Accurate, scalable cohort variant calls using DeepVariant and GLnexus.

MOTIVATION: Population-scale sequenced cohorts are foundational resources for genetic analyses, but processing raw reads into analysis-ready cohort-level variants remains challenging. RESULTS: We introduce an open-source cohort-calling method that uses the highly accurate caller DeepVariant and scalable merging tool GLnexus. Using callset quality metrics based on variant recall and precision in benchmark samples and Mendelian consistency in father-mother-child trios, we optimize the method across a range of cohort sizes, sequencing methods and sequencing depths. The resulting callsets show consistent quality improvements over those generated using existing best practices with reduced cost. We further evaluate our pipeline in the deeply sequenced 1000 Genomes Project (1KGP) samples and show superior callset quality metrics and imputation reference panel performance compared to an independently generated GATK Best Practices pipeline. AVAILABILITY AND IMPLEMENTATION: We publicly release the 1KGP individual-level variant calls and cohort callset (https://console.cloud.google.com/storage/browser/brain-genomics-public/research/cohort/1KGP) to foster additional development and evaluation of cohort merging methods as well as broad studies of genetic variation. Both DeepVariant (https://github.com/google/deepvariant) and GLnexus (https://github.com/dnanexus-rnd/GLnexus) are open-source, and the optimized GLnexus setup discovered in this study is also integrated into GLnexus public releases v1.2.2 and later. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Uncovering the Overlap of Global and Domestic Rural Surgery for Medical Trainees.

INTRODUCTION: Medical trainees who participate in global rotations demonstrate improved cultural sensitivity, increased involvement in humanitarian efforts, and ability to adapt to limited resources. The global coronavirus pandemic halted global rotations for medical trainees. Domestic rural surgery (DRS) may offer a unique alternative. We aimed to understand medical students' perceptions of the similarities and differences between global surgery and DRS and how students' priorities impact career choices. METHODS: An electronic survey was administered at eleven medical training institutions in Indiana, Illinois, and Michigan in spring 2021. Mixed methods analysis was performed for students who reported an interest in global surgery. Quantitative analysis was completed using Stata 16.1. RESULTS: Of the 697 medical student respondents, 202 were interested in global surgery. Of those, only 18.3% were also interested in DRS. Students interested in DRS had more rural exposures. Rural exposures associated with DRS interest were pre-clinical courses (P = 0.002), clinical rotations (P = 0.045), and rural health interest groups (P < 0.001). Students interested in DRS and those unsure were less likely to prioritize careers involving teaching or research, program prestige, perceived career advancement, and well-equipped facilities. The students who were unsure were willing to utilize DRS exposures. CONCLUSIONS: Students interested in global surgery express a desire to practice in low-resource settings. Increased DRS exposures may help students to understand the overlap between global surgery and DRS when it comes to working with limited resources, achieving work-life balance and practice location.

Paracentral Acute Middle Maculopathy in Pregnancy.

ABSTRACT: A 31-year-old previously healthy, pregnant woman presented with acute, unilateral, painless paracentral vision loss in the left eye. The results of neuroimaging studies were normal. Hypercoagulable workup was negative, and fundus examination showed no retinal emboli and no retinal vascular abnormalities. The patient had well-controlled blood pressure and did not have eclampsia/preeclampsia. Although a presumptive referral diagnosis of "optic neuritis" was made, optical coherence tomography (OCT) of the macula showed a hyperreflective band involving the inner nuclear layer, consistent with paracentral acute middle maculopathy (PAMM). Furthermore, OCT angiography (OCT-A) showed flow attenuation of the outer retinal capillary plexus, further supporting a diagnosis of PAMM in pregnancy. Clinicians should be aware of the benefit of OCT-A as a complement to macular OCT in the evaluation of acute monocular vision loss mimicking retrobulbar optic neuropathy, particularly when signs and findings of other retinal vasculopathy are absent. PAMM should be considered in pregnant patients with acute visual changes.

Gender Differences in Insurance, Surgical Admissions and Outcomes at a Kenyan Referral Hospital.

INTRODUCTION: Gender is an important factor in determining access to healthcare resources. Women face additional barriers, especially in low- and middle-income countries. Surgical costs can be devastating, which can exacerbate engendered disparities. Kenya's National Hospital Insurance Fund (NHIF) aims to achieve universal coverage and protect beneficiaries from catastrophic health expenditures. We examine gender differences in NHIF coverage, health-seeking behavior, and surgical outcomes at a tertiary care hospital in Eldoret, Kenya. MATERIALS AND METHODS: All patients ≥13 years admitted to the general surgery service at Moi Teaching and Referral Hospital from January 2018-July 2018 were enrolled. Health records were retrospectively reviewed for demographic data, clinical parameters, NHIF enrollment, and cost information. Descriptive analyses utilized Wilcoxon Rank Sum, Pearson's Chi-square, and Fisher's Exact tests. RESULTS: 366 patients were included for analysis. 48.6% were enrolled in NHIF with significant female predominance (64.8% versus 37.9%, P < 0.0001). Despite differing coverage rates, male and female patients underwent surgery and suffered in-hospital mortality at similar rates. However, women only comprised 39.6% of admissions and were significantly more likely to delay care (median 60 versus 7 days, P < 0.0001), be diagnosed with cancer (26.6% versus 13.2%, P = 0.0024), and require a palliative procedure for cancer (44.1% versus 13.0%, P = 0.013). CONCLUSION: Many financial and cultural barriers exist in Kenya that prevent women from accessing healthcare as readily as men, persisting despite higher rates of NHIF coverage amongst female patients. Investigation into extra-hospital costs and social disempowerment for women may elucidate key needs for achieving health equity.

The role of community health workers in the surgical cascade: a scoping review.

BACKGROUND: Community health workers (CHWs) can increase access to various primary healthcare services; however, their potential for improving surgical care is under-explored. We sought to assess the role of CHWs in the surgical cascade, defined as disease screening, linkage to operative care, and post-operative care. Given the well-described literature on CHWs and screening, we focused on the latter two steps of the surgical cascade. METHODS: We conducted a scoping review of the peer-reviewed literature. We searched for studies published in any language from January 1, 2000 to May 1, 2020 using electronic literature databases including Pubmed/MEDLINE, Web of Science, SCOPUS, and Google Scholar. We included articles on CHW involvement in linkage to operative care and/or post-operative surgical care. Narrative and descriptive methods were used to analyze the data. RESULTS: The initial search identified 145 articles relevant to steps in the surgical cascade. Ten studies met our inclusion criteria and were included for review. In linkage to care, CHWs helped increase surgical enrollment, provide resources for vulnerable patients, and build trust in healthcare services. Post-operatively, CHWs acted as effective monitors for surgical-site infections and provided socially isolated patients with support and linkage to additional services. The complex and wide-ranging needs of surgical patients illustrated the need to view surgical care as a continuum rather than a singular operative event. CONCLUSION: While the current literature is limited, CHWs were able to maneuver complex medical, cultural, and social barriers to surgical care by linking patients to counseling, education, and community resources, as well as post-operative infection prevention services. Future studies would benefit from more rigorous study designs and larger sample sizes to further elucidate the role CHWs can serve in the surgical cascade.

Paracentral Acute Middle Maculopathy Mimicking Retrobulbar Optic Neuropathy.

ABSTRACT: A 70-year-old woman presented with acute awareness of decreased color vision in her right eye. Fundus examination and a flash electroretinography (ERG) were both normal. A multifocal ERG (mfERG) however revealed foveal depression, and thinning of inner nuclear layer was noted on macular optical coherence tomography (OCT), and a diagnosis of resolved paracentral acute middle maculopathy was made. Clinicians should be aware of the complementary role of OCT and mfERG in unexplained acute central visual loss to distinguish retinal from neuro-ophthalmic etiologies. Structural ocular imaging with OCT shows features of inner, middle, and outer retinal localizations to the visual loss.

Arteritic Orbital Ischemia Producing Afferent and Efferent Pupillary Defects.

A 67-year-old woman presented with acute loss of vision to no light perception (NLP), a right afferent pupillary defect, and anisocoria with a nonreactive and dilated pupil in the right eye. Fundus examination showed pallid optic disc edema and a central retinal artery occlusion (CRAO) in the right eye. A temporal artery biopsy showed giant cell arteritis (GCA). Orbital involvement in GCA has been reported previously. However the combination of an afferent and efferent pupillary defect, NLP vision, pallid disc edema, and a CRAO in an elderly patient is likely a unique clinical combination that should strongly suggest GCA. Clinicians should be aware of the myriad presentations of GCA, including orbital ischemia.

Transient vision loss after optic nerve sheath fenestration.

Optic nerve sheath fenestration (ONSF) is a well-known, relatively safe, and effective surgical treatment for visual loss related to papilledema. Visual loss following ONSF is uncommon but can occur from direct surgical trauma, ischemic optic neuropathy, orbital or intrasheath hemorrhage, or arterial occlusion. Transient severe (e.g., light perception (LP) or no light perception (NLP) visual loss) after ONSF is uncommon but has been reported. We describe a case of LP vision following uncomplicated ONSF with orbital imaging demonstrating significant postoperative inflammation and slow recovery after intravenous steroid treatment. We discuss the various mechanisms for this phenomenon after ONSF. To our knowledge, this is the first clinico-radiologic description with follow up and recovery of this postoperative complication of ONSF to be reported in the English language ophthalmic literature.

Modulation of postprandial lipaemia by a single meal containing a commonly consumed interesterified palmitic acid-rich fat blend compared to a non-interesterified equivalent.

PURPOSE: Interesterification of palm stearin and palm kernal (PSt/PK) is widely used by the food industry to create fats with desirable functional characteristics for applications in spreads and bakery products, negating the need for trans fatty acids. Previous studies have reported reduced postprandial lipaemia, an independent risk factor for CVD, following interesterified (IE) palmitic and stearic acid-rich fats that are not currently widely used by the food industry. The current study investigates the effect of the most commonly consumed PSt/PK IE blend on postprandial lipaemia. METHODS: A randomised, controlled, crossover (1 week washout) double-blind design study (n = 12 healthy males, 18-45 years), compared the postprandial (0-4 h) effects of meals containing 50 g fat [PSt/PK (80:20); IE vs. non-IE] on changes in plasma triacylglycerol (TAG), glucose, glucose-dependent insulinotropic polypeptide (GIP), peptide YY (PYY), insulin, gastric emptying (paracetamol concentrations) and satiety (visual analogue scales). RESULTS: The postprandial increase in plasma TAG was higher following the IE PSt/PK versus the non-IE PSt/PK, with a 51 % greater incremental area under the curve [mean difference with 95 % CI 41 (23, 58) mmol/L min P = 0.001]. The pattern of lipaemia was different between meals; at 4-h plasma TAG concentrations declined following the IE fat but continued to rise following the non-IE fat. Insulin, glucose, paracetamol, PYY and GIP concentrations increased significantly after the test meals (time effect; P < 0.001 for all), but did not differ between test meals. Feelings of fullness were higher following the non-IE PSt/PK meal (diet effect; P = 0.034). No other significant differences were noted. CONCLUSIONS: Interesterification of PSt/PK increases early phase postprandial lipaemia (0-4 h); however, further investigation during the late postprandial phase (4-8 h) is warranted to determine the rate of return to baseline values. TRIAL REGISTRATION NUMBER: Clinicaltrials.gov as NCT02365987.

Necrotizing Fasciitis of the Periorbital Region Complicated by Combined Central Retinal Artery Occlusion, Central Retinal Vein Occlusion, and Posterior Ciliary Occlusion.

A 50 year-old man on immunosuppressive agents presented with left eye vision loss, periorbital swelling, pain, and ophthalmoplegia. The patient was clinically found to have a central retinal artery and vein occlusion. A CT scan was performed which demonstrated intraorbital fat stranding, however the patient lacked sinus disease. The etiology of the orbital infection was held in question. The area was debrided in the operating room, and the specimen demonstrated group A streptococcal species consistent with necrotizing fasciitis. Periorbital necrotizing fasciitis should be suspected in patients with rapidly progressive orbital symptoms without sinus disease as lack of surgical intervention can result in poor outcomes. The unusual aspect to this case is the mechanism of vision loss, as the authors hypothesize that there was vascular infiltration of the infection resulting in the central retinal artery occlusion and central retinal vein occlusion which have not been previously reported secondary to necrotizing fasciitis of the orbit.

The rhesus rhadinovirus CD200 homologue affects immune responses and viral loads during in vivo infection.

UNLABELLED: Rhesus macaque rhadinovirus (RRV) is a gammaherpesvirus of rhesus macaque (RM) monkeys that is closely related to human herpesvirus 8 (HHV-8)/Kaposi's Sarcoma-associated herpesvirus (KSHV), and it is capable of inducing diseases in simian immunodeficiency virus (SIV)-infected RM that are similar to those seen in humans coinfected with HIV and HHV-8. Both HHV-8 and RRV encode viral CD200 (vCD200) molecules that are homologues of cellular CD200, a membrane glycoprotein that regulates immune responses and helps maintain immune homeostasis via interactions with the CD200 receptor (CD200R). Though the functions of RRV and HHV-8 vCD200 molecules have been examined in vitro, the precise roles that these viral proteins play during in vivo infection remain unknown. Thus, to address the contributions of RRV vCD200 to immune regulation and disease in vivo, we generated a form of RRV that lacked expression of vCD200 for use in infection studies in RM. Our data indicated that RRV vCD200 expression limits immune responses against RRV at early times postinfection and also impacts viral loads, but it does not appear to have significant effects on disease development. Further, examination of the distribution pattern of CD200R in RM indicated that this receptor is expressed on a majority of cells in peripheral blood mononuclear cells, including B and T cells, suggesting potentially wider regulatory capabilities for both vCD200 and CD200 that are not strictly limited to myeloid lineage cells. In addition, we also demonstrate that RRV infection affects CD200R expression levels in vivo, although vCD200 expression does not play a role in this phenomenon. IMPORTANCE: Cellular CD200 and its receptor, CD200R, compose a pathway that is important in regulating immune responses and is known to play a role in a variety of human diseases. A number of pathogens have been found to modulate the CD200-CD200R pathway during infection, including human herpesvirus 8 (HHV-8), the causative agent of Kaposi's sarcoma and B cell neoplasms in AIDS patients, and a closely related primate virus, rhesus macaque rhadinovirus (RRV), which infects and induces disease in rhesus macaque monkeys. HHV-8 and RRV encode homologues of CD200, termed vCD200, which are thought to play a role in preventing immune responses against these viruses. However, neither molecule has been studied in an in vivo model of infection to address their actual contributions to immunoregulation and disease. Here we report findings from our studies in which we analyzed the properties of a mutant form of RRV that lacks vCD200 expression in infected rhesus macaques.

Multimodal imaging of white and dark without pressure fundus lesions.

PURPOSE: To describe multimodal imaging findings in patients with dark or white without pressure lesions of the fundus. METHODS: Retrospective observational case series of 10 patients with white or dark without pressure lesions. We analyzed multimodal imaging using spectral domain optical coherence tomography, color and near-infrared fundus photography, and fundus autofluorescence imaging to explore the findings associated with these lesions. RESULTS: All patients had geographic dark or white lesions on clinical examination and color photography, which were either hyporeflective or hyperreflective on near-infrared reflectance imaging, respectively. On optical coherence tomography, these lesions correlated with an abrupt change of the photoreceptor reflectivity, with relative hyporeflectivity of photoreceptor zones (ellipsoid and interdigitation zones, as well as outer segments) within the dark, and relative hyperreflectivity within white lesions. Ten patients underwent fundus autofluorescence, which showed well-defined zones of relative hypo-autofluorescence within the lesion, compared with neighboring uninvolved regions, whether dark or white without pressure. In two patients who had a lesion combining white and dark without pressure, we observed the transition in photoreceptor reflectivity from the dark lesion (hyporeflective) to the white lesion (hyperreflective), relative to the surrounding retina. CONCLUSION: Both white and dark without pressure lesions are associated with changes in outer retinal reflectivity on optical coherence tomography, which occur in opposite directions compared with the surrounding unaffected areas. In the face of normal visual field testing to date, the clinical significance of this finding remains uncertain. Recognition of the optical coherence tomography appearance will help clinicians avoid unnecessary workup of these patients for outer retinal dystrophy or degeneration.

Human iPSC-derived retinal organoids develop robust Alzheimer's disease neuropathology.

Alzheimer's disease (AD), characterized by memory loss and cognitive decline, affects nearly 50 million people worldwide. Amyloid beta (Aß) plaques and intracellular neurofibrillary tangles (NFTs) of phosphorylated Tau protein (pTau) are key histopathological features of the disease in the brain, and recent advances have also identified AD histopathology in the retina. Thus, the retina represents a central nervous system (CNS) tissue highly amenable to non-invasive diagnostic imaging that shows promise as a biomarker for early AD. Given the devastating effects of AD on patients, their families, and society, new treatment modalities that can significantly alter the disease course are urgently needed. In this study, we have developed and characterized a novel human retinal organoid (RO) model derived from induced pluripotent stem cells (iPSCs) from patients with familial AD due to mutations in the amyloid precursor protein gene (APP). Using immunofluorescence and histological staining, we evaluated the cellular composition and AD histopathological features of AD-ROs compared to control ROs from healthy individuals. We found that AD-ROs largely resemble their healthy control counterparts in cellular composition but display increased levels of Aß and pTau. We also present proof of principle of an assay to quantify amyloid levels in whole ROs. This in vitro model of the human AD retina constitutes a new tool for drug screening, biomarker discovery, and pathophysiological studies.

Implementation of a pediatric trauma registry at a national referral center in Kenya: Utility and concern for sustainability.

BACKGROUND: Pediatric trauma disproportionately affects low- and middle-income countries, particularly the pediatric trauma systems, are frequently limited. This study assessed the patterns of pediatric traumatic injuries and treatment at the only free-standing public children's hospital in East Africa as well as the implementation and sustainability of the trauma registry. METHODS: A prospective pediatric trauma registry was established at Shoe4Africa Children's Hospital (S4A) in Eldoret, Kenya. All trauma patients over a six-month period were enrolled. Descriptive analyses were completed via SAS 9.4 to uncover patterns of demographics, trauma mechanisms and injuries, as well as outcomes. Implementation was assessed using the RE-AIM framework. RESULTS: The 425 patients had a median age of 5.14 years (IQR 2.4, 8.7). Average time to care was 267.5 min (IQR 134.0, 625.0). The most common pediatric trauma mechanisms were falls (32.7 %) and burns (17.7 %), but when stratified by age group, toddlers had a higher risk of sustaining injuries from burns and poisonings. Over half (56.2 %) required an operation during the hospitalization. Overall, implementation of the registry was limited by the clinical burden and inadequate personnel. Sustainability of the registry was limited by finances. CONCLUSIONS: This is the first study to describe the trauma epidemiology from a Kenyan public pediatric hospital. Maintenance of the trauma registry failed due to cost. Streamlining global surgery efforts through implementation science may allow easier development of trauma registries to then identify modifiable risk factors to prevent trauma and long-term outcomes to understand associated disability.

Automated analysis of diabetic retinopathy images: principles, recent developments, and emerging trends.

Diabetic retinopathy (DR) is a vision-threatening complication of diabetes. Timely diagnosis and intervention are essential for treatment that reduces the risk of vision loss. A good color retinal (fundus) photograph can be used as a surrogate for face-to-face evaluation of DR. The use of computers to assist or fully automate DR evaluation from retinal images has been studied for many years. Early work showed promising results for algorithms in detecting and classifying DR pathology. Newer techniques include those that adapt machine learning technology to DR image analysis. Challenges remain, however, that must be overcome before fully automatic DR detection and analysis systems become practical clinical tools.

Post-traumatic amaurosis secondary to paraophthalmic internal carotid artery pseudoaneurysm treated with pipeline embolization device.

During evaluation for monocular visual loss, a 48-year-old woman was found to have a posttraumatic paraophthalmic internal carotid artery (ICA) pseudoaneurysm. She underwent reconstruction of the ophthalmic segment of the right ICA with a Pipeline embolization device but her vision did not return.

Deletion of the monkeypox virus inhibitor of complement enzymes locus impacts the adaptive immune response to monkeypox virus in a nonhuman primate model of infection.

Monkeypox virus (MPXV) is an orthopoxvirus closely related to variola virus, the causative agent of smallpox. Human MPXV infection results in a disease that is similar to smallpox and can also be fatal. Two clades of MPXV have been identified, with viruses of the central African clade displaying more pathogenic properties than those within the west African clade. The monkeypox inhibitor of complement enzymes (MOPICE), which is not expressed by viruses of the west African clade, has been hypothesized to be a main virulence factor responsible for increased pathogenic properties of central African strains of MPXV. To gain a better understanding of the role of MOPICE during MPXV-mediated disease, we compared the host adaptive immune response and disease severity following intrabronchial infection with MPXV-Zaire (n = 4), or a recombinant MPXV-Zaire (n = 4) lacking expression of MOPICE in rhesus macaques (RM). Data presented here demonstrate that infection of RM with MPXV leads to significant viral replication in the peripheral blood and lungs and results in the induction of a robust and sustained adaptive immune response against the virus. More importantly, we show that the loss of MOPICE expression results in enhanced viral replication in vivo, as well as a dampened adaptive immune response against MPXV. Taken together, these findings suggest that MOPICE modulates the anti-MPXV immune response and that this protein is not the sole virulence factor of the central African clade of MPXV.

Characterization of macaque pulmonary fluid proteome during monkeypox infection: dynamics of host response.

Understanding viral pathogenesis is challenging because of confounding factors, including nonabrasive access to infected tissues and high abundance of inflammatory mediators that may mask mechanistic details. In diseases such as influenza and smallpox where the primary cause of mortality results from complications in the lung, the characterization of lung fluid offers a unique opportunity to study host-pathogen interactions with minimal effect on infected animals. This investigation characterizes the global proteome response in the pulmonary fluid, bronchoalveolar lavage fluid, of macaques during upper respiratory infection by monkeypox virus (MPXV), a close relative of the causative agent of smallpox, variola virus. These results are compared and contrasted against infections by vaccinia virus (VV), a low pathogenic relative of MPXV, and with extracellular fluid from MPXV-infected HeLa cells. To identify changes in the pulmonary protein compartment, macaque lung fluid was sampled twice prior to infection, serving as base line, and up to six times following intrabronchial infection with either MPXV or VV. Increased expression of inflammatory proteins was observed in response to both viruses. Although the increased expression resolved for a subset of proteins, such as C-reactive protein, S100A8, and S100A9, high expression levels persisted for other proteins, including vitamin D-binding protein and fibrinogen γ. Structural and metabolic proteins were substantially decreased in lung fluid exclusively during MPXV and not VV infection. Decreases in structural and metabolic proteins were similarly observed in the extracellular fluid of MPXV-infected HeLa cells. Results from this study suggest that the host inflammatory response may not be the only facilitator of viral pathogenesis, but rather maintaining pulmonary structural integrity could be a key factor influencing disease progression and mortality.