely protected against detectable viremia and substantial body weight loss after challenge with ZIKVPRVABC59. BinJ/ZIKA-prME vaccination thus provided long-term protective immunity without the need for adjuvant or replication of the vaccine in the vaccine recipient, both attractive features for a ZIKV vaccine.

Examining Experiences of Poor Sleep During Pregnancy: A Qualitative Study to Inform the Development of a Prenatal Sleep Intervention.

Background: Poor sleep is common during pregnancy and is associated with increased risk of negative health outcomes. Research indicates that physical discomfort and having an active mind are primary factors for prenatal sleep disturbances. Mindfulness-based interventions have the potential for addressing these factors, but have yet to be optimized for this purpose in this population. Objective: The objective of this study was to gather input from pregnant and postpartum individuals about the value of a mindfulness-based program for improving prenatal sleep and their preferred content and delivery format. Methods: We conducted 2 focus groups with 12 pregnant people experiencing poor sleep quality and 3 individual interviews with postpartum people. Interviews were thematically analyzed. Results: The majority of participants expressed strong interest in a mindfulness program for improving prenatal sleep. Participants reported that pregnancy-specific physical discomfort and worry (both general and pregnancy-specific) affected their sleep. Participants wanted sleep education, and strategies for calming the mind, reducing physical discomfort, reducing impact of bedtime partners on sleep, and tips for improving sleep schedule and quality. Participants recognized the convenience of an online intervention and the social benefits of an in-person intervention and favored a hybrid delivery model. Conclusion: Addressing prenatal sleep problems is an unmet need. Given the challenges and discomfort women face during pregnancy, and the importance of adequate sleep for promoting mental and physical health during pregnancy, sleep difficulties are critical to address. A mindfulness-based intervention for improving prenatal sleep was deemed of high interest to this perinatal population.

A genome-wide CRISPR-Cas9 knockout screen identifies essential and growth-restricting genes in human trophoblast stem cells.

The recent derivation of human trophoblast stem cells (hTSCs) provides a scalable in vitro model system of human placental development, but the molecular regulators of hTSC identity have not been systematically explored thus far. Here, we utilize a genome-wide CRISPR-Cas9 knockout screen to comprehensively identify essential and growth-restricting genes in hTSCs. By cross-referencing our data to those from similar genetic screens performed in other cell types, as well as gene expression data from early human embryos, we define hTSC-specific and -enriched regulators. These include both well-established and previously uncharacterized trophoblast regulators, such as ARID3A, GATA2, and TEAD1 (essential), and GCM1, PTPN14, and TET2 (growth-restricting). Integrated analysis of chromatin accessibility, gene expression, and genome-wide location data reveals that the transcription factor TEAD1 regulates the expression of many trophoblast regulators in hTSCs. In the absence of TEAD1, hTSCs fail to complete faithful differentiation into extravillous trophoblast (EVT) cells and instead show a bias towards syncytiotrophoblast (STB) differentiation, thus indicating that this transcription factor safeguards the bipotent lineage potential of hTSCs. Overall, our study provides a valuable resource for dissecting the molecular regulation of human placental development and diseases.